&EPA
United States
Environmental Protection
Agency
EPA/601/B-15/001 September 2015 www.epa.gov/ord
User's Guide & Metadata to
Coastal Biodiversity Risk
Analysis Tool (CBRAT):
framework for the
ystemization of Life History
and Biogeographic Information
Office of
Research and Development
National Health and
Environmental Effects
Research Laboratory
Western Ecology Division
-------
&EPA
United States
Environmental Protection
Agency
User's Guide & Metadata to
Coastal Biodiversity Risk Analysis Tool
(CBRAT): Framework for the
Systemization of Life History and
Biogeographic Information
Version 1.0
www.cbrat.org
Authors:
Henry Lee II, U.S. EPA, Western Ecology Division
Katharine Marko, U.S. EPA, Western Ecology Division
W. Marshall Hanshumaker, Contractor U.S. EPA Western
Ecology Division
Christina Folger, U.S. EPA, Western Ecology Division
Rene Graham, CSS-Dynamac, Contractor U.S. EPA Western
Ecology Division
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Author and Program Support Affiliations: Pacific Coastal Ecology Branch, Western Ecology Division,
National Health and Environmental Effects Research Laboratory, Office of Research and Development,
U.S. Environmental Protection Agency. Newport, OR 97365
Disclaimer: The information in this document has been funded in part by the U.S. Environmental
Protection Agency (U.S. EPA). This publication was reviewed by the National Health and Environmental
Effects Research Laboratory's Western Ecology Division and has been approved for publication.
However, approval does not signify that the contents reflect the views of the U.S. EPA. The use of trade,
firm, or corporation names in this publication is for the information and convenience of the reader; such
use does not constitute official endorsement or approval by the EPA of any product or service to the
exclusion of others that may be suitable.
Acknowledgements: Special thanks to Deborah Reusser (USGS retired) who provided programming
support and insights into the design of web-based tools. D. Reusser's support for this project was
partially funded through IAG #DW-14-95779101-4 with the U.S. EPA and through the U.S. Fish & Wildlife
Northwest Pacific LCC. Database development and programming was also provided by Dylan McCarthy
and Rachel Nehmer. Emily Saarinen and Melanie Frazier provided many insights into the development of
the framework, while Patrick Clinton provided GIS support. Thanks to all the students and contractors
who helped populate CBRAT including Rebecca Loiselle, Summer Maga, Tracy Hoblit, Anthony Pham,
Rochelle Regutti, Micaela Edelson, Alma Meyer, and others. The authors would like to acknowledge Tim
Counihan and Jill Hardiman of the USGS Western Fisheries Research Center for their assistance in
collating the abundance and distributions of rockfish. Dayv Lowry of Washington Dept. Fish and Wildlife
provided helpful insights on Puget Sound rockfish. Workshops with the Southern California Association
of Marine Invertebrate Taxonomists (SCAMIT) provided expert information on several taxa and usability
of CBRAT; Rick Brusca, Don Cadien, Larry Lovell, Gene Coan, Doug Eernisse, Nora Foster, Greg Jensen,
Paul Valentich-Scott, Ron Velarde, Mary Wicksten, and Roger Clark all shared their time and expertise.
Mary Mahaffy of the U.S. Fish and Wildlife Service helped co-sponsor a workshop on trait-based risk
assessment, which provided key insights into the design of CBRAT. Don Cadien (County Sanitation
Districts of Los Angeles County), Larry Lovell (County Sanitation Districts of Los Angeles County), Dean
Pasko (Dancing Coyote Environmental), Maggie Dutch (Washington Dept. Ecology), and Valerie Partridge
(Washington Dept. Ecology) reviewed an earlier version of this document and provided a number of
insightful suggestions. Finally, Dr. Lee would like to acknowledge the continued support of EPA ORD's
Air, Climate, and Energy (ACE) research program.
Suggested citation: Lee II, H., Marko, K., Hanshumaker, M., Folger, C, and Graham, R. 2015. User's
Guide & Metadata to Coastal Biodiversity Risk Analysis Tool (CBRAT): Framework for the Systemization
of Life History and Biogeographic Information. EPA Report. EPA/601/B-15/001. 123 pages.
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TABLE OF CONTENTS
Contents
I. INTRODUCTION 1
A. User Access and Preferred Browser 1
B. Caveats & Cautions 2
II. SEARCHING FOR SPECIES, PUBLICATIONS, LOCATIONS, & COMMENTS 3
A. Search Species page 3
B. Species Home Screen and Sidebar Menu Options 4
References 5
Comments 5
Images 7
PDFs& Species Profiles 7
C. Publications Search 13
D. Locations Search 13
E. Comments Search 14
III. BIOGEOGRAPHY 15
A. Distribution Map 16
B. Relative Abundance Map & Relative Abundance Schema 17
C. Population Trends 22
D. Classification Map - Native/Non-Native Status 25
E. Vulnerability 28
F. Comments 28
IV. ENVIRONMENT 28
A. Regime 29
B. Ecosystem/Habitat 29
C. Depth 33
D. Salinity 34
E. Substrate 35
F. Energy 38
G. Temperature 38
V. LIFE HISTORY 39
A. Trophic Level and Feeding 39
B. Reproduction 43
C. Development 45
D. Habitat Association 46
E. Mobility 48
VI. SPECIALIZATION 49
A. Habitat 49
B. Trophic 54
C. Reproduction 55
D. Symbiotic 55
VII. MORPHOLOGY AND PHYSIOLOGY 57
VIII. INVASION VECTORS 57
IX. DATA EXPORT 59
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A. Step One - Choosing a Taxon & Ecoregion or Ecoregion Group 61
B. Species Info Queries 61
1. Output Species Comments 61
2. Output References 62
3. Output Species Taxonomy 63
C. Biogeography Queries 63
1. Abundance by Ecoregion 63
2. Abundance by Citation 64
3. Master Abundances Table 65
4. Abundance across Ecoregions 66
5. Classification / Population Values - Status of Nonindigenous Species 68
6. First Record Values - Dates of First Record of Nonindigenous Species 68
D. Environment Queries 69
1. Environmental Class queries 69
2. All Life History & Environmental Information query 70
X. DOCUMENTS 71
A. User's Guide and Metadata 71
B. Vulnerability Framework 71
C. Acronyms and Abbreviations 71
D. Glossary of Terms 71
E. Museum Abbreviations 71
F. Taxa Codes 72
G. NEP and U.S. Arctic Ecoregions 72
H. All MEOW Ecoregions 72
I. Small Island Ecoregions 72
J. Tropical Ecoregions 72
XI. ABOUT 72
A. User's Guide and Metadata 72
B. Site Map to CBRAT 72
C. Acknowledgements 72
D. Version 72
XII. REFERENCES 73
XIII. APPENDICES 75
Appendix I: CBRAT Access Levels 75
Appendix Table 1: Summary of the privileges associated with each level of access in CBRAT 76
Appendix Table 2: Qualitative descriptions and quantitative cut points of dominance normalized
relative abundance for the three-level relative abundance classifications (Figure 16) 77
Appendix Table 3: Definitions for the regime classes (Figure 20) 81
Appendix Table 4: Definitions for ecosystem/habitat classes (Figures 22-23) 82
Appendix Table 5: Definitions for the depth classes for the benthic and pelagic zones (Figure 25) 93
Appendix Table 6: Definitions for the salinity classes in practical salinity units (psu) (Figure 27) 94
Appendix Table 7: Definitions for substrate classes (Figure 29-30) 95
Appendix Table 8: Definitions for the wave energy classes (Figure 31) 98
Appendix Table 9: Definitions for the current energy classes (Figure 31) 98
Appendix Table 10: Definitions for the physiological temperature classes (Figure 32) 98
Appendix Table 11: Definitions for the trophic modes (Figure 34) 99
Appendix Table 12: Definitions for trophic interactions among symbionts (Figure 34) 100
Appendix Table 13: Definitions for the terms describing reproductive classes (Figure 36) 101
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Appendix Table 14: Definitions for breeding strategy (Figure 38) 102
Appendix Table 15: Definitions for juvenile development and dispersal (Figure 38) 104
Appendix Table 16: Definitions for adult development (Figure 38) 105
Appendix Table 17: Definition for alternation of generations classes (Figure 38) 106
Appendix Table 18: Definitions for habitat-association classes (Figure 40) 106
Appendix Table 19: Definitions of mobility classes (Figure 42) 109
Appendix Table 20. Taxa codes used to identify major taxonomic groups 112
Appendix Table 21: List of the MEOW ecoregions classified as tropical 115
Appendix Table 22: List of small island MEOW ecoregions 118
Appendix Table 23: Primary invasion vectors (Figure 51) 120
FIGURES
Figure 1: CBRAT home page (http://www.cbrat.org) 3
Figure 2: Species Search page 4
Figure 3: Taxonomy page - General page for Metacarcinus magister 5
Figure 4: References page listing sources linked to species 6
Figure 5: Bibliographic reference page 6
Figure 6: Comment page for Metacarcinus magister 7
Figure 7: First of three pages of the Species Profile for Metacarcinus magister 8
Figure 8: Second of three pages of the Species Profile for Metacarcinus magister 9
Figure 9: Third of three pages of the Species Profile for Metacarcinus magister 10
Figure 10: Publications search page 13
Figure 11: Search Locations page showing a global view of all 254 MEOW ecoregions 14
Figure 12: Search Comments page 15
Figure 13: Species distribution map of Metacarcinus magister 17
Figure 14: Relative abundance map for Metacarcinus magister 18
Figure 15: Legend for the relative abundance map (Figure 14) 19
Figure 16: Three-level relative abundance classification schema 19
Figure 17: Hybrid approach to assigning ecoregional-scale relative abundance classes 22
Figure 18: Population trends by ecoregion for Metacarcinus magister 23
Figure 19: Native/non-native status of the amphipod Grandidierellajaponica by ecoregion 26
Figure 20: Regime page for Metacarcinus magister 29
Figure 21: Ecosystem/Habitat page for Metacarcinus magister 30
Figure 22: All the major unconsolidated ecosystems/habitats on the Ecosystem/Habitat page 31
Figure 23: All the major consolidated, pelagic, and specialized systems on the Ecosystem/Habitat page.
32
Figure 24: Depth page for Metacarcinus magister 33
Figure 25: All the benthic and pelagic depth classes on the Depth page 34
Figure 26: Salinity page for Metacarcinus magister 34
Figure 27: All the salinity classes on the Salinity page 35
Figure 28: Substrate page for Metacarcinus magister 36
Figure 29: Consolidated substrate classes on the Substrate page 36
Figure 30: Unconsolidated sediment classes on the Substrate page 37
Figure 31: All the wave and current classes on the Energy page 38
Figure 32: Temperature page for Metacarcinus magister 39
Figure 33: Trophic Level and Feeding page for Metacarcinus magister 40
IV
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Figure 34: Major classes on the Trophic Level and Feeding page 40
Figure 35: Reproduction page for Metacarcinus magister 43
Figure 36: Reproduction page showing all reproductive classes 44
Figure 37: Portion of the Development page for Metacarcinus magister 45
Figure 38: Major reproductive and developmental characteristics on the Development page 46
Figure 39: Habitat Association page for Metacarcinus magister 47
Figure 40: All habitat association classes on the Habitat Association page 48
Figure 41: Mobility page for Metacarcinus magister 48
Figure 42: All mobility classes available on the Mobility page 49
Figure 43: Specialized Habitat page for Metacarcinus magister 51
Figure 44: All the specialized unconsolidated habitats on the Habitat Specialization page 52
Figure 45: All specialized consolidated and pelagic habitats and specialized systems on the Habitat
Specialization page 53
Figure 46: Trophic specialization page for Metacarcinus magister, a generalist feeder 54
Figure 47: Trophic specialization page for the globose kelp crab, Taliepus nuttallii, a specialist feeder...54
Figure 48: Symbiotic page for Fabia subquadrata 56
Figure 49: Shell Structure (left) and Skeletal Composition (right) pages available from the Morphology
and Physiology tab 57
Figure 50: Primary Vectors for Metacarcinus magister 58
Figure 51: Invasion vectors available on the Primary Vectors page 59
Figure 52: Data Export page - Extracting environmental ranges, habitats, distributions, and abundances.
60
Figure 53: Comments linked to brachyuran crabs in the Cortezian Ecoregion 62
Figure 54: References linked to brachyuran crabs in the Cortezian Ecoregion 62
Figure 55: Higher order taxonomy of brachyuran crabs in the Cortezian Ecoregion 63
Figure 56: Abundance by Ecoregion query for brachyuran crabs in the Cortezian Ecoregion 64
Figure 57: Abundance by Citation query for brachyuran crabs in the Cortezian Ecoregion 65
Figure 58: Master Abundance Table query for brachyuran crabs in the Cortezian Ecoregion 66
Figure 59: Abundance across Ecoregions query for brachyuran crabs occurring in the Cortezian
Ecoregion 67
Figure 60: Classification / Population Values - Invasion status of the brachyuran crabs in the Northern
California Ecoregion 68
Figure 61: First Record Values - First records of nonindigenous brachyuran crabs in the Northern
California Ecoregion 69
Figure 62: Environment Depth Class query - Intertidal and shallow subtidal brachyuran crabs in the
Cortezian Ecoregion 70
Figure 63: All Life History & Environmental Information query on brachyuran crabs in the Cortezian
Ecoregion 71
TABLES
Table 1: Key to Species Profiles (Ver. 1.0) 11
Table 2: Numerical codes and abbreviations used for relative abundance in the Abundance across
Ecoregions query 67
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SIDEBARS
Sidebar #1: Hierarchical Approach to Environmental and Life History Data 2
Sidebar #2 MEOW Biogeographic Schema 16
Sidebar #3: Relative Abundance Classification Schema 20
Sidebar #4: Dominance Normalized Relative Abundances & Hybrid Approach to Assigning Relative
Abundances 21
Sidebar #5: Population Trend Classes 24
Sidebar #6: Time Intervals for Population Trends 25
Sidebar #7: Native vs. Nonindigenous Classifications 27
Sidebar #8: Population Establishment Status 28
Sidebar #9: Classifying the Extent of Trophic Specialization 41
Sidebar #10: Rules Used to Automate the Degree of Trophic Specialization 42
VI
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I. INTRODUCTION
This document provides instructions for using the web-based tool "Coastal Biodiversity Risk Analysis Tool" (CBRAT;
http://www.cbrat.org) developed by researchers from the U.S. Environmental Protection Agency (U.S. EPA) and U.S.
Geological Survey (USGS). CBRAT is an ecoinformatics platform that synthesizes biogeographical distributions,
abundances, life history attributes, and environmental tolerances for near-coastal invertebrates and fishes on a regional
scale. The current version focuses on the North American Pacific Coast from the Beaufort Sea down through the Gulf of
California, though any portion of the world's ocean can be captured. The public version, which is described here,
summarizes these data for taxonomic groups that have undergone quality assurance checks. Currently, this includes the
true brachyuran crabs (Infraorder Brachyura, 367 species), king crabs (Family Hapalogastridae and Lithodidae, 21
species) and rockfish (Genus Sebastes, 74 species). Species in these taxa are limited to oceanic (offshore) and estuarine
species that occur from the supratidal to a depth of 200 m. As additional taxa are quality assured, they will be made
available.
The ultimate objective of CBRAT is as a risk-assessment tool that automatically calculates the relative vulnerability of
species to individual and multiple climate change drivers based on traits that make species vulnerable (e.g., endemic) or
resilient (e.g., nonindigenous) to climate change. This functionality is not currently implemented in the public version,
but should be available within the next year. A companion document that will be available shortly, the Expert CBRAT
Guide, describes how to enter data into CBRAT by taxonomic and ecological experts (Lee et al., in progress). Finally, a
framework document describing the conceptual approach to assessing climate vulnerability (Lee et al., in progress) using
the trait data synthesized in CBRAT will be available in the next year. We want to emphasize that while the objective of
CBRAT is to generate regionally-specific vulnerabilities to climate change, CBRAT can inform other research and
management issues including, but not limited to, developing adaptation strategies to climate change, developing
conservation strategies for commercially and recreationally important species regardless of the stressor(s), evaluating
pollution impacts in term of functional responses vs. changes in species composition, and generation of indicators of the
impacts of climate change.
CBRAT has a fairly simple construct based on the Search function (by species, publication, location, or comment), but
also includes a Data Export function, as well as a Document database. Herein, we describe each of the pages in CBRAT
and provide an example screen shot for a species, usually the Dungeness crab Metacarcinus magister. Additionally, we
provide screen shots of all the options available for each particular life history or environmental characteristic.
Definitions for the terms (metadata) are given in the appendix tables. The sidebars provide more detailed information
on the conceptual and theoretical background of the approaches used in CBRAT. For example, Sidebar #1: Hierarchical
Approach to Environmental and Life History Data provides background information on the use of hierarchical schema to
synthesize biotic and environmental data, one of the signature characteristics of CBRAT. However, information in the
sidebars is not required to understand how to use CBRAT. We note that CBRAT is an active research endeavor and the
species listed, the types of information synthesized, and the web-site functionality will continue to expand.
A. User Access and Preferred Browser
The public, non-password protected version of CBRAT is available at http://www.cbrat.org. This version allows users
access to the taxa that have undergone quality assurance checks. Besides viewing data, public users can download
distributional, abundance, and life history data in PDFs or spreadsheets on the quality assured taxa. The public version
does not allow users to add data or to submit issues to CBRAT. Managers and experts who wish to view draft data must
sign up for access with the database administrator by clicking the "Sign Up" button at the right top corner on the CBRAT
home page. The different levels of access are described in Appendix I.
Due to the structure of this database, the optimal web program to view CBRAT from is Google Chrome or Firefox.
Depending upon the version, Internet Explorer may not display all of the features and menus within CBRAT at an
optimum level.
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Sidebar #1: Hierarchical Approach to Environmental and Life History Data
Much of the information in CBRAT is synthesized and displayed in a hierarchical fashion.
Specifically, we developed or adopted hierarchical topologies for biotic and environmental
information that captures data at different levels of resolution. For example, an estuarine salinity
could be classified as brackish (0.5 to <30 psu), polyhaline (18 to <30 psu), or beta-polyhaline (18
to <25 psu), depending on the data available. This hierarchical approach to life history and
environmental data was first proposed in Reusser and Lee (2011) and then expanded and
implemented in an analysis of nonindigenous species in the North Pacific (Lee and Reusser, 2012).
In CBRAT, hierarchical topologies were developed for both quantitative data (e.g., numerical
depth ranges) and qualitative classes (e.g., depth classes, reproductive type). One advantage of
hierarchical schemas is that data at different resolutions can be captured, thus increasing the
amount of information that can be synthesized for a species. Using salinity as an example, simply
knowing a species occurs in an estuary indicates that a "brackish" salinity range could be linked to
the species. A related advantage is that when information has been synthesized at different levels
of detail, a formal hierarchical schema allows rolling up the more detailed information to allow
analysis at the lower level of resolution. Another advantage is that the researchers and managers
can analyze the information at the level of resolution best suited to the specific question or
managerial need.
B. Caveats & Cautions
From the home page (Figure 1), and on every page in CBRAT, the user can read the Terms of Use by clicking on the link
on the bottom of the page. This is the legalese that states that the U.S. EPA and USGS do not provide any warranty
regarding the accuracy of the data or the utility of CBRAT. In more practical terms, we urge the user to check the linked
references, or other references, if any piece of information synthesized in CBRAT is critical in making an important
management decision. The user also needs to recognize that values of several species' traits, especially relative
abundance and population trends, were often estimated using incomplete data. While we strove to assign these values
accurately and without bias using the best available data, new data may require modifications to these values.
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Species List
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Acantholithodes h/spidus
Acantholobulus mirafloresensis
Acanthonvx oetiverii
Achelous guavmasensis
Achelous iridescens
Achelous tuberculatus
Addops fimbriatus
Actaea anausta
Aethra scutata
Ala cornuta
Aratus oisonii
Arenaeus mexicanus
Armases maadalenense
Austinixa felioensis
Austinotheres angelicus
Displaying all 15 Species found under 'A1
As of 10:20AM on 08/05/2015, 469 species are publicly available.
Species: Scientific Name
^^^^^^Q
Common Name
Also Reported As
Search
Figure 2: Species Search page.
Clicking on a letter at the top will list the available species that start with that letter. Alternatively, enter a portion or
complete scientific name, common name, or "Also Reported As" name (e.g., synonym) into the text box and click Search.
B. Species Home Screen and Sidebar Menu Options
After selecting your species of interest, you will be directed to the Taxonomy - General page (Figure 3). This page lists
the higher order taxonomy (on left of page), the Author who first described the species, Type Locality (geographical
location where the described species was initially collected), Location of Type (museum where the holotype or other
types are maintained), Also Reported As (alternate names used for the species), and Common Name(s) of the species.
The taxonomy follows that in the World Register of Marine Species (WoRMS; http://www.marinespecies.org/index.php)
unless there are recent, regional taxonomic standards indicating a different taxonomy. If different, "Taxonomy different
than WoRMS" will be displayed below the WoRMS link. If the taxonomy is the same as WoRMS, clicking on "World
Register of Marine Species (WoRMS) Record" link will open up the WoRMS page for that species in a new browser tab.
The names given under Also Reported As include true taxonomic synonyms as well as other versions of the species
name, such as misspellings and misidentifications. The primary purpose of the Also Reported As is to help users
"translate" alternate species names to be able to extract distributional and ecological information from earlier literature.
It is not an exhaustive synonymy listing. A user who needs a detailed taxonomic review should consult the original
taxonomic literature for synonyms. With the common names, the scientific name is appended to the common name
when the same common name is applied to multiple species.
From the species page, you can use the sidebar menu (gray shaded area on the far left in Figure 3) to access additional
information on references, comments, images, and linked PDFs.
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Metacarcinus magister (Dana, 1852)
Taxonomy
Biogeography Environment Life History Specialization Morphology and Physii
|Kingclom;| Aninialia
Phylum: Arthropoda
||SLibphyluin:| Crustacea
Superclass: Multicrustacea
World Register of Marine Organisms (WoRMSi Record
[Author: I (Dana, 1852)
Class: Malacostraca
[Type Locality: | San Francisco Bay, California, USA
[location of Type: | Unspecified
||subclass:| Eunialacostraca
||superorder:| Eucarida
||suborder:| Pleocyeniata
||lnfraorder:| Brachylira
Section: Enbrachyiira
[Also Reported As; |
• Cancer magister | Synonym
[Common Name(s); |
• Dungeness crab
• America-fcho-gani
[[Subsection:] Heterotreniata
||superfamily:| Cancroidea
[Family:] Cancridae
Genus: Metacarcinus
l|Taxacode:| DEC
17 taxonoinic levels have been hidden
from the list because they are blank. To
(see them, <
Figure 3: Taxonomy page - General page for Metacarcinus magister.
This page provides the higher order taxonomy for the species and type locality, as well as common names and other
scientific names used in the literature (Also Reported As). Clicking on the "World Register of Marine Species (WoRMS)
Record" will open the WoRMS page for the species. The Species Profile Key on the left sidebar opens a PDF of the
Species Profile Key (see Table 1).
References
Clicking on References provides a list of references that were used to populate CBRAT with data on the species of
interest, as well as what type of information (e.g., biogeographic, taxonomic, etc.) that the reference provided (Figure 4).
Whenever you click on a citation listed in CBRAT you will be taken to the full bibliographic reference for that citation
(Figure 5). All the species linked to the reference are highlighted on the left side; clicking on a species' name will open its
Taxonomy Page.
Comments
The link to call up the comments is available in the sidebar on the left of the Taxonomy page (Figure 3) as well as most
other pages. The Comments page will always open in a new tab (Figure 6). CBRAT uses comments linked to individual
species to document the information used in assigning different attributes to that species. Comments include excerpts
from the literature, key information synthesized from the literature, personal communications from experts, and CBRAT
decisions. In general, comments focus on environmental tolerances, life history attributes, and distribution and
abundance. Taxonomic comments are primarily limited to those required to resolve taxonomic conundrums. CBRAT has
a function that allows users to search through comments across multiple species (see Section II. D.).
Comments using "CBRAT" as the citation are used to document our interpretations. Comments using "#Master
Comment" are comments that will be printed out on the Species Profile (see Section II. B.). To date, #Master Comments
-------
have primarily been used to document decisions regarding nonindigenous species (MIS), but may be used to synthesize
any type of information.
Metacarcinus magister (Dana, 1852)
taxonomy Bioaeograpny Lnvironment Life History Specialization Morphology and f'fwsiology Invasion
References
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Figure 4: References page listing sources linked to species.
References page listing the papers, reports, databases, and personal communications linked to Metacarcinus magister.
Source is the first paper linked to the species, and is used for quality assurance but otherwise has no special significance
(not shown in this section of the page). The information provided by each paper is indicated by checkmarks. Source,
Biogeographic, Comment, Abundance, Classification, Establishment, and First Record are filled in automatically by
CBRAT. Taxonomic, Ecological, Key Word, and Other are filled in manually.
Species reterenced:
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Citation: Jensen, 2014
Figure 5: Bibliographic reference page.
All the species linked to the reference are listed on the left. Clicking on a species name will open the species' Taxonomy
Page (Figure 3).
-------
Metacarcinus magister (Dana,
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M«rt«*rclin!•- ni.i-iF-,!.-i s .nrii.-Klal, i**cr«aMorMil onul itltml Iflndln^s of D«ng*inw crnlj In Pugwt Swmd f«i»g»d from approximately 6 lo 9 million pounds
per >ea*on (lit(p://vrww.copg>c>l:sourKl.ar9/ait»cFcsr'dunocni»&-tra&»*pug(rt-KHin4}. In conipnnbon, Oiooort cornnicrtMjl landing* avciiaycd ie,l million
iHJi per -jiM-jnfi iiym ]»77-j979 through 2012-2011 Masons, with a maxlinum. cornnvi mil Umhri-j of 33.5 .million pound* In Ulc 2004-^005 s«ftson
''• •' -
k'.tt-n {Jfll?'.Liiv.'y [CPA, l^w^^r.ninil i".. IT,IIJ,-.I;I-I in tfji>g F
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'.r-siy, Duivg*fn*-.s c«ab itockt havo lil»to rtporl "coilaps*' b dafiln»i3 as a rtoch having declined by 90%, 10% ol ttic stMk rcmaina.'
ConwUdfli•'•'i ii" .t:-n. n,-ir.aii.T-r.- u.s pi - .
,;,,.>!-. ,. i"./r,.uE In. hr-rMlrsf. su«w..y> fir*m H*i.- Or^onJarl fcori-glmi. A MaUif -ifiS Mmplpv m«r» tak«n In «,lij.srU-s (t-..huiiv) -mil H(t vimpF** totari
ofhhoro (Oc*an). Sdn»p£i.-s wci« lakun ftmn ttw Inlftlldi,! ID U^ m depth. Mo&t wni(rfes takpn wlH» * 0.1 ml giab though some biteiUdal Mimpln w«r»
n vrith sariftlU'r -kompli'fS 01 ^uh--.flmjJk'd du* to Ills dmgunl Of dutirtua, wllh dll rtlMjrKS.in.: ••-. sE.inr|,ndi/<-d Co the nimth*lJ d! «Mr^ni^n'iS FHT m?. Al!
ples proo«Scm rncvh siav*. Abundance and TrcduertLy Jtie analyjed lor the loljj data i«t (ALL) (N-£65]l and for the wtuaiy «nd
• ; - • -- !' . i- • ' -
Figure 6: Comment page for Metacarcinus magister.
Currently, there are 47 comments for M. magister. Less well studied species may only have one or two comments.
Clicking on the citation will open the bibliographic reference page (Figure 5).
Images
Any images of species in CBRAT are accessed from this link. At this point, most species do not have images associated
with them, but they will be added over time. However, this page also has a link to Google Image Search, which accesses
the images available via the Internet. This link is external to CBRAT and there is no assurance of the accuracy of these
images.
PDFs & Species Profiles
Clicking on "PDFs" in the left sidebar (Figure 3) opens a page with two functions. First, PDFs that have been linked to a
species are listed under the linked PDF documents heading. Clicking on a listed file will open the PDF document. A linked
PDF may be an informational report relevant to that species, or a synthesis of the distribution and/or relative abundance
of the species from a particular study. If no files are linked to the species, the statement "There are no current species
pdfs" will appear on the top of the page.
Second, the options below the linked PDFs allow the generation of a "Species Profile" that displays summarized data for
the chosen species (Figures 7-9). The Species Profile includes most of the data on the species in a highly synthesized
fashion along with maps of its relative abundance, native/non-native status, and population trends at an ecoregion scale
(MEOW ecoregions discussed in Sidebar #2). A key to the abbreviations used in the profiles is given in Table 1, which can
be downloaded as a PDF from the General Taxonomy page (Figure 3). Selecting the Species Profile Generator allows the
user to create the default summary with all the available data by clicking the "Generate Standard Species Profile (PDF)"
button. Defaults include a world map and "magnification" for the Puget Trough/Georgia Basin Ecoregion, which makes it
easier to view in the maps.
Unchecking the attributes that are not desired, and clicking the button "Generate Custom Species Profile (PDF)" on the
bottom of the page will generate a customized Species Profile. For example, if not interested in outputting the
taxonomy, uncheck the "Show Taxonomy". The user also has the option to change the scale of each map using the
dropdowns for each map. The options are world (default), Atlantic NW (east coast of US and Canada), Pacific NE (west
coast of US, Canada, and northern Mexico), North America (all of US, Canada, and Mexico), South America, and USA (US
and Canada and northern Mexico). The world and North America options display the Hawaii ecoregion. Remember to
use the "Generate Custom Species Profile (PDF)" button if any of the map options are changed.
-------
CBRAT
Species report for Meiacarcinus magister (121)
Metacarcinus magister
Tanarade: DEC
Kingdom: An-i:;ii:i
Subphylum: Crustacea
Subclass: Cuniiilarostn
Order: Oscapoda
Superlamiy: Canomidaa
Tribe:
CcTrr™r NimnVl:.
Ainarica-AdtD-gani
IM«th» Abmdance Map Dmnl: Pacic NE
Type Locality: Sim Frauds™ Bay, California. USA
Subklngdom:
Superclass: MuJtauslaoea
lrlracla=s:
Subardor: PlBOcyaina[a
Rafntty: Caiicaidtui
Qenua:
Phylum:
Class: MabuosKac
Superarder: t ,• ,j ..:.,
InFraordor: D-;. :' . ,i i
Subfamily:
| AbjnCalT! ^ MLduiiSdy Abu Karri gg M::doral*y Ra
g' Rma ^ Hypw Ran)
Tiansiaitt Cancel
Vixiindigiixiuu Q C-yu::x.n,--!iL Q ~rai-s wil ^ LfcidassifitK:
Generated on 2015-09-06 16:39:10 -0700
Page 1 of 3
Figure 7: First of three pages of the Species Profile for Metacarcinus magister.
Species Profile generated using the "Custom Species Profile (PDF)" button at the bottom of the Species Profile
Generator. Relative abundance was mapped at the "Pacific NE" scale while the native/non-native classification was
mapped at the "World" scale. In both cases, the "Show Puget Sound magnification?" was chosen to expand the Puget
Sound/Georgia Basin Ecoregion. Choosing the Generate Standard Species Profile (PDF) will produce a map at the world
scale.
-------
CBRAT
Population Trend Map BcKnt US*
Species report for Metacarcinus magister (121)
Dteaaae 1%-25%
Unknewn
Mrtwtwlmi* m*tf«W (- C«now m«Mw> hw
V, USA-1K notMMNllwt In Mwroftil
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Generated on 2015-09-06 16:39:10-0700
Page 2 of 3
Figure 8: Second of three pages of the Species Profile for Metacarcinus magister.
Population trend was mapped at the "USA" scale. O = observed class (default); P = preferred class; X = species possess
trait or falls within class.
-------
CBRAT
Species report for Metacarcinus magister (121)
R I BR I BUD I HP I BO C I OVS M I WR I CA K I RA MAM I DW O I ART RR P I H.B Oh
IBR I BLD I UP I BO C I OYS M I WR I CA K I
I I I P I I I I I I I
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P P O P P
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aproduelivB TmnparatHB. 1*1 Ofe-PWWnj: VJ U H.I ObJBrrM): 20.0 MB PMfcmfl: 10.0 lfc» PmlMT«d U.D
Ljki Walue Ccid [ wmpunLta Mid TcurEjarali} . Outer Tropca! Inim T-uuiirjl I SlmiulfwiiiTal
Taniparatn
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MM-U
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Generated on 2015-09-06 16:39:10-0700
Page 3 of 3
Figure 9: Third of three pages of the Species Profile for Metacarcinus magister.
O = observed class (default); P = preferred class; X = species possess trait or falls within class.
10
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Table 1: Key to Species Profiles (Ver. 1.0).
Test Species (Authority)
Taxacode: Abbreviations for major
taxonomic groups.
Kingdom:
Subphylum:
Subclass:
Order:
Superfamily:
Tribe:
Tvoe Localitv* Location where species first described. For Provisional species,
'" *' general location where species description may apply.
Subkingdom:
Superclass:
Infraclass:
Suborder:
Family:
Genus:
Phylum:
Class:
Superorder:
Infraorder:
Subfamily:
ID:# Species ID no.
Common Name(s):
Synonym(s):
Types of Also Reported As::
Alternate representation
Ambiguous synonym
Convention
Misidentified
Misspelling
Nomen nudum
Partial synonym
Subspecies
Synonym
MAPS: Up to three maps can be generated at different spatial extents.
1) Relative abundance at ecoregion scale
2) Population trends at ecoregion scale
3) Native / non-native classification
comment- D'sP'avs tne "Master Comment", which is usually a summary of decisions that have been made from
'the comments and/or from taxonomic or ecological experts.
Many of the environmental and life history attributes are classified either as Observed
range) or Preferred ("P", favored habitat or environmental range).
'O", secondary habitat or environmental
Regime See Appendix Table 3 for definitions
Terrestrial
Rivers, Streams, and
Creeks (Lotic)
Lakes and Ponds
(Lentic)
Coastal
Fringe
Estuaries
Estuaries and
Lagoons
Coastal bay
Open Near Shore
Waters
Shelf
Oceanic
£ Inland Seas
>200m
Ecosystem See Appendix Table 4 for definitions
Unconsolidated Ecosystem
UNVSED
Unvegetated
Sediment
UV-CS
Unvegetated
Sediment-
UV-TF
Unvegetated
Sediment-
UV-SUB
Jnvegetate<
Sediment-
Coastal Shore Tide Flats Subtidal
Rl
Rocky
RI-TP
Rl-
Tide Pool
RI-P
Kl -
Phyllospadix
RI-C
Rl-Caves
SAV
Submerged Aquat
Vegetation
MAC-BEDS
' Macroalga
• .jl.
EM
Emergent
March
MAN
Mangrove
Dune
Dune
W
Wrack
Oth
Other
Consolidated Ecosystem
SUB-R
Subtidal Rocks
CR
Coral
OB
Oyster Beds
WR
Worm Reef
CA
coralline
Algae
K
Kelp Beds
Oth
Other
Pelagic Ecosystem
Water Column
Floating Vascular Plants
Flotsam
Depth See Appendix Table 5 for definitions
Min Observed:* (m) Max Observed:* (m) Min Preferred:* (m) Max Preferred:* (m) Numerical depth ranges
Benthic Depth
Coastal Fringe Supralittoral
Intertidal
Neritic
Upper
Mid
Lower
Shallow
Upper Intertidal Mid Intertidal Lower Intertidal Shallow Subtidal Deep Subtidal
Deep
Pelagic Depth
Epipelagic
Meso pelagic
Bathypelagic
Abysso pelagic
Surface
Shallow
Deep
Salinity See Appendix Table 6 for definitions
Min Observed:* Max Observed:* Min Preferred:* Max Preferred:*
Fresh
Brackish Oligo Oligohaline
Brackish MesoMesohaline
Brackish Poly Polyhaline
Marine/euhaline
Hyper
Freshwater
Beta
Beta-oligohaline
Alpha
Beta
Alpha-oligohaline
Beta-
mesohaline
Alpha
Beta
Alpha-
Beta-polyhaline
Alpha
Beta-euhaline
Alpha-Polyhaline
Alpha-
euhaline
Hypersaline
11
-------
Substrate See Appendix Table 7 for definitions
Mean PHI:
Min Observed:# Max Observed:# Min Preferred:* Max Preferred:* Numerical phi ranges
% Fines:
Min Observed:* Max Observed:* Min Preferred:* Max Preferred:* Numerical % fines ranges
Mean %TOC:
Min Observed:* Max Observed:* Min Preferred:* Max Preferred:* Numerical %TOC ranges
Unconsolidated Substrate
Mud
Sand
Mixed Fines
Gravel
Cobble
Mixed Sediments
Organic
Mud & Sand w/
Organic Sediments
Consolidated Substrate
>5% gravel/cobble
BR BID
HP
BIO
OYS
M WR CA
, Worm Coralline , Rooted Drift Artificial Rip Hulls &
Rock|Bedrock|Boulder|Hardpan|Biogenic| Coral | Oyster |Mussel| Reef | A|gae | Kelp |AquaticlMangrovelwoodl other Isubstratel Rap I Plllng I Ballast
K RA MAN
DW
ART
RR
H+B Oth
Tanks
Energy see Appendix Tables 8 and 9 for definitions
Wave Energy
Exposed
Semi-exposed
Semi-protected
Protected
Very Protected
Current Energy
No Energy
High Energy
Moderate Energy
Low Energy
Temperature See Appendix Table 10 for definitions
Adult Temperature: Min Observed:* Max Observed:* Min Preferred:* Max Preferred:* Numerical temperature range for adults
Reproductive Temperature: Min Observed:* Max Observed:* Min Preferred:* Max Preferred:* Numerical temperature range for reproductior
Cold Water
Cool Temperate
(
Mild Temperate
Warm
Temperate
.... Not currently used ....
Outer Tropical
Inner Tropical
)
Stenothermal
Mesothermal
Eurythermal
Trophic Level Feeding See Appendix Tables 11 and 12 for definitions
PAR
Parasite/
SA
Symbiotic
Algae
PP
Primary
Producer
H
Herbivore
P
Predator
S
Scavenger
DET
Detritivore
DEC
Decomposer
SF
Suspension
Feeder
DF
Deposit
Feeder
DF-SUR
Surface
Deposit
DF-SUB
Subsurface
Deposit
Feeder Feeder
Reproduction
See Appendix Table 13 for definitions
Sexual Reproduction
H/M
Hermaphrodite/
Monoecious
SynH
Synchronous
Hermaphrodite
SeqH
Sequential
Hermaphrodite
G/D
Gonochoristic/
Dioecious
SF
Spawning/
Fertilization Type
IF
Internal
Fertilization
FEE
External
Fertilization
Asexual Reproduction
BF
Binary Fission
BUD
Budding and
PAR/AGA
Parthenogenesis/Agamospermy
VP
Vegetative Propagation
FCS
Freecast
Spawner
(animals)
P
Pollination (plants)
SP
Sporogenesis
Fragmentation
Development See Appendix Tables 14 and 15 for definitions
ED-V
Egg
development-
ED-OVI
Egg
development-
ED-OVO
Egg
development-
DD
Direct
Development
LP
Larval phase
LP-B
Larval phase-
benthic
LP-P
Larval phase-
planktonic
FR
Fragments
SD
Seeds
SP
Spores
Viviparous
Oviparous
Ovoviviparous
Habitat Association See Appendix Table 18 for definitions
SURSurficial epibenthic
ryptofauna Borer Nestler Infauna
Pleuston NeustonPelagic-submerged
Epibenthic
swimming
Epibenthic
jnconsolidated
Mobility See Appendix Table 19 for definitions
IMM
Immobile
IMM-U
Immobile-
unattached
IMM-A
Immobile-
attached
IMM-R
Immobile-
rooted
FM
hacuitatively
Mobile
FM-U
Facultatively
Mobile-
FM-A
Facultatively
Mobile-
PM
Passively
mobile
PM-P
Passively
mobile
PM-D
Passively
mobile
PM-0
passively
mobile
AM
Actively
mobile
AM-SED
Actively
mobile
AM-SW
Actively
mobile
unattached attached -planktonic -drift -other -sedentary -swimming
Invasion Vectors See Appendix Table 23 for definitions
SH BW S
Ships & Ballast So
Boats water Bal
B HF MS
id ""II
ast =ouling 1
AF
Moveable
Structures
S/R
1
AE
Intentional
Stocking/
Release
r 1
AA
1
AO
Atlantic
Ovsters
i
Aquaculture
Associated
PO
Pacific
Ovsters
IR
1
ID
i
Intentional
Illegal
Release i
Aquaculture Aquaculture
and Fisheries Escapees
RE
1
AP
i
Research and
Education
r i
A
1
P
Aquarium
Escapees and
Hitchhikers
' T
REC
1
SF
Recreational
Boating and
Fishing
r i
HR
1
O
Other
Habitat
Restoration
and Mitigation
r
Infrastructure Aquarium Ornamental Seafood
Development and Plant Plant Escapees Processing
Trade and Hitchhikers and Release
12
-------
The public version of CBRAT limits users to generating single Species Profiles. Because of the size of the
files, CBRAT uses email notification for multiple species profiles, which requires a higher level of access.
As additional traits are synthesized in CBRAT they will be added to the Species Profiles. In particular,
future versions will map species' vulnerability to climate by ecoregion.
C. Publications Search
The Publications function searches for references in CBRAT (Figure 10). References can be searched for
by citation, author, title, or publication ID. Citation is the abbreviated form used within text (e.g., Garth
et al., 1987), while author can include any of the authors (e.g., Garth, Haig, or Knudsen). Search options
include "starts with", "contains", and "is exactly". To find all publications with an author, use the author
and contains options. The output lists all the references in CBRAT that meet the criteria, and clicking on
the title will open the reference on the Publications page (Figure 5).
Publications
i |!iilili..jtki..-,: Citalkm • slallsBWTT] fonn. 154
Publications List
"Ciartlij I'M" ^Turned :i records:
*.IMII.- ii. '.v '.|ii'j i,-, nl lir.ii liyiinin [.nibs trwill M< *i< ii ond Ml-- r i-nl r.il .in'l Sli«Tion id: i(]/S9^B
n.)^: I'-I I."i
Citation: Oarth. 1940
Aulln)i(s): CailPi. J.S.
Liltoral bracliynran faima of the Galapagos Archipelago
Publication Id: 100993
Djlc: 1046
t.irarmn: t^rrri, 14"lh
Authors): Garth, J,s,
The IM.I. hyiir-« "I ' !»• "A'-kny" Expedition, wild rvilldrkv OH . ,in innlmjH ,i I , .illi'i t m.j in tlic P.m.i in-i Biylil
publication id: 3C]/SH<*[)
Date: 1948
Citation: Garth. 1048
: CJith. J.S.
Figure 10: Publications search page.
The Publications page searches for references in CBRAT. The first option is whether to search by
"citation", "author", "title", or "publication ID". The second options is whether to search by "starts
with", "contains", or "is exactly". Note that "author" can include any author when there are multiple
authors as long as "contains" is used. In this example, the search was for all references with Garth as the
first author that were published in the 1940s.
D. Locations Search
The Locations function is used to associate a geographical location (e.g., town, bay) to a MEOW
ecoregion. Clicking on Locations from the Search tab opens a Locations search page with the world's
ocean partitioned into Marine Ecoregions of the World (MEOW) ecoregions (Figure 11). A location can
be searched by name by typing in the name, or part of the name, in the text box. We recommend
searching using "contains" rather than "starts with" or "is exactly". The search may return multiple sites,
from which the user can select one, which is then plotted on the map and the corresponding MEOW
ecoregion listed on the bottom. If the query returns too many sites, it is possible to limit the search by
using "Select Country". It is important to recognize that the same name, or very similar name, is often
used in different countries, and in some cases in the same country or state. We attempted to mitigate
confusion by appending the state and/or country name to a location name when we were aware of the
problem; however, the user is cautioned that a general knowledge of the location of a site will reduce
the likelihood of plotting the wrong location.
13
-------
In addition to names, it is possible to search by latitude and longitude by clicking on the "Lat. & Long."
tab next to "Location Search" tab. This search is designed to use decimal degrees (e.g., Newport Bay, CA
= latitude: 33.6, longitude: -117.9). However, there is a built-in function to convert degrees - minutes -
seconds to decimal degrees. We remind users to negate longitudes on the U.S. Pacific Coast (or to input
"W" for degrees - minutes).
Figure 11: Search Locations page showing a global view of all 254 MEOW
ecoregions.
In this example, we searched for a location that contains "Newport" with no country selected. This
search returned 19 locations, of which the "Newport Bay Estuary" was selected, indicated by the red
arrow. The default scale for the maps is the NEP and U.S. Arctic; the globe in the upper left corner was
selected to obtain a global view. It is also possible to search using latitude and longitude by clicking on
the "Lat. & Long." tab in the upper right. Maps of all the MEOW ecoregions can be downloaded as PDF
files from the Documents tab.
E. Comments Search
This function allows the user to search for a word or phrase across all the comments within the CBRAT
database. Selecting Comments from the Search tab will open a page for this purpose (Figure 12), which
allows searches using one or more keywords (including phrases), a taxa code to limit the search to a
specific taxonomic group (see Appendix Table 20), citation for a particular reference, and/or a date
range when comments were added to CBRAT. A search can be based on one or more combinations of
these criteria by clicking in the box alongside the appropriate search criteria. At least one criterion must
be selected to enable the search operation. Searches are based on the "and" operator (vs. "or"
operator); thus the more criteria added, the more narrow the returned search result will be. Filtering is
recommended so as not to generate a very long list of comments; clicking the keyword box without
entering any text generates over 5700 comments in the current public version.
14
-------
5,769 comments exist.
0 of those have one or more empty timestamps and as such may not appear in a date search.
Search by keyword? *
planktotrophic
Add Keyword
Search by taxa code? "*
DEC
Search by citation?
Abbott, 1974
Search by date?
Created? ' Updated?
From: 2008 » January » 1 "To:
2015 * September * 9 »
(Note that a search by date will not include
any undated comments)
2 search options are enabled. You may proceed.
Search Reset Export CSV Export XLS
Figure 12: Search Comments page.
In this example, the search is for comments that have the words "larvae" and "planktotrophic" among
decapods (DEC), as indicated by the checkboxes. This search returned two comments with the data
currently in the public version of CBRAT. The returned comments can be exported as a csv or Excel file.
III. BIOGEOGRAPHY
From within the Biogeography menu, the user can generate separate maps of distribution (Figure 13),
relative abundances (Figure 14), population trends (Figure 18), and native/non-native classifications
(Figure 19) at the MEOW ecoregion scale. In the future, an additional map will display the relative
vulnerability to climate change by ecoregion. Clicking on the Biogeography tab from the top row of tabs
opens a map of the species' global distribution by Marine Ecoregions of the World (MEOW) ecoregions
(see Sidebar #2: MEOW Biogeographic Schema). In the public version, the Biogeography page defaults to
the Distribution map because in some cases the information is sufficient to determine a species' global
distribution but not its relative abundance pattern.
15
-------
Sidebar #2: MEOW Biogeographic Schema
We use the "Marine Ecoregions of the World" (MEOW) biogeographic schema (Spalding et al.,
2007) as the framework for synthesizing the distributions and abundance patterns of near-coastal
species as well as climate projections (e.g., sea surface temperature) at a regional scale. MEOW is a
hierarchical schema for marine coastal waters to a depth of 200 m. The original three levels of
MEOW include ocean basin realms divided into smaller provinces and then smaller ecoregions. To
capture differences in the eastern and western sides of the Atlantic and Pacific, we modified the
MEOW schema by adding a fourth level, the region which is between a realm and province (Reusser
and Lee, 2011; Lee and Reusser, 2012). Our analysis is primarily at the MEOW ecoregion scale,
which is defined by Spalding et al. (2007) as "Areas of relatively homogeneous species composition,
clearly distinct from adjacent systems. The species composition is likely to be determined by the
predominance of a small number of ecosystems and/or a distinct suite of oceanographic or
topographic features." In total, there are 254 MEOW ecoregions in the world's oceans. As discussed
in Section II.D., the MEOW ecoregions can be viewed in the Search-Locations page while a PDF of
the ecoregions is available from the Document tab (Section X).
A. Distribution Map
The distribution map shows the global distribution of where the species has been reported by MEOW
ecoregions (Figure 13). Note that a single reported occurrence will link the species to an ecoregion. It is
also important to note that the distribution map displays ecoregions where the species has been
reported but which we consider absent because of regional extinction or taxonomic mistakes. The
region displayed can be changed by panning the map, while the scale of the map can be changed with
the scaling bar in the upper left corner of the map. Clicking on the globe symbol will expand the map to
a global view. Clicking on an area on the map identifies the MEOW ecoregion on the bottom of the map.
Clicking on the ecoregion also opens a sidebar menu on the right with links to the abundance,
classification, and population trend maps.
16
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Metacarcinus magister (Dana, 1852)
Figure 13: Species distribution map of Metacarcinus magister.
Map displaying the reported distribution of the chosen species by MEOW ecoregions. Distributions
include all reports, which may include ecoregions where the species is considered absent due to regional
extinction, such as a nonindigenous species that was reported but which did not become established.
Distribution maps also include ecoregions where the species has been incorrectly reported. The relative
abundance map (Figure 14) identifies ecoregions where the species is classified as absent, while the
population trends map (Figure 18) identifies whether the species is absent either due to extinction or
incorrect taxonomy. Clicking on a region identifies the ecoregion on the bottom as well as calling up
links to the Abundance, Classification, and Population Trend maps.
B. Relative Abundance Map & Relative Abundance Schema
From the Distribution map, clicking on the Abundance link on the sidebar menu on the left will open a
map of the relative abundance of the species by MEOW ecoregion (Figure 14). A key to the color codes
can be accessed via the "Legend" in the upper left corner of the map, reproduced here as Figure 15.
With relative abundance classifications, the classification for an ecoregion may be assigned a "master"
classification. A master classification is the official CBRAT classification, which is based on a weighting of
all the evidence for that particular ecoregion. Because of resource limitations, master abundance
classifications are primarily limited to the twelve Northeast Pacific (NEP) and U.S. Arctic ecoregions.
Master classifications are indicated on the map by a yellow border around the ecoregion. Master
classifications are also used with population trends and native/non-native classifications.
To view and/or identify a particular ecoregion, click on the area on the map. A list of citations used for
the designation of the distribution and/or relative abundance of that species in that ecoregion will
appear on the right. Citations highlighted in a darker gray are "key" references in making the decision as
to the master abundance classification. This approach is used to lend transparency to the decision
process and is especially pertinent when there are multiple conflicting references as to the relative
abundance of a species. However, in many cases the Comments were the primary information used in
assigning a master abundance, in which case no key reference(s) may be highlighted.
17
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Metacarcmus magister (Dana, ass2)
EtitKFfHlHjr.IllllV
Figure 14: Relative abundance map for Metacarcinus magister.
The codes for the relative abundance classes can be viewed by clicking on the Legend link (see Figure
15). Ecoregions with "master" relative abundance classifications are highlighted in yellow. The vertical
yellow line running through the Aleutians is a computer artifact and not a delineation of another
ecoregion. The ecoregions on the East Coast and in Japan coded in black indicates that M. magister has
been reported from these ecoregion but is currently absent. Cause for each absence is summarized
under the population trends map (Figure 18). The citations on the right are those that linked M.
magister to the chosen ecoregion, while the grayed citation identifies a key reference used in assigning
the relative abundance to that ecoregion. The CBRAT citation highlighted in yellow indicates the master
classification. At this scale, the Puget Trough/Georgia Basin Ecoregion is difficult to see, and the map can
be expanded using the scaling bar in the upper left of the map.
We developed a three-level classification schema for ecoregion-scale relative abundances (Figure 16).
Details on the classification schema are given in Sidebar #3: Relative Abundance Classification Schema.
The color codes for the relative abundance classes are available on the legend on the map (Figure 15),
which also provide a short definition. Definitions and quantitative cut points of each level of relative
abundance are available in Appendix Table 2. The conceptual framework for assigning relative
abundance classes is explained in Sidebar #4: Dominance Normalized Relative Abundances & Hybrid
Approach to Assigning Relative Abundances.
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Abundance
Very Abundant
High Moderate
Abundant
Moderately Abundant
Moderately Rare
O Moderate
Low Moderate
Rare
Present
Reported Absent
Very Rare
Transient
Hyper Rare
Conflict
Very Abundant
The most numerous species within an
ecoregion, usually inhabit a habitat of
large spatial extent and/or multiple
habitats.
Figure 15: Legend for the relative abundance map (Figure 14).
Clicking on a class in the legend will bring up a short definition.
Moderately Abundant
Not Reported
(default)
Transient
(Not Established)
Figure 16: Three-level relative abundance classification schema.
Species are classified at the lowest level based upon the available data. See Appendix Table 2 for
definitions of the terms.
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Sidebar #3: Relative Abundance Classification Schema
Knowledge of a species' abundance provides additional insights into its vulnerabilities than are provided by
biogeographic distributions alone. Distributions identify where a species can survive while geographic
patterns of abundance help elucidate preferred and marginal environmental conditions. Additionally,
numerous studies have shown that rarity is a practical predictor of vulnerability to anthropogenic stressors
(Davies et al., 2000; Duncan and Young, 2000; IUCN, 2014). Here, we provide a summary of the approach we
developed to assess relative abundances at an ecoregion scale; a more complete discussion can be found in
the climate vulnerability framework document (Lee et al., in progress).
Our approach is to assess relative abundance based on classes rather than absolute abundance, where
relative abundance is total population size of a species normalized to the abundances of the other species in
the defined taxon or guild. Relative abundances are frequently used when comparing studies in which
sampling techniques are not directly comparable or when comparing species across taxa, habitats, or spatial
scales. Abundance classes are used when quantitative data are not available and/or when integrating
quantitative and qualitative assessments. Relative abundance ranks depend upon what taxon or guild is used
to normalize the abundances. In general, the relative abundance of a particular species is greater the more
narrow the taxon or guild used to normalize the abundances, (e.g., a crab species may be abundant within its
family but rare when all decapods are considered).
To be able to assess species with different levels of information, we developed a three level classification
system, with the level of resolution chosen primarily based on data availability (Figure 16). Level I is a
"present/not reported" analysis, with the addition of Absent and Transient classes. Absent is used to capture
cases when a species was reported from an ecoregion but does not actually occur either because the species
was incorrectly identified or because the species went extinct. Transient is used to capture cases when a
species shows up in an ecoregion due to "unusual" climatic or oceanographic events, including cyclical events
like El Nino. However, the key aspect is that the species does not establish a permanent reproductive
population. Level II is a basic three-class system (Abundant/Moderate/Rare). Level III then splits each of the
Abundant / Moderate / Rare classes into two subclasses. Additionally, there is a Hyper-Rare subclass in Level
III for species that have not been observed in 50+ years, assuming at least a moderate sampling effort. As a
guide, Appendix Table 2 provides generalized definitions for the abundance classes as well as phrases
commonly associated with the different classes.
We want to emphasize that we are assessing relative abundance at the ecoregion scale, with each species
compared to all other species within the target taxon across all habitats within the ecoregion. Because
relative abundance is assessed at the ecoregion scale, the area of the habitat occupied by a species becomes
a key factor in determining relative abundance. A species that is very abundant in a habitat of limited areal
extent might be classified as moderate, or even rare, depending on the area of the occupied habitat. The only
exception to comparing across all habitats is that oceanic and estuarine populations are assessed separately,
with the relative abundance assigned to the larger of the two. Thus, a crab that was moderately abundant in
estuaries but rare in the ocean would be assigned a relative abundance class of moderately abundant.
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Sidebar #4: Dominance Normalized Relative Abundances & Hybrid Approach to Assigning Relative Abundances
Even when there is ample quantitative data, there is no agreement as how to define what constitutes an
abundant versus a rare species (see Gaston, 1994, 1997 for discussion of rarity). Our approach is to use
"dominance normalized relative abundances" (DNRA) as a standard methodology to compare relative
abundances across a suite of species from multiple quantitative studies. We define dominance normalized
relative abundance as the target species' proportional abundance in comparison to the mean abundance of the
numerically dominant species, defined here as those species making up >75% of the individuals in the study (see
Swartz et al., 1985). Thus, it is a measure of how abundant the species is in comparison to the most common
species in the study, and a value of 0.05 indicates that the particular species has an abundance equal to 5% of the
average abundance of the numerical dominants. Each species' dominance normalized relative abundance value is
then used to assign it to one of the abundance classes defined in Sidebar #3 using the quantitative cutpoints
defined in Appendix Table 2.
In many cases, it is not possible to rely solely on quantitative studies because of the paucity of such studies
especially at regional scales, difficulties in comparing studies across different habitats, and because many
organisms are not detected in quantitative studies due to rarity or sampling biases. Thus, we developed a
"hybrid" approach that integrates quantitative analysis when available, qualitative reports (e.g., taxonomic
treatises), online databases (e.g., OBIS; http://iobis.org/home), approximations of the area of the habitat
occupied by the species, and expert opinion (Figure 17). Using weight of evidence, species are assigned to a Level
I, II, or III abundance class, depending upon the type and amount of information. While quantitative studies are
generally considered the most important type of information, key questions in deciding how heavily to weight
them are: 1) was the study at a regional scale or limited to a localized area; 2) what habitats were sampled and
how much of the area of the ecoregion do these represent; and 3) were the sampling techniques suitable for the
target species? A localized quantitative study might be given less weight in assigning an ecoregion-scale
abundance class than a qualitative assessment across multiple habitats covering much of the ecoregion.
Approximate ranges of the percentages of species falling into the various relative abundance classes are provided
in Appendix Table 2. These ranges are derived from our analyses of the relative ecoregional abundances of
brachyuran crabs and bivalves in the Southern California Bight, Northern California, Oregon, Washington,
Vancouver Coast and Shelf, and Puget Trough/Georgia Basin ecoregions, where 98-100% of the species in each
ecoregion are classified to at least Level II. Percentages for the Level III classes had to be extrapolated as only 31-
61% of the crabs and bivalves were classified at this level of resolution. These percentages are presented as
general examples, and the percentages for other taxa or regions may fall outside these ranges, in particular when
a small number of species occurs within an ecoregion such as in "extreme" environments. An example of an
extreme case is the Beaufort Sea - Continental Coast and Shelf Ecoregion which only has three brachyuran crabs,
of which two (66%) are classified as abundant and the third is classified as high moderate (33%).
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Inputs
I
Natural History
& Taxonomic
Literature
Quantitative Surveys | Web-based biogeographic
distributions
(OBIS & GBIF)
Regional vs. Site
Probabilistic vs. Targeted
Weight Information
•MiH
Relative Abundance Estimate
Figure 17: Hybrid approach to assigning ecoregional-scale relative abundance
classes.
The approach weights abundances from regional-scale and local quantitative studies, natural history and
taxonomic texts, online databases, and expert opinion. In general, regional-scale, probabilistic surveys
are given the greatest weight, assuming the sampling techniques were appropriate for the chosen
species.
C. Population Trends
The user can display a map of the extent of a species' population increase or decrease within ecoregions
by clicking on the Population Trends link in the sidebar (Figure 18). Navigation on the Population Trend
page is the same as on the Abundance page. Clicking on the "Legend" link in the upper left corner of the
map provides the color codes to the trend classes as well as short definitions for each class. Ecoregions
with master (CBRAT) classifications are highlighted in yellow. The numerical cutpoints used for the trend
classes are discussed in Sidebar #5: Population Trend Classes while Sidebar #6: Time Intervals for
Population Trends discusses the time periods used to evaluate population trends.
Clicking on an ecoregion will display the CBRAT master classification (if any) and the references linking
the species to the ecoregion whether they addressed population trends or not. Both the start interval
and end interval for the trend are given for each reference. In nearly all cases for master classifications,
"Continuing" is the End Time, indicating that the population increase or decrease is presumably still
occurring; an exception is when the date interval for the extinction of a failed nonindigenous species is
known. Information on population trends in near-coastal species is very limited, and in most cases the
master classifications were generated from an expert analysis of the information synthesized in the
Comments. Thus, nearly all references linking a species to an ecoregion are given an "Unknown" trend
classification, indicating either that no population trend is associated with the reference or that the
population trend data in the reference was not linked separately.
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Metacarcinus magister (Dana, 1852)
Figure 18: Population trends by ecoregion for Metacarcinus magister.
Our estimates of the extent of population increases or decrease are indicated by the color coding, with
the trend classes discussed in Sidebar #5: Population Trend Classes. Master (CBRAT) assignments are
highlighted in yellow. All the citations linked to an ecoregion are displayed on the right by clicking on the
ecoregion, with the Master trend classification listed on top. The start and end time intervals of the
population trend are listed under the trend classification. The red cross-hatched coloring off Japan and
New England indicates that A/7. magister has been reported from these ecoregions but that it did not
become established (i.e., it is absent).
23
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Sidebar #5: Population Trend Classes
CBRAT uses population decline as an indicator of a species' general vulnerability to climate change,
based on the concept that a currently stressed population is less likely to be able to adapt to the
imposition of additional stressors related to climate. Further, smaller populations are at greater risk in
general to environmental stressors and/or catastrophes. Conversely, a population that is increasing
presumably would be less vulnerable. To capture this aspect of a species' vulnerability, we assign a
population trend class to each ecoregion a species occupies.
Values for the cutpoints for the population decline classes were taken from the IUCN A2-A4 criteria to
assess species at risk of extinction ("red list"; IUCN, 2014). Though we do not apply these population
decline values in exactly the same manner as the IUCN, they do represent generally accepted criteria
for species vulnerability. For population increases, we used the IUCN values converted increases. In
many cases, the extent of population change had to be interpreted from verbal descriptions of
changes in population size and/or by extrapolating the effects of habitat loss (see IUCN for use of
different types of data). While such extrapolation likely introduces some error, it is environmental
more protective to assign classes based on incomplete data compared to simply defaulting to
"unknown", or data deficient in IUCN terms, and not accounting for current population declines.
Population Trend Classes:
Order-of-Magnitude: Greater than a 10-fold population increase. Most likely to occur during the
expansion phase of NIS and, potentially, during climate-related range expansions of native
species.
Major increase: Population increase of >100% and <10-fold.
Substantial increase: Population increase of 50% to 100%.
Moderate increase: Population increase of 30% to 49%.
No apparent trend: No sustained population trend within the ecoregion, with a margin of error of
-29% to +29% in population size.
Moderate decline: Population decline of -30% to -49%.
Substantial decline: Population decline of -50% to -79%.
Extreme decline: Population declines of -80% to -99%.
Unknown: Unknown extent of population change. Default value in absence of any data.
Conflict: A conflict occurs when two non-master citations disagree as to the extent of the
population increase or decrease. As with abundance, there is no master conflict.
Absent: Extirpated: Species went extinct within the ecoregion.
Absent: Mistake: Species does not occur in the ecoregion because previous reports were based
on incorrect taxonomy.
Transient: Transient species are treated separately since they are not established, and hence are
not undergoing a population trend per se.
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Sidebar #6: Time Intervals for Population Trends
All population trends are keyed to a descriptive time period or a specific date (year or decade) for both
the beginning and the end of the population increase or decrease. Whether descriptive or quantitative
timeframes are used depends, in part, upon the resolution of the population trend data. The following
definitions are used for the time periods:
Descriptive Terms: The beginning and end of the population change is linked to the following:
Continuing: A population increase or decrease that is assumed to be ongoing. This is only
available as an end date. Unless there is information indicating otherwise, "continuing" is used as
the end date for population trends.
Recent: A population increase or decrease that began and/or ended within approximately the last
10 years. The IUCN (2014) uses "10 years or three generations (whichever is longer)"; however
given the paucity of information on generation time in most invertebrates we only use the 10
year criterion.
Long-term: Long-term is defined here as a population increase or decrease that began and/or
ended between 1950 (post-World War II) to 10 years ago (i.e., beginning of "recent"). Unless
more detailed information is available, long-term is assumed as the start date for population
declines.
Historical: Historical is defined here as a population increase or decrease that began and/or ended
between 1750 (approximate beginning of the Industrial Revolution) to 1950.
Preindustrial: A population increase or decrease that began before 1750.
Unknown: Unknown is the default start and/or end time period if no information is available.
Decades: The beginning and end of the population change is linked to specific decades, from 2010-
2019 to 1900-1909, and then 50 year intervals to 1800.
Years: The beginning and end of the population change is linked to specific years, from 2000 to 2020.
Used for recent events, such as the ongoing starfish declines.
D. Classification Map - Native/Non-Native Status
A map of a species' native/non-native status by ecoregion is available by clicking on the Classification
link in the sidebar menu (Figure 19). Within each ecoregion, a species is classified as a native,
nonindigenous, cryptogenic, transient, or unknown (default) as indicated by the color key in the legend.
Navigation on the Classification page is the same as on the Abundance page and ecoregions with master
classifications are highlighted in yellow. Additionally, there is a conflict class when two or more non-
master publications disagree about a species' classification. Conflicts are generated automatically and
there is no master conflict classification. These classes are discussed in Sidebar #7 Native vs.
Nonindigenous Classifications.
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Species are also classified according to their population status within the ecoregion. With one exception
population status is not mapped, but is available in the sidebar on the right by clicking on the ecoregion
of interest. Establishment classes include established, not established, and unknown (default).
Additionally, there is a subclass where a species can be classified as stocked if it is cultured (e.g.,
aquaculture) in the ecoregion. All native and cryptogenic species are assumed to be established, and
species that are classified as Absent in the Abundance map due to incorrect taxonomy are not displayed
on the Classification map. However, failed introductions in an ecoregion are given a special class of "MIS
- Not Established" and color coded in red hatched marks. Population status classes are discussed in
Sidebar #8 Population Establishment Status.
Clicking on an ecoregion displays the linked references in a sidebar on the right, along with date and
location of first record (if known) for invaded ecoregions. The colored boxes next to the references
indicate both the invasion and establishment status of the species according to that reference, and
whether the species is stocked (Figure 19). Another important component of invasion biology are the
vectors by which species were transported to non-native ecoregions. Because the importance of
different invasion vectors relate strongly to the life history characteristics of the species, vectors are
considered species traits rather than an ecoregion characteristic and are not displayed on the
Classification maps. Rather, vectors linked to non-native species are available through the "All Life
History & Environmental Information" query on the Data Export page (see Section IX.).
Grandidierella japonica Stephenson, 1938
Figure 19: Native/non-native status of the amphipod Grandidierella japonica by
ecoregion.
The master (CBRAT) native/non-native classifications are outlined in yellow. Clicking on an ecoregion
displays the references that link the species to the ecoregion. Citations in gray are key references in
making the decision as to the classification for that ecoregion, though in many cases key information
used to assign classifications is summarized in the Comments. The upper colored box just below each
citation is the species' native/non-native status according to that reference, using the color key in the
legend. The lower colored box is the population establishment status, again using the color key in the
legend. If the species is stocked, a third yellow box will be displayed. If known, the location and date of
first record for the species in the ecoregion is displayed on the top of the master classification; clicking
on the location/date will display the associated reference.
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Sidebar #7: Native vs. Nonindigenous Classifications
Species are classified within each ecoregion using the following definitions:
a) Native: Species that occur naturally in the ecoregion with no human intervention.
Natives are assumed to be established within the ecoregion.
b) Nonindigenous Species (NIS): Species that have been introduced into an area through
human activities, whether accidently or on purpose. NIS may be established or not
established in an ecoregion.
c) Cryptogenic: Cryptogenic species are not clearly native or introduced. As originally
defined, this term was to capture uncertainty regarding a species biogeography and
invasion history (Carlton, 1996). However, "cryptogenic" is increasingly for species with
taxonomic uncertainties, such as cryptic species. To avoid mixing uncertainty over
invasion history with taxonomic uncertainty, we restrict the use of cryptogenic to cases
where there is some evidence for invasion.
d) Transient: Transient species are those that temporarily migrate into an area as a result
of unusual or extreme climatic conditions, including cyclical events such as El Nino. Their
movement into the area is via climatic and oceanographic mechanisms rather than
mediated through direct human activities, and are not considered as NIS. By definition,
transient species are not established.
e) Unknown: A species is classified as unknown when there is insufficient information to
make a judgment as to its origin. This is the default classification in the absence of any
evidence. In some cases, species outside of the North Pacific may have an unknown
classification because we have not yet analyzed the taxon and/or geographical region in
terms of classification status. We also note that some authors use cryptogenic when there
is very limited information rather than unknown, however we believe that this can be
misleading.
27
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Sidebar #8: Population Establishment Status
In addition to native/non-native origin, species are classified in terms of their population status
according to one of three primary classes and one subclass:
a) Established: A species with a self-maintaining, natural population as indicated by its
population size, occurrence overtime, wide-spread geographical distribution, presence of
juveniles, and/or presence of reproductive adults. Native and cryptogenic species are
assumed to be established.
b) Not Established: A species that has been reported from an area but that does not
maintain a self-reproducing population. Indicators of non-establishment include not
observing the species for >25 years and lack of juveniles or reproductive adults. By
definition, transient species are considered not established. Nonindigenous species are
classified as either established or not established.
c) Unknown: Species for which there are insufficient spatial and/or temporal records to
assess population status. This is the default population status. Unknown is used for stocked
species that have not been reported from the wild but which have a high potential to
escape containment. This is particularly used in Asia where little information is available
other than that a non-native species is being cultured.
d) Stocked: Stocked species are a subclass, and are defined as species maintained through
active human intervention, usually via aquaculture. Stocked species known only to exist in
an ecoregion through human intervention are given a population status of not established.
Stocked species that have been reported from the wild are assigned a population status of
established, not established, or unknown, as appropriate. In many cases it will be unclear
whether a stocked species occurs in the wild, in which case the stocked species is assigned
an unknown population status.
E. Vulnerability
Maps of a species' relative vulnerability to climate change by ecoregion are not currently available.
F. Comments-
This is another access point for the species' comments section. Anywhere you see this link, you will be
able to access the comments for the selected species.
IV. ENVIRONMENT
The Environmental pages provide information on a species habitat requirements and environmental
tolerances. Click on the "Environment" tab from the list under the species' name to open a figure of the
species' regime. The sidebar menu includes additional tabs to access information on the species' specific
habitat requirements and environmental tolerances. Our approach is to classify habitats and
environmental ranges as either "observed" (in purple) or "preferred" (in green). We make this
28
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distinction because many marine/estuarine species can be found across a wide range of habitats and
environmental conditions, yet the majority of the population occurs in a much more restricted range.
Preferred habitats or environmental ranges are those that the species "normally" occurs in, as indicated
by high densities or frequencies, breeding individuals, and/or presence of juveniles. "Observed"
indicates that the species has been collected in a particular habitat or within an environmental range
(e.g., salinity). Observed is the default classification when there is insufficient information to decide on
the relative suitability of the habitat or environmental range for a species. Most of the terms on the
environmental pages have a "?" next to the attribute; clicking on these will provide a brief definition.
A. Regime
This page displays the broad geomorphological regions that near-coastal species may occupy (Figure 20).
These regimes are primarily defined by depth and salinity and secondarily by energy level, and multiple
ecosystems and habitat types occur within each regime. Filled purple boxes indicate that a species
occurs within that regime, while filled green boxes indicate a preferred regime for the species.
"Oceanic" is used in a broad fashion, and includes ecosystems that occur at depths >200 m in inland
seas, such as Puget Sound. For definitions of the terms see Appendix Table 3.
Metacarcinus magister (Dana, 1852)
Taxonomy Biogeography
Environment
Life History Specialization Morphology and Physiology
Ecosystem / Habitat
Depth
Temperature
Terrestrial s
Rivers, Streams,
and Creeks
(Lotfc) -
Coastal Bay ;
Oceanic
(>ZOOm bathymetric
isopleth) A
ZOOm bathymetric isopleth)
-------
are different. For example, the surfgrass, Phyllospadix torreyi, occurs in the rocky intertidal ecosystem
but its roots actually grow in the sand (an unconsolidated substrate) accumulated in tide pools or
between rocks. One way of looking at this is that ecosystems are contained within regimes, while
substrate types are contained within ecosystems.
A hierarchical view of the all the ecosystems and habitats in CBRAT is displayed by clicking on "Full List
View" in the upper left of the page (Figures 22-23), while definitions for the terms are available in
Appendix Table 4. If a species resides in one of the pre-defined specialized habitats, clicking on the
"View Specialized Habitats" link on the top right of the page will direct you to the Habitat page under
Specialization, as discussed in Section VI.A.
Metacarcinus magister (Dana, iS52)
Figure 21: Ecosystem/Habitat page for Metacarcinus magister.
The page displays the near-coastal ecosystems and habitats occupied by the species (purple squares) or
preferred by the species (green squares). Clicking on "Full List View" in the upper left corner displays the
full list of ecosystems and habitats (see Figures 22-23), while definitions for the terms are available in
Appendix Table 4. The boxes under Zostera marina indicates that juvenile M. magister have a facultative
relationship with Z. marina, which is considered a specialized habitat. Clicking on the "View Specialized
Habitats" in the upper right opens the Habitat page under the Specialization tab, in this case displaying
the facultative relationship with Z. marina.
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Metacarcinus magister (Dana, 1852)
I •,
Metacarcinus magister (Dana, 1852)
U Mimcjruvc
I Linergtfiit Mar*ti
H<
a
Otliur/Utikn
a
a
a
Specialized
Systems
Figure 22: All the major unconsolidated ecosystems/habitats on the Ecosystem/Habitat page.
31
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Metacarcinus magister (Dana, 1852)
—
• Rocky Iiitertidal £
Metacarcinus magister (Dana, 1852)
Metacarcinus magister (Dana,
Metacarcinus magister (Dana, 1852)
Figure 23: All the major consolidated, pelagic, and specialized systems on the Ecosystem/Habitat page.
32
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C. Depth
This page contains the categorical (qualitative) and numerical (quantitative) observed and preferred
depth ranges for a species (Figure 24). Based on standard usage, different depth classes are used for
benthic versus pelagic species. Quantitative depth ranges are entered when available, though in most
cases the qualitative information using the depth classes is more complete. A user can view all the
available depth ranges by clicking on the "Full List View" at the top left corner and a hierarchal view of
all the available depth ranges will be displayed (Figure 25). Definitions for the terms are given in
Appendix Table 5.
Metacarcinus magister (Dana, 1852)
Taxonomy Bkxjeography
Environ menl:
Life History Spe<
Depth Ranges (meters)
Min Max
Observed: [
Preferred:!
Temperature
Intertidal (MLLW
MHHW)
Mid Intertidal
Lower Intertidal
I Shallow Subtirial (>0
- 30m) 9
\ Deep Subtidal (>30
200m) t
Bathyal (> 200
2000m)
Figure 24: Depth page for Metacarcinus magister.
The purple boxes are observed depths while the green boxes indicate preferred depths. Clicking on "Full
List View" in the upper left corner displays the full list of depth classes (Figure 25), while definitions for
the terms are available in Appendix Table 5.
33
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Metacarcinus magister (Dana, 18S2)
Metacarc/'nus magister (Dana, 1852)
Figure 25: All the benthic and pelagic depth classes on the Depth page.
D. Salinity
This page displays the salinity classes over which a species has been reported, as well as the quantitative
salinity range when available (Figure 26). The hierarchical salinity schema used in CBRAT was derived
from the Venice system (Anonymous, 1958), and all the salinity classes can be viewed by clicking the
"Full List View" at the top left corner (Figure 27). All salinity values are given in practical salinity units
(psu). Purple boxes indicate an "observed" salinity range while green boxes indicate a "preferred"
salinity range. The definitions for the terms used on this page are given in Appendix Table 6.
Metacarcmus magister (Dana, 1S52)
Figure 26: Salinity page for Metacarcinus magister.
The purple boxes are observed salinities while the green boxes indicate preferred salinities. Click on "Full
List View" in the upper left corner to display the full list of salinity classes (see Figure 27).
34
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Metacarcinus magister (Dana, 1852)
Salinity
(Freshwater (<0.5 -
psu)
• Brackish (0.5
Q<30psu) 0
a Marine / Euhaline ,
(30 - <40 psu) H
[
1
Oligohaline (0.5 - &)
<5 psu) H
Mesohaline (5 - ©
<18psu) B
Polyhaline (18- '„<
<30 psu) D
SBeta-euhaline (30 -
- <36 psu)
aAlplia-euhaline
(36 - <40 psu)
BHypersaline (>-
40 psu)
BBeta-oligohaline
(0.5 -3 psu)
aAlpha-oligohaline
(3 - <5 psu)
SBeta-mesahaline
(5 - <10 psu)
Alpha-mesohaline -
(10 - <18 psu)
SBeta-polyhaline
(18 - <25 psu)
Alpha-polyhaline Q
(25 - <30 psu)
Figure 27: All the salinity classes on the Salinity page.
E. Substrate
This page displays the substrate(s) the organism lives in or on (Figure 28). As with the other
environmental attributes, a purple box indicates an "observed" substratum and a green box indicates a
"preferred" substratum. This page also shows the quantitative range for three attributes related to
unconsolidated sediments; specifically phi (particle size expressed as negative Iog2 of size in mm),
percent fines (combined percent of silts and clays), and percent total organic carbon (TOC) content of
the sediment. The definitions of the substrate classes are available in Appendix Table 7. Clicking the "Full
List View" at the upper left corner of the Substrate page will display a hierarchal view of all the substrate
classes (Figure 29-30).
There are two nuances that are important in understanding the substrate classification. The first is that
cobble up to 256 mm in diameter is considered an unconsolidated substrate because the particles are
"movable" and allow water to flow through the sediment bed. However, this can result in species
normally associated with hard substrates (e.g., barnacles) being linked with unconsolidated substrates if
they occur on gravel or cobble. The other nuance is the difference between the ecosystem type and
substrate type. In most cases there is a simple relationship between habitat and substrate type.
However, as discussed in Section IV.B., there are cases when a species, such as surfgrass, is linked to a
consolidated ecosystem but actually grows in sediments. Conversely, barnacles that live on the shells of
semi-infaunal bivalves would be linked to an unconsolidated habitat but live on a consolidated
substrate.
35
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gfster (Dana, 18S2)
Figure 28: Substrate page for Metacarcinus magister.
The purple boxes are observed substrates while the green boxes indicate preferred substrates. Clicking on the Full List View link in the upper left
corner displays the full list of ecosystems (see Figures 29-30).
«_,
Figure 29: Consolidated substrate classes on the Substrate page.
36
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Metacarcmus magtster (Dana, las?)
Metacarcinus magister (IMH.I, 1852)
Figure 30: Unconsolidated sediment classes on the Substrate page.
Minimum and maximum numerical values for phi, percent fines, and percent TOC are captured in the boxes on the top of the page.
37
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F. Energy
This page contains information about wave energy and current energy that a species may encounter
across the range of habitats it occupies (Figure 31). Wave energy classes are derived from Howes et al.
(1999) based on fetch. Definitions for wave energy classes are provided in Appendix Table 8. Tidal and
ocean current energy classes are based on Madden et al. (2005), who proposed a general energy
intensity classification based on current velocity and wave energy. The values used here only utilize the
classification based on current velocity. The definitions for current energy can be found in Appendix
Table 9. Note that in many cases, energy classifications were assigned by the general energy regime of
the occupied habitat(s) and/or from comments in the literature.
Metacarcinus magister (Dana, 1852)
Environment lIUJilUM.IM-ff
Exposed
Semi-exposed
Semi-protected
Protected
Very Protected '^
High Energy
Moderate Energy
Low Energy
a
No Energy
Figure 31: All the wave and current classes on the Energy page.
G. Temperature
This page displays numerical temperature tolerances for adult survival and for reproduction (Figure 32).
Temperature ranges for adults are based on temperatures recorded from species' collection sites or
laboratory studies. Temperature for reproduction is based on data from laboratory tests and/or field
observations. Because of limited temperature data, the observed numerical temperature ranges likely
underestimate the full thermal ranges of many species. Species can also be classified according to extent
of their thermal range, with species having a narrow (stenothermal), moderate (mesothermal), or wide
(eurythermal) temperature tolerance range. These classes are used in a qualitative fashion as specific
temperature ranges have not been defined in the literature for the three classes. The qualitative
definitions are given in Appendix Table 10. In future versions, we will provide "ecoregional thermal
indices" based on species' distributions in relation to recent sea surface temperature data at an
ecoregion scale (Payne et al., 2012).
38
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Metacarcinus magister (Dana, 1852)
Environment
Life History Specialization Morphology and Physiology Invasi
Adult Temperature
Mill Max
Observed: |^
Preferred: I
Reproductive Temperature
Min Max
Observed:
Preferred:
Figure 32: Temperature page for Metacarcinus magister.
The green box indicates that M. magister is classified as eurythermal, which was based on its wide
geographical and depth ranges.
V. LIFE HISTORY
Clicking on the "Life History" tab on the top of the page opens the Trophic Level and Feeding page
(Figure 33) along with a set of other links in the sidebar on the left. These pages summarize key
information on the life history of the species, including feeding, reproduction, development, habitat
associations, and mobility.
A. Trophic Level and Feeding
This page displays the feeding mechanism(s) of the adult stage of the species (Figure 33). As with the
environmental attributes, a purple box indicates an "observed" feeding type and a green box indicates a
"preferred", or major, feeding type. Multiple selections of feeding types are used to generate different
types of omnivore strategies. For example, with Metacarcinus magister an omnivore strategy is
indicated by the linkages to predator, scavenger, and herbivore, though the first two feeding types
predominate. Clicking on the "Full List View" at the top left corner will display a hierarchal view of all the
available feeding strategies (Figure 34). Definitions for the terms are found in Appendix Table 11 and 12.
The buttons at the top of the page indicate the level of specialization of the species' diet, using
Generalist, Moderate, and Specialist classifications along with an Unknown default. Sidebar #9:
Classifying the Extent of Trophic Specialization discusses the criteria used to assign a species to each of
these classes, including the rules to automatically assign the degree of specialization, though the
automatic assignment can be manually overwritten by experts. Clicking on "View Trophic Specialization"
in the upper right of the page opens a page displaying the specifics of the species' diet, assuming such
information is available and/or has been captured in CBRAT.
39
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Metacarcinus magister (Dana, 1852)
Figure 33: Trophic Level and Feeding page for Metacarcinus magister.
Click on the "View Trophic Specialization" to open the trophic specialization page for M. magister (Figure
46).
Metacarcinus magister (Dana, 1852)
Figure 34: Major classes on the Trophic Level and Feeding page.
Click on the "View Trophic Specialization" to open the trophic specialization page (see Figures 46 & 47).
40
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Sidebar #9: Classifying the Extent of Trophic Specialization
Species are classified as to their degree of trophic specialization to identify species most likely to be
impacted by climatic changes affecting their food sources. The basic rule is that trophic specialists are
more likely to be susceptible to climate alterations than are generalists that have the flexibility to shift to
different foods. The different feeding modes used in CBRAT are defined in Appendix Table 11 and 12 and
can be viewed on the "Trophic Level and Feeding" page (Figure 34). The four trophic specialization classes
are:
Generalist: Species feeding on multiple food sources, utilizing multiple feeding modes, and/or
utilizing a general food source unlikely to be strongly impacted by climate change. These species
are considered robust to climate change via impacts on food availability.
Moderate: Species that feed on more than one but still limited number of food sources and utilize
a single feeding mode or, at most, two feeding modes. These species are considered to have a
moderate level of vulnerability to climate change via impacts on their food sources.
Specialist: Species feeding on a single or restricted number of food sources and which usually
utilize only a single feeding mode. These species are considered vulnerable to climate change via
trophic impacts unless there are mitigating factors, such as their prey item(s) increasing under
climate change.
Unknown: When there is insufficient information, the trophic specialization is set to "unknown",
which is the default value.
In CBRAT, classification of trophic specialization is automated to the extent feasible by assigning
classifications to broad feeding types and combinations of feeding models as shown in Sidebar #10: Rules
Used to Automate the Degree of Trophic Specialization. Our preliminary rules for classifying herbivores
and predators based on the number of prey items are given below:
Herbivore: Depends on number of plant species consumed
Specialist if < 5 prey items.
Moderate if >5 prey items and <10 prey items.
Generalist if >10 prey items.
Predator: Depends upon the number of prey items consumed
Specialist if < 5 prey items.
Moderate if >5 prey items and <10 prey items.
Generalist if <10 prey items.
These criteria for generalist-specialist herbivores and predators were based on comparing the breadth of
diets of specialists (e.g., several nudibranchs) versus generalists (e.g., Dungeness crabs), and are not
theoretically based. We also note that experts have the ability to overwrite the automatically generated
classification.
41
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Sidebar #10: Rules Used to Automate the Degree of Trophic Specialization
Classification of combined feeding types in terms of degree of trophic specialization. Values in the diagonal in gray are the classifications for a single
feeding type. "Varies" indicates that the degree of specialization depends on specifics of the species' feeding requirements, such as the number of prey
types for a predator. The text in red indicates an unlikely trophic combination, but which are included for completeness.
Combined
Feeding Types
Parasite /
Disease
Symbiotic Algae
Primary
Producer
Herbivore -
grazer
Herbivore -
folivore
Predator
Scavenger
Detritivore
Decomposer
Suspension
Feeder
Deposit Feeder
Other
Parasite /
Disease
Varies
Symbiotic
Algae
Varies
Specialist
Primary
Producer
Varies
Moderate
Moderate
Herbivore -
grazer
Generalist
Generalist
Generalist
Generalist
Herbivore -
folivore
Varies
Varies
Generalist
Generalist
Varies
Predator
Varies
Varies
Generalist
Generalist
(omnivore)
Generalist
(omnivore)
Varies
Scavenger
Generalist
Generalist
Generalist
Generalist
Generalist
Generalist
Generalist
Detritivore
Generalist
Generalist
Generalist
Generalist
Generalist
Generalist
Generalist
Generalist
Decomposer
Generalist
Generalist
Generalist
Generalist
Generalist
Generalist
Generalist
Generalist
Generalist
Suspension
Feeder
Generalist
Specialist
Generalist
Generalist
Generalist
Generalist
Generalist
Generalist
Generalist
Moderate
Deposit
Feeder
Generalist
Generalist
Generalist
Generalist
Generalist
Generalist
Generalist
Generalist
Generalist
Generalist
Generalist
Other
Varies
Varies
Varies
Generalist
Varies
Varies
Generalist
Generalist
Generalist
Varies
Generalist
Varies
42
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B. Reproduction
This page captures the basic reproductive characteristics of the target species. The opening page shows
the reproductive attributes for the target species (Figure 35). Clicking on the "Full List View" at the top
left corner of the Reproduction page shows the full reproductive hierarchy, shown in Figure 36. The
definitions for the terms related to reproductive classes are given in Appendix Table 13.
Metacarcinus magister (Dana, 1852)
Trophic Level And Feeding
Reproduction
Development
Habitat Association
Mobility
Comments
Taxonomy Biogeography Environment
I Full List View
Life History
Specialization Morphology i
Sexual Reproduction'
Gonochoristic /
Dioecious
Fertilization /
Spawning Type
Copulation
Figure 35: Reproduction page for Metacarcinus magister.
43
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Metacarcinus magister (Dana, 1852)
Life History
Parthenogenesis
/ Agamospermy D
Figure 36: Reproduction page showing all reproductive classes.
44
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C. Development
This page displays adult life history characteristics of a species related to the production and/or nurture
of their young, as well as various juvenile characteristics. Figure 37 is a portion of the Development page
for Metacarcinus magister, while all the attributes are shown in Figure 38. Attributes on this page
include breeding strategy (e.g., semelparous vs. iteroparous), juvenile characteristics (e.g., larval type
and duration) and adult characteristics related to reproduction (e.g., age or size at first reproduction,
fecundity, and maximum size). When available, durations of larval phases are recorded. These larval
durations are the maximum lengths reported for a species converted to days. Durations for age at
earliest reproduction and maximum age are in months. All sizes are reported in millimeters, with the
specific size measurement dependent upon the taxon. For example, the size of a fish would be recorded
in total length, standard length, and/or fork length while the size of a crab would be recorded in
carapace width and/or carapace length. Additionally, there is an Alternations category that indicates
whether the life cycle includes an alternation of a sexual reproductive phase, such as an alternation of a
polypoid benthic stage and a free-living medusoid stage as in some Cnidaria or an alternation of haploid
and diploid phases as in some macroalgae.
Clicking the "Full List View" at the top left corner of the page will show the hierarchical schema used for
all the reproductive strategies and attributes (Figure 38). Definitions for the terms can be found in:
Appendix Table 14 for definitions of breeding strategy; Appendix Table 15 for definitions of juvenile
development/dispersal; Appendix Table 16 for definitions related to adult development; and Appendix
Table 17 for definitions of the terms associated with alternation of generations.
Metacarcinus magister (Dana, 1852)
Figure 37: Portion of the Development page for Metacarcinus magister.
45
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Metacarcinus magister (Dana,
Metacarcinus magister (Dana, 1852)
•ceding Strategy .
Juvenile
Development
Adult
Development
Maturation (1st f
Reproduction)
Fecundity
Max. Life Span
Max Size C
von Bertalanffy
(k)-
Female
Male
Unknown
Haploid-Diploid
Medtisa-Palvp
Figure 38: Major reproductive and developmental characteristics on the
Development page.
D. Habitat Association
This page displays the organism's relationship to the habitat, specifically classifications of where the
adult of the species lives in relationship to the air/water and water/substrate interfaces. Figure 39 is an
example for Metacarcinus magister, while Figure 40 lists all the attributes. One source of potential
confusion is that many benthic organisms are closely associated with the bottom but do not
permanently live in or on the substrate. Species capable of swimming that live on the surface of the
sediment, such a flounders, are referred to as "Demersal - Epibenthic swimming". Species that
46
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periodically leave the sediment and swim into the water column are referred to as "Demersal -
Benthopelagic - Hyperbenthos". Examples include many of the corophiid amphipods. Species that
permanently live in the water column above the sediments are referred to as "Demersal - Benthopelagic
- Permanent benthopelagic", which includes both fish, such as shiner perch, and certain invertebrates,
such as some mysids. Species that live directly on the substrate and do not swim up into the water
column are referred to as "Surficial epibenthic non-swimming", which includes both species that live on
sediments (Epibenthic - unconsolidated) or rocks or other hard substrates (Epibenthic - consolidated).
The classifications are not mutually exclusive, and, as an example, certain corophiid amphipods would
be classified as infaunal, hyperbenthos, epifauna-consolidated, and epizoic. Definitions for the habitat
association classes are given in Appendix Table 18.
Metacarcinus magister (Dana, 1852)
Figure 39: Habitat Association page for Metacarcinus magister.
47
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Metacarcinus magister (Dana, 1852)
1 tyiilr.f „><•<>.
%i-r»l»l.fy *|Mti-
tiutdt-t no
Figure 40: All habitat association classes on the Habitat Association page.
E. Mobility
This page displays the classification of a species' mobility. That is, how the species moves through or on
the sediment, hard surfaces, and/or water column. An example of an opening page is Figure 41 for
Metacarcinus magister. Figure 42 gives the full list of attributes available on this page. The same
information can be viewed by clicking the "Full List View" at the top left corner. The definitions for the
terms can be found in Appendix Table 19.
Metacarcinus magister (Dana, 1852)
Taxonomy Biogeography Environment
i-. L :: V •;•
Life History
Specialization Morphology and Physiology Invasion
Reproduction
Development
Habitat Association
Actively mobile
Sedentary
Figure 41: Mobility page for Metacarcinus magister.
48
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X Metacarcinus magister (Dana, 1852)
Metacarcinus magister (Dana, 1852)
Figure 42: All mobility classes available on the Mobility page.
VI. SPECIALIZATION
Species with specialized environmental requirements are often more vulnerable to anthropogenic
stressors, including those associated with climate change. Clicking on the Specialization tab opens the
Habitat Specialization page with links on the left to trophic and reproductive specialization and
symbiotic relationships. On the habitat and trophic specialization pages, purple indicates an observed
habitat/food (the default) while green indicates a preferred habitat/food. The reproduction and
symbiotic information is not color coded.
A. Habitat
This page summarizes specialized habitat requirements, specifically those related to "unique habitats of
limited distribution", which we define as habitats of relatively small areal extent with a physical
structure substantially different than other habitats, thus providing distinctive environmental
conditions. If a species occupies one or more of the specialized habitats, we identify, to the extent that it
is known, whether it is the adult stage, juvenile stage(s), or both adults and juveniles that utilize the
49
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habitat, with "adult only" as the default. The degree of reliance of the species on the habitat is classified
as obligate, facultative, or incidental. Obligate indicates that the species requires the habitat, and its loss
would presumably result in a major (>90%) decline, if not loss, of the species. Facultative indicates that
the specialized habitat constitutes a major, but not sole, habitat for the species, and loss of the habitat
would presumably result in a substantial decline (>30% and <90%) of the species. Incidental indicates
that the while the species uses the specialized habitat, it does not constitute a major portion of its
habitat, and loss of the habitat would presumably have only minor impacts on the species population.
Another view of the strength of the habitat relationships is the expected population decline in the target
species in relation to the relative area of the specialized habitats:
Obligate: Population decline » relative area of specialized habitat.
Facultative: Population decline > relative area of the specialized habitat.
Incidental: Population decline < relative area of the specialized habitat.
In addition to the specialized habitats, we identify several "specialized ecosystems". These systems are
physically separated from other habitats, have distinctive environmental conditions and are of limited
spatial extent compared to other marine and estuarine ecosystems (with exception of sea ice in the
Arctic). We treat these as systems rather than habitats because they consist of several distinct habitats
(e.g., whale falls include the whale carcass as well as organically enriched sediment surrounding the
carcass).
Figure 43 shows the habitat specialization for Metacarcinus magister. The seagrass, Zostera marina, is
an important habitat for juveniles crab, but M. magister does not absolutely require seagrass. Thus, we
classify this as facultative. Clicking on the Full List View on the Specialization page displays the full list of
specialized habitats and systems (Figures 44 and 45), which is repeated below:
Unconsolidated Ecosystems/Habitats
1) Burrowing shrimp beds
2) Submerged aquatic vegetation (SAV) beds, all species including Zostera marina
3) Emergent marshes
4) Mangrove forests
5) Dunes
6) Wrack beds
Consolidated Ecosystems/Habitats
1) Rocky Intertidal - Supratidal Splash Pools
2) Rocky Intertidal -Tide pools
3) Rocky Intertidal - Phyllospadix
4) Corals - Coral Reef Ecosystem (living coral reefs)
5) Corals - Non-Reef Corals - Isolated coral heads
6) Corals - Non-Reef Corals - Deep/cold water corals
7) Oyster Beds (all)
8) Non-Coral Reefs (sponge, polychaete, and vermetid)
9) Algal Tufts
10) Kelp
11) Wood
12) Mussel Beds (all)
13) Rhodoliths/Maerl
14) Solitary sponge
50
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Pelagic Ecosystems/Habitats
1) Water Column - Microlayer
2) Floating Plants
3) Floating Debris
Specialized Systems
1) Saline Lagoons
2) Sea Mounts
3) Cold Seeps
4) Hydrothermal Vents
5) Sea Ice
6) Whale Falls
Metacarcinus magister (Dana, IBS2)
Figure 43: Specialized Habitat page for Metacarcinus magister.
Juvenile M. magister frequently occupy beds of the seagrass Zostera marina butZ. marina is not a
required (obligate) habitat, and thus this is classified as a facultative habitat relationship. Clicking on the
"Full List View" link in the upper left lists all the specialized habitats/ecosystems (Figures 44-45). Clicking
on "View Full Ecosystem/Habitat List" link in the upper right lists all the habitats/ecosystems (same as in
Figures 29 and 30).
51
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Metacarci'nus magister (Dana, 1852)
Figure 44: All the specialized unconsolidated habitats on the Habitat Specialization
page.
52
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Metacarcinus magister (Dana, 1852)
Figure 45: All specialized consolidated and pelagic habitats and specialized systems
on the Habitat Specialization page.
53
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B. Trophic
The Trophic Specialization page summarizes the plant and/or animal food items consumed by the target
species. Details on the plants or animals consumed can be summarized at different taxonomic levels,
from kingdom (e.g., Animalia) to species (e.g., Macoma nasuta) depending upon the available
information and the required level of specificity. The green boxes indicate preferred or major food
items, while the purple boxes indicate a food item of secondary, or unknown, importance. The overall
classification of the degree of trophic specialization from the Trophic Level and Feeding page (see
Section V.A.) is repeated on the top of the page. The Trophic Specialization page can be used to
summarize the diet of generalist feeders (Figure 46) or specialist feeders (Figure 47). However, this
information has primarily been populated for species with limited diets since such trophic specialists are
more likely to be vulnerable to climate change.
Metacarcinus magister (Dana, 1352)
Trafrtlk- spoclaluatton:
I Modi-rate
(value »«
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C. Reproduction
The purpose of the Reproduction specialization page is to synthesize environmental and/or habitat
requirements for successful reproduction, especially as they relate to vulnerability to climate change. An
example might be specific water temperatures required to induce spawning. This page is currently under
development.
D. Symbiotic
The Symbiotic page captures specialized biotic relationships where one species lives in close association
with another. Symbiosis is now generally accepted as the overarching term for such long-term biological
interactions between two species, and includes mutualism (+/+ relationship), commensalism (+/0
relationship), neutralism (0/0 relationship), and parasitism (+/- relationship). While symbiotic
relationships can be considered as a type of habitat specialization, we treat them separately. We
separate them, in part, because symbiotic relationships are potentially vulnerable to climate due to
additional factors such as the potential for disruption of the cues required to find the hosts.
Figure 48 shows the Symbiotic page for the pinnotherid crab, Fabia subquadrata, a known associate of
bivalves and other invertebrates. The information on the page includes the strength of the relationship
(obligate, facultative, or incidental), the type of the relationship (mutualism, commensalism, parasitism,
or neutralism), the presumed function of the relationship for the symbiont (habitat, trophic, dispersal
(phoresy) or other), and a list of hosts categorized as observed or preferred. We note that increasingly
detailed studies on purported "commensal" relationships have shown that the symbiont harms the host
(e.g., Martin and Britayev, 1998; Mena et al., 2014), and we categorize these relationships as parasitic
(i.e., +/- relationship). As with food types (Section VLB.), hosts can be entered at different taxonomic
levels, from kingdom to species. Preferred hosts are indicated by a green box while secondary hosts and
hosts of unknown importance are indicated by a purple box.
The climate vulnerability of a symbiont will depend, in part, on the vulnerability of its hosts. However, at
this stage, it is not feasible to conduct risk assessments on all the hosts, which is further compounded by
hosts being reported at taxonomic levels above a species in many cases. As a first step in addressing this
issue, we provide a general assessment of whether the hosts are likely to be impacted by climate
change; this assessment will be most predictive when there are a few hosts sensitive to climate change.
55
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Fabia subquadrata Dana, 1851
I OmiM* Ch*f«g* G." A iv^ib'tii depend, in p*il, bit wheltivr die A
will iii^i eau if, detreai* ov«r i*,e -4nu« at 1*\f ivmhion; will b* ai
it ol the process of assgninq ttw restive srnsti*i!f . As i ist asseswn^nts ac
ic hOH(*J increase* or *ee*ii« m response 10 tlim jt? clung«. In the avrenl version o* CBB*T. irte Ilkfrlitood (ha; the
i opinion. To il>- cxeenl ?>i»i (he riW; MMHrnenti have ftcen compleied. Che vulnerably Of The hoitt thoutit be ie
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VII. MORPHOLOGY AND PHYSIOLOGY
Intuitively, a species' physical form and structure and its physiology should be fundamentally related to
its sensitivity to climate stressors. However, identifying the specific morphological and physiological
attributes predictive across multiple taxa has proven challenging, especially when attempting to
extrapolate to population impacts. Because of this uncertainty, we limited our current synthesis of
morphology and physiology to shell and skeleton structure and composition. This focus derives from the
well-documented effects of reduced pH on coral exoskeletons (e.g., National Research Council, 2010),
though the vulnerability of certain taxa are not simply related to their shell structure and composition as
suggested by the presence of mussels located near low pH vents (Gazeau et al., 2013).
Clicking on the Morphology and Physiology tab opens the Shell Structure page with a link to the Skeletal
Composition page on the left. The Shell Structure page (Figure 49) displays a hierarchical schema we
developed from various sources (e.g., Taylor, Kennedy, and Hall, 1969) to synthesize bivalve shell
structure, though it may be applicable to other taxa with a calcium carbonate shell. The Skeletal
Composition page (Figure 49) is general and applies to all taxa, including those with hydrostatic
skeletons. The Skeletal Composition page also captures attributes based on the chemical composition of
the skeleton, such as whether it is composed of calcite or the more soluble aragonite.
/ Metacarcinus magistcr (Dana, 1852]
' Metacardnus magister (Dana,
Figure 49: Shell Structure (left) and Skeletal Composition (right) pages available
from the Morphology and Physiology tab.
The Shell Structure was developed for bivalve shells, while the Skeletal Composition applies to all taxa.
VIII. INVASION VECTORS
Invasion status was detailed in Section III.D. and Sidebar #7: Native vs. Nonindigenous Classifications and
Sidebar #8: Population Establishment Status. The information on the Invasion page summarizes another
aspect of invasion biology, the primary invasion vectors. Primary invasion vectors are the anthropogenic
mechanisms by which a nonindigenous species was likely introduced (transported) from its native
ecoregion into the non-native ecoregion. In contrast, secondary invasion vectors are mechanisms by
which nonindigenous species are transported into new areas within an invaded ecoregion. Secondary
vectors are not addressed in CBRAT, though we note that most primary vectors also operate within a
region.
57
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Figure 50 shows the potential primary invasion vectors for Metacarcinus magister. As is often the case,
there are several non-exclusionary vectors by which M. magister could be transported from its native
ecoregions. Figure 51 shows the full primary vector hierarchy for near-coastal species. In interpreting
these vectors it is important to recognize that the importance of vectors can vary geographically. Their
importance may also vary historically, such as the historical importance of solid ballast versus the
current importance of ballast water.
Metacarcinus magister (Dana, 1852)
Taxonomy Biogeography Environment Life History Specialization Morphology and Physiology
Invasion
I Full List View
Ships and Boats
Commercial
Ballast Water
Aquaculture and
Fisheries
Intentional Stocking /
Release
Intentional Illegal
Release
Live Seafood
Figure 50: Primary Vectors for Metacarcinus magister.
This page displays the presumed anthropogenic vectors by which M. magister can be transported from
native to non-native ecoregions.
58
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Metacarcinus mag/ster (Dana, 1852}
f Metacarcinus magister (Dana, 1352}
I , i/,.,. .ill I.T- .111.1
I'.n it,. Ov*ler»
Um,irin-nMil PI,tin
Live B..SI IIH!
pKfctng
Figure 51: Invasion vectors available on the Primary Vectors page.
IX. DATA EXPORT
The Data Export tab opens a page that allows users to export different types of data at several spatial
scales (Figure 52). This ability to export large amounts of data is one of the powerful features of CBRAT,
but as with all powerful functions, it is incumbent on the user to understand both what data they want
and how to use the various options. The queries on the Data Export page are divided into three general
sets: Species Info, Biogeography, and Environment, with key queries under each of these sets explained
below. Results from the queries can be exported as Excel (.xls) or csv files for analysis; in most cases we
have found it better to initially export the information as a csv file and then save this as an Excel file.
Additionally, the comments, references and taxonomy can be exported as a PDF.
When conducting multiple queries, we caution the user to click on the Clear Outputs or Reset All button
to assure that all the previous filters have been cleared. We also caution not to combine several
different filters that are not discussed here - we cannot verify the accuracy of such queries.
59
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Search Data Export
Documents
Data Export
Select Additional Values to Output:
Species Info
Biogeography
Environment
Species Comments
Output References
Species Taxonomy
Abundance by Ecoregion
Abundance by Citation
Master Abundances Table
Abundances across Ecoregions
Options:
Numeric Values
Short Abbreviations
Classification / Population Values
First Record Values
Q Regime Classes
• • Q Depth Classes
U select all
Benthic
Coastal Fringe
Supralittoral
Intertidal
•t- (MLLW -
MHHW)
Upper Intertidai
1 Q Salinity Classes
• Q Substrate Classes
• Q Ecosystem/Habitat Classes
• B Energy Classes
•_' Q Temperature Classes
All Life History & Environmental
Information
Generate Results
Clear Outputs
Reset All
Figure 52: Data Export page - Extracting environmental ranges, habitats,
distributions, and abundances.
The Data Export page generates queries on a specific taxon from a single ecoregion or from preassigned
ecoregion groups. The "N.E. Pacific & U.S. Arctic" group generates results based on all species that occur
in any of the 9 NEP or 3 U.S. Arctic ecoregions. After choosing a taxon and an ecoregion or ecoregion
group, queries can be run on Species Info, Biogeography, or Environment. Under Biogeography, the
Abundance by Ecoregion query will generate a unique list of all the species reported for an ecoregion
(single record per species), including those classified as absent. CBRAT is listed as the publication if a
master classification has been assigned, else it is the first publication associated with a species. The
Abundance by Citation generates a list of all the species X citation linkages for the taxon (multiple
records per species), sorted by abundance classes. The Master Abundance Table generates a table of all
the species with a master abundance, sorted by abundance class. The Abundance across Ecoregions
outputs the distribution/abundance of the chosen taxon across all 254 MEOW ecoregions. The
Environment queries output the species meeting the chosen environmental class(es). In the example
above, the query would output all the crabs that occur in the intertidal in any of the 12 NEP and U.S.
Arctic ecoregions, along with their depth classes. The All Life History & Environmental Information query
generates a large output of nearly all the environmental and life history information on the chosen
group of species, and includes both numerical and class values for attributes. The "Clear Outputs"
button clears all the information in the lower portion of the page, while "Reset AN" clears the selected
taxon and ecoregion/ecoregion group as well.
60
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A. Step One - Choosing a Taxon & Ecoregion or Ecoregion Group
The first step in all the queries is to select the taxonomic level (kingdom to genus) at which to search
using the Taxonomic Ranks dropdown list. First enter the appropriate taxonomic level and then choose
the specific taxon from the second dropdown list. In the examples given here, we use the true crabs
(Infraorder Brachyura). Use WoRMS (http://www.marinespecies.org) to determine the taxonomic level
if it is unknown. Note that while the full range of taxonomic levels is available in the dropdown list, only
species that have gone through quality assurance checks will be displayed in the public version.
The second step is to narrow the geographic range of the output by using the "Locations" dropdowns.
Choosing "Single Ecoregion" will open a dropdown list of all the MEOW ecoregions. Choosing one of
these ecoregions limits the output to species in the chosen taxon that occur in the selected ecoregion. In
the examples given below, we used the Cortezian Ecoregion. The other option is to search across
multiple ecoregions using the "Ecoregion Group" function. There are four options under Ecoregion
Group:
Select All Ecoregions: This option returns the selected attribute for all species in the chosen
taxon occurring in any of the 254 ecoregions. It is the broadest of the options.
N.E. Pacific & U.S. Arctic: This option returns the selected attribute for all the species in the
chosen taxon occurring in any of the nine NEP ecoregions (Cortezian through Aleutians) and
three U.S. Arctic ecoregions (Eastern Bering, Chukchi, and Beaufort Sea - Continental Coast and
Shelf). This is the standard choice for generating outputs for the U.S. Pacific Coast.
Non-N.E. Pacific Data: This option returns the selected attribute for all species in the chosen
taxon that occur in ecoregions other than the twelve NEP and U.S. Arctic ecoregions, but it does
not exclude species that occur in the NEP and U.S. Arctic group.
Do not include Ecoregion data: This option is used when the output is not ecoregion specific. For
example, it could be used with Depth Class - Intertidal to generate a list of species that occur in
the intertidal. Since this output is not filtered by ecoregion, the list of intertidal crabs would
include all intertidal crabs in CBRAT and not just those that occur in the NEP and U.S. Arctic
group.
B. Species Info Queries
This set of queries outputs the comments, references, or higher level taxonomy associated with the
species in the chosen taxon.
1. Output Species Comments
This query outputs the comments associated with the chosen taxon. The query can be limited to the
species occurring in a single ecoregion by using the "Single Ecoregion" option. Alternatively, all the
comments associated with all the species in the chosen taxon can be outputted by using one of the
ecoregion groups. An example output is given in Figure 53.
61
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Data Export
.-..--.,-.,.
taw*** csv
Acantholobulus mirafioresensis
lltaflairwrnw* WAI capturpij in Tli« ii
aiw lour' ChDfntMrt of ttir Mif Aflorr* Loclci of [Iw Panama Ctiial. Hi* tocln h<
a Ullnicy rang* of 0 1ft 30 pw.
'MEASUREMENTS. 'H
, rti I.S-9. 1 mm;
. (6 3.0-S.9 mm; OV*8*rmi*
d> 3.0-9.1 mm.'
"The recori9 of OW p*nopet4 A<*rW»wli>*uliis nil* aflovewrn.! i AbeM & Kim. 1999 (a* P*ne»«u* m.f«niwe**r.*n] '""om ftw Grande tfo Note (FerrCita \ iant^ankutt/ 1
"
> not valid. Tim ft
.
fxrt ftMer » MattJtt g
•AcamtiololMiKrtni.faflot-*s*nSi (Abcfe ft Ktm, 1909), "ew omtenahen, (o
s mir*fto«i*m«t, ir*dudit>(| fo
P. tofrmaOvmtt, from,
rKdnihofvlntfia LAr-D
mlrjItorttM-n^i* [ '
AutnthDtiiliuba '„
uulhem ji,l<- af the northern tapo [IUt«ro Gl tferd*. Gulf of C
mangle L. cotoiatO by the MHV« qxdti of oyg>f.'
ly (olletted an lubme-ijed
Figure 53: Comments linked to brachyuran crabs in the Cortezian Ecoregion.
Currently there is a total of 305 species and 3433 comments. The comments can be exported as an
Excel, csv, or PDF file.
2. Output References
This query outputs the references linked to the species within the chosen taxon. The query can be
limited to the species occurring in a single ecoregion by using the Single Ecoregion option. Alternatively,
all the references associated with all the species in the chosen taxon can be outputted by several
ecoregions using the Ecoregion Group function. An example output is given in Figure 54.
Data Export
WaoFDF
Infr«ordcr-8racl
Jcymal af Zeoh^jy 134:1S>22,
. £-, Ouarratanja, S.. Witic - .', '-.--< ....[Li- ,-.-:-.- i-T i -1--- •••- ^diMnwin
.. ..
i--1 M r >-'•= ' v a v ,- v . ;• = . .-,.- " C>rircn : 1
.
l »*.'»:T». t.l.f... j
«) from vmlficrn ttahm, (k«il, lalin
10 Wv*r«z-L« k-^«-,
t ««i0dixtKM»» 0' ma«Trw IMntfwj info f(*YO Mr tr; Pro«W(ff inyajl^n .i.l» an
ri toj*vsft«rri with d on the
, CM» CenCr'l N«ursl MMOrvMutcum J&unwl
Figure 54: References linked to brachyuran crabs in the Cortezian Ecoregion.
Currently there is a total of 514 references linked to brachyuran crabs that occur in the Cortezian
Ecoregion. The references can be exported as an Excel, csv, or PDF file.
62
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3. Output Species Taxonomy
This query outputs the higher order taxonomy (genus to kingdom) of the species within the chosen
taxon. As discussed in Section II.B., the higher order taxonomy follows WoRMS except in cases when an
authoritative regional reference is chosen over WoRMS. The query can be limited to the species
occurring in a single ecoregion by using the Single Ecoregion option. Alternatively, the taxonomy for all
the species in the chosen taxon can be outputted for several ecoregions using the Ecoregion Group
function. An example output is given in Figure 55.
Figure 55: Higher order taxonomy of brachyuran crabs in the Cortezian
Ecoregion.
The taxonomy can be exported as an Excel, csv, or PDF file. In most cases, the higher order taxonomy
follows WoRMS (http://www.marinespecies.org).
C. Biogeography Queries
This set of queries outputs the distribution and relative abundance of the species in the chosen taxon as
well as the native/non-native status of the species and its first record location.
1. Abundance by Ecoregion
This query generates a single record of all the species reported from an ecoregion or multiple ecoregions
within an ecoregion group, including species without master abundance classifications and absent
species. This query is useful to evaluate the completeness of reported species for an ecoregion, but the
absent species (if any) need to be removed for an assessment of regional biodiversity. An example
output is given in Figure 56.
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1 Home Search Data Export Documents About
Data Export
Generate PDF
Generate XLS
Generate CSV
Infraorder-Brachyura Abundance by Ecoregion, in Cortezian
305 results.
No. Species Family {Location Taxacode|Abundance Class {Abundance Values Publication Abundance Values Master
1 lAcantholobulus mirafloresensis
2 Acanthonvx Detiverii
3 Achelous nuaviliasensis
4 Achejmis iridescens
S JAchelous tiibercuiatus
6 Acidops fimbriatus
7 |Actaea anausta
8 |Aethra scutata
9 Ala coruuta
10 Aratus p sonii
11 Arena eus mexica mis
12 Armases maadalenense
13 Austinixa felipensis
14 Austinotheres anaelicus
15 Bathvrhombila furcata
16 Calappa convexa
17 Calappula saussurei
IS Callinectes arcuatus
19 [Callinectes bellicosus
20 Callinectes toxotes
Panopeidae |cortez anJDEC |veryRare |CBRAT t
Epialtidae
Portunidae
Cortez an DEC |LOW Moderate
Cortez an DEC IveryRare
CBRAT
CBRAT
Portunidae | Cortez an| DEC | High Moderate | CBRAT
Portunidae
Acidopsidae
CottezanDEC | Moderate |cBRAT
Cortez an DEC 1 Moderately Rare IcBRAT
t
t
t
t
t
Xanthidae |cortez an|DEC | Low Moderate |CBRAT
Ae-i-ndae CcitezanDEC |very Rare |CBRAT
Mithracidae |CottezanDEC [Abundant |CBRAT
Sesarmidae | Cortez an| DEC (Moderate | CBRAT
Portunidae |cortezanDEC | Low Moderate |CBRAT
Sesarmidae |CortezanDEC (Moderately Rare |cBRAT
Pinnotheridae |coitez an[DEC | Very Rare |CBRAT
Pinnotheridae | Cortez an DEC |Rare | CBRAT
Pseudorhombilidae
Calappidae
Calappidae
Cortez an DEC
Cortez an DEC
Cortez an DEC
Moderately Rare
Low Moderate
Moderate
CBRAT
CBRAT
CBRAT
|
-
t
-
t
t
t
t
t
Portunidae | Cortez an[ DEC (Moderately Abundant] CBRAT t
Portunidae |cortezanDEC |Very Abundant |cBRAT
t
Portunidae |cortezanDEC | Low Moderate |CBRAT |t
Figure 56: Abundance by Ecoregion query for brachyuran crabs in the Cortezian
Ecoregion.
This query outputs a list of all the species from an ecoregion or multiple ecoregions within an ecoregion
group, including species without master abundance classifications and absent species. The "CBRAT"
citation indicates a master abundance classification; the first citation linked to the species is listed if
there is no master classification. The last column, "Abundance Values Master" indicates whether the
record is a master value (t = true) or a non-master record (f = false). The query can be exported as an
Excel, csv, or PDF file.
2. Abundance by Citation
This query outputs each record linking the species in the chosen taxon from an ecoregion or multiple
ecoregions within an ecoregion group. If a single ecoregion is chosen (Figure 57), each record is sorted
by citation within each relative abundance class (from Very Abundant to Absent). If multiple ecoregions
are chosen, the species are first sorted by ecoregion and then relative abundance class. Note that most
species are likely to be listed under multiple abundance classes, in particular under the Present class. To
collate all the records by species, export the data as an Excel or csv file and then sort by species. The
master classifications are indicated by the "CBRAT" citation and "t" (= true) in the "abundance values
master" column.
64
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1 Home
Search Data Export Documents About
Data Export
| Generate PDF
Generate XLS
Gent
rate CSV
Infraoi dei -Br achyura Abundance Values by Citation, in Cortezian
1334 results.
No. [species Family Location|Taxacode Abundance Class
1
2
3
4
5
6
7
9
10
11
12
13
14
15
16
17
18
19
20
Callinectes arcuatus
Callinectes bellicosus
Portunidae
Portunidae
Callinectes bellicosus Pcrtunidae
Cataleptodtus occidentalis
Cataleotodius occidentalis
Cataleptodius occidentalis
pjssoda
Eiii,,lt,i!
Eoialtus
ctylus lockinatoni
Xanthiclae
Xanthidae
Xanthiclae
Pinnothei dae
des paradigimis JEpialtidae
minimus 1 Epialttdae
Epiattus minimus Epialtida
EurvDanooeus ovatns
Eurvtium affiue
Graosus araosus
Panopeid e
Panopeid e
Grapsida
Grapsus arapsus Graosida
Graosus arausus
PachvQrapsus socius
Ala con
uta
Ala cornuta
Callinectes arcuatus
Coitez an|DEC
Cortez an|DEC
Very Abundant
Very Abundant
abundance_values publication abuiidance_values master
Arzola-Gonzalez et al., 2010 f
CBRAT t
Cortezan|DEC [very Abundant |EPA/SCAMIT Workshop, 2012
Coitez an|DEC
Cortez an|DEC
Cortez an|DEC
Cortez an| DEC
Cortez an|DEC
Cortez an|DEC
Very Abundant |CBRAT t
Very Abundant
Arzola-Gonzalez et al., 2010 f
Very Abundant | EPA/SCAMIT Workshop, 2012 f
Very Abundant
Very Abundant
Very Abundant
EPA/SCAMIT Workshop, 2012 ?
EPA/SCAMIT Workshop, 2012 f
CBRAT t
Cortez an|DEC Vei-y Abundant | EPA/SCAMIT Workshop, 2012 f
Cortez an| DEC
Coitez an|DEC
Cortez an|DEC
Very Abundant
Very Abundant
Very Abundant
Arzoia-Gonzalez et al., 2010 f
Arzola-Gonzalez et al., 2010 f
CBRAT t
Grapsida |cottez an|DEC
Grapsida
Mithracid e
Mithracidae
Poitunidae
Cortez an| DEC
Cortez an|DEC
Cortez an|DEC
Cortez anlDEC
Very Abundant | EPA/SCAMIT Workshop, 2012 f
Very Abundant
Abundant
Abundant
Arzola-Gonzalez et al., 2010 f
CBRAT t
EPA/SCAMIT Workshop, 2012 f
Abundant 1 EPA/SCAMIT Workshop, 2012 f
DKsodartvlus lockiiiatoni Pinnotherdae |coitez an|DEC Abundant |cBRAT t
Figure 57: Abundance by Citation query for brachyuran crabs in the Cortezian
Ecoregion.
This query outputs each species in the Cortezian by individual record (citation). The species are sorted
by relative abundance class, from Very Abundant to Absent on the bottom. The "CBRAT" citation
indicates a master classification. Additionally, the last column, "abundance values master" indicates
whether the record is a master value (t = true) or a non-master record (f = false). The query can be
exported as an Excel or csv file for sorting by species or as a PDF.
3. Master Abundances Table
This query generates a table of all the species in the chosen taxon in the selected ecoregion that have a
master abundance classification, sorted by abundance class (Figure 58). The table is useful for evaluating
the breakout of species among the abundance classes. However, since it does not include species
without master classifications, it may not include all species (i.e., those only classified as Present). Note
that while the output has a column labeled "Present", this is limited to species that have a master
Present classification, which is rarely used. The query can be run using the Ecoregion Group option, but
since species are sorted by ecoregion and then by abundance the resulting table is not as easy to
understand as the single ecoregion output.
65
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Data Export
r Rr.n-hyiir.i lict l.y M.i^lfr AlumilAii, <- I.,hi,-, 1,1 K,,t-i:
nwfWMM
.-. .. -. ,
".• - • I- '•..'
J
'
Chltmecarunui
.
CO->0*t»turtH*rt
£-;-*-KV *K e*'»a>
-------
Table 2: Numerical codes and abbreviations used for relative abundance in the
Abundance across Ecoregions query
Numerical Code
3
4
5
6
7
8
9
10
11
12
13
14
15
Abbreviation
Ab
T
P
HR
VR
R
MR
LM
M
HM
MA
A
VA
Long Name
Absent
Transient
Present
Hyper Rare
Very Rare
Rare
Moderately Rare
Low Moderate
Moderate
High Moderate
Moderately Abundant
Abundant
Very Abundant
Data Export
..... .iflllL-M-lpsK
HI P
ft
U.S.
••..ii
H
-------
5. Classification / Population Values - Status of Nonindigenous Species
This query outputs the species in the chosen ecoregion that have master native/non-native
classifications. The classification of each species is indicated by which of the five columns (Native,
Nonindigenous, Cryptogenic, Transient, Unclassified) contains a "True" (= master classification of the
species). The population status of the species is indicated by which of the three columns (Established,
Not Established, Unknown) contains a "True" (= master population value). Species artificially maintained
in the ecoregion (e.g., via aquaculture) are identified by a "True" in the Stocked column. An example
output is given in Figure 60.
Data Export
Infi.o.dc. B.achvuia Clmifiuticn/Population V.luei, in Northern California
1 I'1"" <" Mir.!
Oivrtlu
•'•
ulM . 1. * I,. Ml
i |Lrtunnte>naiui
-------
Data Export
Generate PDF
Generate XLS
Generate CSV
Infraorder-Brachyura First Record Values, in Northern California
4 results.
No.
1
2
Species
Callinectes sapidus
Carcimis maenas
3 Eriocheir sinensis
Family
Location |jaxacode
Portunidae | Northern California] DEC
Citation
First Record
Cohen and Carlton, 1995|l897, San Francisco Bay
Portunidae (Northern California|DEC |cohen and Carlton, 1995
Varunidae
Northern California|DEC
Light et al., 2005
1989, Estero Americano
1992, San Francisco Estuary
iLight et al., 2005 11937, Lake Merrltt, San Francisco Bayl
Figure 61: First Record Values - First records of nonindigenous brachyuran crabs
in the Northern California Ecoregion.
D. Environment Queries
This set of queries outputs the environmental ranges, ecosystems/habitats occupied, and life history
attributes of the chosen species. Queries are available by classes for regimes, depths, salinities,
substrates, ecosystems, energy, and temperature. Additionally, there is a query that outputs most of the
environmental, ecosystem, and life history attributes in a single output, including both classes and
numerical values when available (e.g., numerical salinity range).
1. Environmental Class queries.
As mentioned, queries based on class ranges are available for regimes, depths, salinities, substrates,
ecosystems, energy, and temperature, and these will be discussed together. Each of these queries
outputs the species in the chosen taxon in the selected ecoregion or ecoregion group that are included
within the specified environmental or habitat class(es). The output is formatted as a table of the values
across all the attribute classes. The output includes Absent species. An example output for depths in
crabs that occur in the Cortezian Ecoregion is given in Figure 62.
The procedure is to initially choose the taxon and an individual ecoregion or ecoregion group. Then,
after clicking on the button next to the attribute name (e.g., Depth Classes), use the dropdown (see
Figure 52) to select all the classes, several classes, or a single class. These are "or" queries and adding
additional classes will output all the species that are contained within any of the chosen classes. Note
that failure to click the button next to the attribute name will generate a list of all the species in the
ecoregion not filtered by the chosen class(es).
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ln!f,«wi|ff (U.w Jiynr-t f
2"?5rmts.
+- h
Figure 62: Environment Depth Class query - Intertidal and shallow subtidal
brachyuran crabs in the Cortezian Ecoregion.
Both the Intertidal and Shallow Subtidal Neritic (>0 to 30 m) classes were chosen. With the combined
depth classes a total of 275 species were returned. In comparison, 187 species were returned with just
Intertidal and 227 with just Shallow Subtidal. O = observed depth class; P = preferred depth class.
2. All Life History & Environmental Information query.
Use the All Life History & Environmental Information query to output the majority of the environmental
and life history information on the species in the chosen taxon. Specifically, the output includes all
environmental ranges, most life history attributes including shell structure and composition,
reproductive attributes, species size ranges, and invasion vectors. The output includes both class and
numerical values for environmental ranges, when numerical ranges are available (e.g., depth, salinity,
percent fines). Many of the class ranges are keyed as O for an observed environmental range/habitat or
P for a preferred environment range/habitat. The output is large, about 700 columns, and in most cases
the information should be exported to an Excel or csv file. We also note that since the query outputs
attributes for everything, there are many blank columns (e.g., columns related to seed type with a
brachyuran crab). Be patient, the query can take some time with multiple ecoregions and a large taxon.
A portion of an output is shown in Figure 63.
70
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Data Ex pott
f BrAtfiyiira All Life History ft Environ men I ill Information, in Coftc,
Figure 63: All Life History & Environmental Information query on brachyuran
crabs in the Cortezian Ecoregion.
This figure shows a small portion of the output for brachyuran crabs in the Cortezian Ecoregion. In
nearly all cases, it will be necessary to export the results to an Excel or csv file to navigate through the
almost 700 columns.
X. DOCUMENTS
The Documents tab provides access to PDF files related to how to use CBRAT, documentation and
metadata, and the conceptual basis of the vulnerability analysis.
A. User's Guide and Metadata
A link to download the most recent version of this document.
B. Vulnerability Framework
An U.S. EPA document explaining the conceptual framework to predict species' vulnerability to climate
change from information on life history traits and biogeographic patterns of distribution and abundance.
Also, this document presents the results from the proof-of-concept risk analysis with true crabs, king
crabs, and rockfish on the U.S. Pacific Coast. Currently in draft form, and not presently available on the
public site.
C. Acronyms and Abbreviations
List of acronyms and abbreviations used in the User's Guide and on the CBRAT website.
D. Glossary of Terms
Definitions of terms used in the User's Guide and on the CBRAT website. Primarily taken from the
metadata appendices in this document, but listed alphabetically rather than thematically as in the
appendices.
E. Museum Abbreviations
The abbreviations used in the Location of Type on the General Taxonomy page to indicate where the
type specimens are stored.
71
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F. Taxa Codes
The list of taxa codes, which are short-hand abbreviations for major taxonomic groups (see Appendix
Table 20).
G. NEP and U.S. Arctic Ecoregions
A PDF illustrating the MEOW regions of the World's oceans and the Northeast Pacific and U.S. Arctic
eco regions.
H. All MEOW Ecoregions
PDFs illustrating all 254 MEOW ecoregions.
I. Small Island Ecoregions
A list of small island ecoregions, defined as island ecoregions smaller than Hawaii and that do not abut
the mainland. A species' population on a small island ecoregion is used as an indication that the species
was a good colonizer and able to maintain a small population. For completeness, this list is repeated in
Appendix Table 22.
J. Tropical Ecoregions
A list of the MEOW ecoregions that we classify as tropical. Occurrence in a tropical ecoregion is used in
evaluating potential resilience to temperature increases. For completeness, this list is repeated in
Appendix Table 21.
XI. ABOUT
The PDF documents under the About tab provide information on the implementation CBRAT.
A. User's Guide and Metadata
A link to the most recent version of this document is available under the About tab. This is the same
version as under the Documents tab.
B. Site Map to CBRAT
The site map provides an overview of the structure of CBRAT in a hierarchical format.
C. Acknowledgements
The Acknowledgements lists both the organizations who helped support the development of CBRAT as
well as the experts and students who helped to populate CBRAT.
D. Version
The most current version number of CBRAT is listed under the About tab.
72
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XII. REFERENCES
Anonymous. 1958. The Venice System for the Classification of Marine Waters. Limnology and
Oceanography 3:346-347.
Bush, A.M., Bambach, R.K. and Daley, G.M. 2007. Changes in theoretical ecospace utilization in marine
fossil assemblages between the mid-Paleozoic and late Cenozoic. Paleobiology 33:76-97.
Carlton, J.T. 1996. Biological invasions and cryptogenic species. Ecology 77:1653-1655.
Davies, K.F., Margules, C.R., and Lawrence, J.F. 2000. Which traits of species predict population declines
in experimental forest fragments? Ecology 81:1450-1461.
Duncan, R.P. and Young, J.R. 2000. Determinants of plant extinction and rarity 145 years after European
settlement of Auckland, New Zealand. Ecology 81:3048-3061.
Gaston, K.J. 1994. Rarity. Chapman and Hall, London, U.K. 205 pages.
Gaston, K.J. 1997. What is rarity? In Kunin, W.E. and Gaston, K.J. eds. The Biology of Rarity, pp. 30-47.
Chapman & Hall, London, U.K. 280 pages.
Gazeau, F., Parker, L.M., Comeau, S., Gattuso, J.-P., O'Connor, W.A., Martin, S., Portner, H.-O., and Ross,
P.M. 2013. Impacts of ocean acidification on marine shelled molluscs. Marine Biology 160:2207-
2245.
Howes, D.E. and Kenik, E. 1997. Terrain classification system for British Columbia. Version 2. Resource
Inventory Branch, Ministry of Environment, Lands and Parks, Ministry of Crown Lands Province
of British Columbia. (Available at
http://ilmbwww.gov.bc.ca/risc/pubs/teecolo/terclass/covel.htm)
Howes, D.E., Morris, M., and Zacharias, M. 1999. British Columbia Estuary Mapping System.
Resource Inventory Committee, Province of British Columbia, Victoria, British
Columbia. 62 pages. (Available at
http://ilmbwww.gov.bc.ca/risc/pubs/coastal/estuarv/assets/estuary.pdf)
IUCN Standards and Petitions Subcommittee. 2014. Guidelines for Using the IUCN Red List Categories
and Criteria. Version 1.1. Prepared by the Standards and Petitions Subcommittee. 87 pages.
(Available at http://www.iucnredlist.org/documents/RedListGuidelines.pdf)
Lee II, H. and Reusser, D. A., 2012. Atlas of Nonindigenous Marine and Estuarine Species in the North
Pacific. Office of Research and Development, National Health and Environmental Effects
Research Laboratory, EPA/600/R/12/631. 1915 pages.
Madden, C.J., Grossman, D.H., and Goodin, K.L. 2005. Coastal and Marine Systems of North
America: Framework for an Ecological Classification Standard: Version II. NatureServe,
Arlington, Virginia. (Available at
http://www.natureserve.org/getData/CMECS/cm pub.pdf)
73
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Martin, D. and Britayev, T.A. 1998. Symbiotic polychaetes: Review of known species. Oceanography and
Marine Biology: an Annual Review. 36:217-340.
Mena, S., Salas-Moya, C. and Wehrtmann, I.S. 2014. Living with a crab: effect of Austinotheres angelicas
(Brachyura, Pinnotheridae) infestation on the condition of Saccostrea palmula (Ostreoida,
Ostreidae). Nauplius 22:151-158.
National Research Council. 2010. Ocean Acidification: A National Strategy to Meet the Challenges of a
Changing Ocean. National Academies Press. 188 pages. (Available at
http://www.nap.edu/catalog/12904/ocean-acidification-a-national-strategv-to-meet-the-
challenges-of)
Payne, M.C., Brown, C.A., Reusser, D.A., and Lee, H. II. 2012. Ecoregional analysis of nearshore sea-
surface temperature in the North Pacific. PLoS ONE 7(1): e30105.
doi:10.1371/journal.pone.0030105 (Available at
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fiournal.pone.0030105)
Reusser, D.A. and Lee II, H. 2011. Evolution of natural history information in the 21st century -
developing an integrated framework for biological and geographical data. Journal of
Biogeography 38:1225-1239.
Spalding, M., Fox, H.H., Allen, G.R., Davidson, N., Ferdana, Z.A., Finlayson, M., Halpern, B.S., Jorge, M.A.,
Lombana, A., Lourie, S.A., Martin, K.D., McManus, E., Molnar, J., Recchia, C.A., and Robertson, J.
2007. Marine ecoregions of the world: A bioregionalization of coastal and shelf areas. Bioscience
57:573-583.
Swartz, R.C., Schults, D.W., Ditsworth, G.R., DeBen, W.A., and Cole, F.A. 1985. Sediment toxicity,
contamination, and macrobenthic communities near a large sewage outfall. In: Boyle, T.P. (Ed.),
Validation and Predictability of Laboratory Methods for Assessing the Fate and Effects of
Contaminants in Aquatic Ecosystems. American Society for Testing and Materials, Special
Technical Publication 865. American Society for Testing and Materials, Philadelphia,
Pennsylvania, pp. 152-175.
Taylor, J.D., Kennedy, W.J. and Hall, A. 1969. The shell structure and mineralogy of the Bivalvia. I
Nuculacea - Trigoniacea. - Bull. Brit. Mus. (Nat. Hist.), Zool., Suppl. 3:1-125.
Taylor, P.O. and Wilson, M.A. 2002. A new terminology for marine organisms inhabiting hard substrates.
Palaios. 17:522-525.
Todd, J.A. 2001. Introduction to molluscan life habits databases. Part of the Neogene Marine Biota of
Tropical America (NMITA). (Available at
http://porites.geologv.uiowa.edu/database/mollusc/mollusclifestyles.htm)
74
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XIII. APPENDICES
Appendix I: CBRAT Access Levels.
Depending on the user's expertise and interest, the administrator will assign them to one of the
following categories with the corresponding privileges. A summary of these privileges is displayed in
Appendix Table 1.
Public: The first level is public access. No login is required to view biological or environmental
information that has been reviewed and released by the U.S. EPA. Information on individual species
and/or taxonomic groups of species will be released to the public as the information is finalized through
the review process.
Manager/Beta Tester: This level requires a user name and password to gain access to biological and
environmental information that has not been released to the public yet. Users with this access level are
able to view all information, test tools, and evaluate risk analyses. Users with this access level are not
able to edit information contained in the database but they do have the ability to submit issues related
to any bugs encountered, incorrect information about a species, or suggestions on how to improve the
website.
Expert User/Taxonomic Expert: This third level of access also requires a user name and password and
provides the additional ability to add/edit all the information contained in CBRAT. At this access level,
data that are entered into CBRAT is marked as changed and awaiting approval. These data will not be
displayed right away and are not viewable by the public or other experts until they get approved by
Gatekeepers or Administrators.
Gatekeepers: Requires a user name and password for access. Gatekeepers have all the access privileges
of expert user/taxonomic experts and have the added ability to approve information that has been
entered by other expert user/taxonomic experts. Once a datum has been approved, it becomes visible
to other expert user/taxonomic experts for review or revision.
Administrator: Requires a user name and password for access. Administrators have all the access
privileges of gatekeepers. Administrators can approve making information public. Additionally,
administrators have access control to manage access levels for all other users.
75
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Appendix Table 1: Summary of the privileges associated with each level of
access in CBRAT.
Login Required
View Public Species
Generate Spreadsheet Summaries of
Abundance and Life History Data for
Public Species
Generate PDF Profile for a Single
Public Species
View Non-Public Species
Generate Spreadsheet Summaries of
Abundance and Life History Data for
Non-Public Species
Generate PDF Profiles for Multiple
Public & Non-Public Species
Test Tools
Submit Issues
Enter Data
Approve Data
Create Master Records
Modify Data Structure
Modify or Approve User Accounts
Approve Species QA and Public
Viewing
Public
X
X
X
Manager/
Beta Tester
X
X
X
X
X
X
X
X
X
Expert
X
X
X
X
X
X
X
X
X
X
Gatekeeper
X
X
X
X
X
X
X
X
X
X
X
X
Administrator
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
76
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Appendix Table 2: Qualitative descriptions and quantitative cut points of dominance normalized relative
abundance for the three-level relative abundance classifications (Figure 16).
Dominance normalized relative abundances (DNRA) are the values used with quantitative studies to assign relative abundance classes. Phrases
commonly used in relation to the abundance class both in terms of abundance and frequency of occurrence are provided as a guide. Most of the
phrases are not unique to a single level of abundance class; interpretation of these terms needs to be taken in context of scope and spatial scale
of the study (e.g., local habitat or regional scale). The basis of the approximate range of species in each class is discussed in Sidebar #4:
Dominance Normalized Relative Abundances & Hybrid Approach to Assigning Relative Abundances.
Abundance
Class
Qualitative Description
Common Key
Ph rases -
Abundance
Common Key Phrases
- Frequency of
Occurrence
Dominance
Normalized
Relative
Abundance
Cut Points
Approximate Ranges of
Percentage of Species
in an Ecoregion
Level 1
Present
Not Reported
Absent
Transient
Valid quantitative or qualitative records
exist for a species within an ecoregion.
There are no records known for the species
in an ecoregion. This is the default.
Species that have been incorrectly
reported as present in a region due to
incorrect taxonomy or taxonomic revisions,
or that have gone extinct within the
ecoregion.
Species that temporarily occur in an
ecoregion due to unusual climatic or
oceanographic events but do not establish
a permanent population.
Present, Observed,
Reported, Found,
Occurs
No mention of the
species within the
ecoregion.
Misidentified,
Taxonomic revision,
Extinct, Extirpated
Transient,
Extralimital,
Temporary,
Migrant, Not
established, Outside
normal range
Frequency >0
Frequency = 0
NA
Varies
(Often low frequency)
>0
NA
NA
NA
95 - 100%
NA
0-5%
0-10%
77
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Abundance
Class
Qualitative Description
Common Key
Ph rases -
Abundance
Common Key Phrases
- Frequency of
Occurrence
Dominance
Normalized
Relative
Abundance
Cut Points
Approximate Ranges of
Percentage of Species
in an Ecoregion
Level II
Abundant
Moderate
Rare
Hyper-Rare
Numerous and usually observed in
collections in suitable habitat(s). Often
inhabit a habitat of wide spatial extent
and/or multiple habitats.
Includes both species that are abundant in
habitats of small to moderate spatial
extent as well as species that are regularly
found at multiple sites but which do not
normally constitute a major portion of the
individuals.
Species with low total population sizes.
Often inhabit habitats of limited spatial
extent. May be relatively abundant in a
spatially limited habitat.
Species that have not been observed
within an ecoregion for 50+ years, with the
caveat that there has been at least a
moderate sampling effort.
Abundant,
Common, Plentiful
Moderate,
Relatively common,
Not uncommon
Rare, Uncommon,
Specialized
Extremely rare,
Possibly extinct
Widespread,
Frequently observed,
High rate of capture
Moderate rate of
capture, Often
observed
Infrequently
observed, Low
frequency, Rarely
observed, Low rate of
capture
Not observed, Not
seen for over 50 years
>0.1
>0.01<0.1
<0.01
NA
4-17%
18-45%
39-66%
0-4%
78
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Abundance
Class
Qualitative Description
Common Key
Ph rases -
Abundance
Common Key Phrases
- Frequency of
Occurrence
Dominance
Normalized
Relative
Abundance
Cut Points
Approximate Ranges of
Percentage of Species
in an Ecoregion
Level III
Very
Abundant
Moderately
Abundant
High
Moderate
Low Moderate
Moderately
Rare
The most numerous species within an
ecoregion, usually inhabit a habitat of
large spatial extent and/or multiple
habitats.
Abundant species within an ecoregion, but
not numerically dominant.
Species frequently observed in one or
several habitats though usually not among
the most numerous species.
Species that occur in high abundances in
relatively spatially limited habitats.
Uncommon species, but often observed in
low numbers in large collections. May
inhabit specialized habitats and/or
habitats of limited area. May also include
generalist species at the end of their
biogeographic range.
Numerical
dominant, Very
abundant
Abundant, Very
common
Common, Not
uncommon, May be
abundant in suitable
habitats
Common, Not
uncommon
Rare, Sparse
Ubiquitous, Very
widespread, Nearly
always collected
Widespread, Regularly
captured
Frequent, Often
observed
Regularly observed,
Routinely collected
Infrequent
>0.5
>0.1<0.5
>0.03<0.1
>0.01 <0.03
^0.005 <0.01
2-8%
2-12%
5-25%
5-25%
8-25%
79
-------
Abundance
Class
Very Rare
Qualitative Description
The least abundant species in an
ecoregion, often inhabit specialized
habitats or habitats of limited area.
Usually sparse even in suitable habitats.
Can include species at the end of their
biogeographic range.
Common Key
Ph rases -
Abundance
Rare, Very rare,
Unusual
Common Key Phrases
- Frequency of
Occurrence
Rarely observed,
Seldom found
Dominance
Normalized
Relative
Abundance
Cut Points
<0.005
Approximate Ranges of
Percentage of Species
in an Ecoregion
10-50%
80
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Appendix Table 3: Definitions for the regime classes (Figure 20).
Regimes are the broad physical and environmental divisions based on a combination of salinity,
geomorphology, and depth (Madden et al., 2005).
Regime Class
Terrestrial
Lakes and Ponds (Lentic)
Rivers, Streams, and Creeks (Lotic)
Estuaries and Lagoons
Coastal Fringe
Coastal Bay
Open Nearshore Waters
Shelf
Oceanic
Definition
Land areas not directly impinging upon aquatic ecosystems.
Body of standing fresh water, including freshwater wetlands.
Flowing bodies of freshwater, including riparian zones.
Estuary: A semi-enclosed coastal water body with one or more rivers
or streams flowing into it and with a connection to the ocean.
Salinities in estuaries are normally below that of the
bordering ocean water, though in some cases there may be
very little reduction in salinity or even an increase ("negative
estuaries").
Lagoons: Shallow coastal water bodies separated from the ocean by a
barrier island or by shallow or exposed sandbanks or coral
reefs. Depending upon freshwater inputs and connection to
the ocean, salinity in lagoons can range from essentially fresh
to hypersaline.
Area between terrestrial and nearshore or estuarine ecosystems with
primarily terrestrial characteristics but strongly effected by bordering
aquatic ecosystem (e.g., sand dunes, estuarine shrub/scrub wetland,
estuarine forest wetland).
A semi-enclosed segment of a coastline that has marine salinities or
only slightly reduced salinities. Not meant to be used for very large
indentations in the coast, such as Monterey Bay.
0-30 m. The outer coast; from the intertidal to 30 m bathymetric
isobath.
30-200 m bathymetric isobaths. Includes the benthos and water
extending out to where there is an increased slope of the seafloor,
approximately 200 m depth. Shelf is also used with inland seas like
Puget Sound.
>200 m bathymetric isobath. Includes the benthos and water above
the continental slope and ocean floor. "Oceanic" is also used for
waters >200 m in inland seas like Puget Sound.
81
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Appendix Table 4: Definitions for ecosystem/habitat classes (Figures 22-23).
Major
Ecosystem Type
Level 1
Unconsolidated
Ecosystems
Ecosystem/Habitat
Class
Level 2
Unvegetated
Sand/Mud
Ecosystem/Habitat
Class
Level 3
Coastal Shore
Tide Flats
Subtidal
Ecosystem/
Habitat
Class
Level 4
Clastic
Sediment
Carbonate
Sediment
Burrowing
Shrimp
Clastic
Sediment
Carbonate
Sediment
Burrowing
Shrimp
Clastic
Sediments
Definition
Ecosystem types associated with
sediment.
Sediment environments where
plants or algae do not dominate.
Exposed sediment.
Sediment environments along
the coast affected by the tides
and water activity (shore waves).
Sandy beaches.
A sediment environment (beach)
composed of rock fragments.
A sediment environment (beach)
composed of calcium carbonate,
including shells, calcified algae,
and/or coral skeletons.
Relatively flat, sediment areas
submerged or exposed by the
changing tides. Includes mud
flats.
Sediment environments
composed of shrimp burrows.
These environments are usually
dominated by one species of
shrimp (e.g., Neotrypaea sp.).
A tidal flat where the sediment is
composed of rock fragments.
A tidal flat where the sediment is
composed of calcium carbonate.
Sources include shells, calcified
algae, and/or coral skeletons.
Sediment covered by a body of
water at all times, without
exposure to air due to tides.
Sediment environments
composed of shrimp burrows.
Sandy subtidal where the
sediment is composed of rock
fragments.
82
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Major
Ecosystem Type
Level 1
Ecosystem/Habitat
Class
Level 2
Rubble/Hash
Ecosystem/Habitat
Class
Level 3
Coastal Shore
Tide Flats
Subtidal
Ecosystem/
Habitat
Class
Level 4
Carbonate
Sediment
Clastic
Sediment
Carbonate
Sediment
Burrowing
Shrimp
Clastic
Sediment
Carbonate
Sediment
Burrowing
Shrimp
Clastic
Sediment
Definition
Sandy subtidal where the
sediment is composed of calcium
carbonate. Sources include
shells, calcified algae, and/or
coral skeletons.
Sediment environments where
the bottom is composed mostly
of rubble (broken rock or coral)
and/or shell hash (loose shell
accumulations).
Rubble/hash sediment
environments along the coast
(beaches) affected by the tides
and water activity (shore waves).
A rubble/hash sediment
environment composed of rock
fragments.
A rubble/hash sediment
environment composed of
calcium carbonate, including
shells, calcified algae, and/or
coral skeletons.
Relatively flat, rubble/hash
sediment areas submerged or
exposed by the changing tides.
Rubble/hash sediment
environment with high density
of shrimp burrows.
A rubble /hash tidal flat where
the sediment is composed of
rock fragments.
A rubble/hash tidal flat where
the sediment is composed of
calcium carbonate. Sources
include shells, calcified algae,
and/or coral skeletons.
Rubble/hash sediment that is
covered by a body of water at all
times, without exposure to air
due to tides.
Subtidal sediment environments
with high density of shrimp
burrows.
Subtidal where the sediment is
composed of rock fragments.
83
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Major
Ecosystem Type
Level 1
Ecosystem/Habitat
Class
Level 2
Under Rock
Submerged Aquatic
Vegetation (SAV)
Ecosystem/Habitat
Class
Level 3
Zostera
Posidonia
Halodule
Cymodocea
Syringodium
Thalassodendron
Ecosystem/
Habitat
Class
Level 4
Carbonate
Sediment
Zostera
marina
Zostera
japonica
Other/
Unknown
Definition
Subtidal where the sediment is
composed of calcium carbonate.
Sources include shells, calcified
algae, and/or coral skeletons.
Species living under rocks or
other hard substrates (e.g., shell
rubble) located on
unconsolidated sediments.
Sediment environments that
include and are dominated by
aquatic plants (seagrasses)
periodically or regularly
submerged by water.
SAV environments dominated by
the seagrass Zostera (eelgrass).
SAV environments dominated by
the seagrass Zostera marina. Z.
marina is native to the Northeast
Pacific (NEP).
SAV environments dominated by
the seagrass Zostera japonica. Z.
japonica is introduced to the
NEP and native in the Northwest
Pacific (NWP).
SAV environments dominated by
the seagrass Zostera but the
exact species is either unknown
or not listed above.
SAV environments dominated by
plant species within the genus
Posidonia.
SAV environments dominated by
plant species within the genus
Halodule.
SAV environments dominated by
plant species within the genus
Cymodocea.
SAV environments dominated by
plant species within the genus
Syringodium (manatee grass).
SAV environments dominated by
plant species within the genus
Thalassoden dron .
84
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Major
Ecosystem Type
Level 1
Ecosystem/Habitat
Class
Level 2
Macroalgal Beds
Ecosystem/Habitat
Class
Level 3
Amphibolis
Enhaulus
Thalassia
Ruppia
Halophila
Other/ Unknown
Coastal Shore
Ecosystem/
Habitat
Class
Level 4
Ulva
Gracilaria
pacifica
Fucus
gardneri
Sargassum
muticum
Definition
SAV environments dominated by
plant species within the genus
Amphibolis.
SAV environments dominated by
plant species within the genus
Enhaulus.
SAV environments dominated by
plant species within the genus
Thalassia (turtle grass).
SAV environments dominated by
plant species within the genus
Ruppia (widgeon grass).
SAV environments dominated by
plant species within the genus
Halophila.
Sedimentary environments
dominated by SAV but the exact
species is either unknown or not
listed above.
Sediment environments where
macroalgae are dominant and
shape the habitat characteristics
(e.g., algal mats of Ulva,
Porphyra).
Macroalgae dominated sediment
environments along the coast
affected by the tides and water
activity (shore waves). Beaches.
Areas of coastal shores with a
dense cover of green algal
species within the genus Ulva.
Areas of coastal shores with a
dense cover of the red alga
Gracilaria pacifica.
Areas of coastal shore with a
dense cover of the brown alga
Fucus gardneri (rockweed).
Areas of the coastal shore with a
dense cover of the brown alga
Sargassum muticum (Japanese
wireweed). 5. muticum is
introduced to the NEP and
Europe from Asia.
85
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Major
Ecosystem Type
Level 1
Ecosystem/Habitat
Class
Level 2
Ecosystem/Habitat
Class
Level 3
Tidal Flats
Subtidal
Ecosystem/
Habitat
Class
Level 4
Other/
Unknown
Ulva
Gracilaha
pacifica
Fucus
gardneri
Sargassum
muticum
Other/
Unknown
Ulva
Gracilaha
pacifica
Fucus
gardneri
Sargassum
muticum
Other/
Unknown
Definition
Areas of coastal shore with a
dense cover of other or
unidentified species of
macroalgae.
Relatively flat, macroalgae
dominated sediment areas
periodically exposed by the
changing tides.
Areas of tide flats with a dense
cover of the green alga Ulva.
Areas of tide flats with a dense
cover of the red alga Gracilaria
pacifica.
Areas of tide flats with a dense
cover of the brown alga Fucus
gardneri (rockweed).
Areas of the tide flat with a
dense cover of the brown alga
Sargassum muticum (Japanese
wireweed). 5. muticum is
introduced to the NEP and
Europe from Asia.
Areas of the tide flat with a
dense cover of other or
unidentified species of
macroalgae.
Macroalgae dominated sediment
that is covered by a body of
water at all times, without
exposure to air due to tides.
Areas of subtidal with a dense
cover of the green alga Ulva.
Areas of the subtidal with a
dense cover of the red alga
Gracilaria pacifica.
Areas of the subtidal with a
dense cover of the brown alga
Fucus gardneri (rockweed).
Areas of the subtidal with a
dense cover of the brown alga
Sargassum muticum (Japanese
wireweed). S. muticum is
introduced to the NEP and
Europe from Asia.
Areas of the subtidal with a
dense cover of other or
unknown species of macroalgae.
86
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Major
Ecosystem Type
Level 1
Ecosystem/Habitat
Class
Level 2
Emergent Marsh
Mangrove
Ecosystem/Habitat
Class
Level 3
Distichlis
S part in a
Sarcocornia
Juncus
Other/
Unknown
Rhizophora
Ecosystem/
Habitat
Class
Level 4
alterniflora
anglica
densiflora
foliosa
patens
townsendii
Definition
Intertidal sediment
environments dominated by
vegetation that is rooted in the
soil (i.e., marsh grasses and salt
tolerant succulents).
Marshes dominated by plant
species within the genus
Distichlis.
Marshes dominated by plant
species within the genus
Spartina (cord grasses).
Dominated by S. alterniflora, an
invasive species in the NEP.
Dominated by S. anglica, an
invasive species in the NEP.
Dominated by S. densiflora, an
invasive species in the NEP.
Dominated by S. foliosa
(California cordgrass), a native
species in the NEP.
Dominated by S. patens, an
invasive species in the NEP.
Dominated by the hybrid S.
townsendii, an invasive species
in the NEP.
Marshes dominated by plant
species within the genus
Sarcocornia (glasswort,
pickleweed).
Marshes dominated by plant
species within the genus Juncus.
Marshes dominated by other or
unidentified marsh plants.
Intertidal sediment
environments dominated by
salt-tolerant trees and shrubs.
Found in tropical and subtropical
areas.
Mangrove forests dominated by
plant species within the genus
Rhizophora (includes red
mangroves).
87
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Major
Ecosystem Type
Level 1
Consolidated
Ecosystems
Ecosystem/Habitat
Class
Level 2
Dune
Wrack
Other /Unknown
Rocky Intertidal
Ecosystem/Habitat
Class
Level 3
Avicennia
Laguncularia
Conocarpus
Other/ Unknown
Supratidal Splash
Pool
Tide Pool
Phyllospadix
Caves
Under Rocks
Ecosystem/
Habitat
Class
Level 4
Definition
Mangrove forests dominated by
plant species within the genus
Avicennia (includes black
mangroves).
Mangrove forests dominated by
plant species within the genus
Laguncularia (includes white
mangrove).
Mangrove forests dominated by
plant species within the genus
Conocarpus (includes
buttonwood).
Mangroves habitat dominated
by other or unidentified
mangrove plants.
Sand hills or ridges on land
created by wind.
Dried vegetation and associated
debris usually left behind by the
receding tide.
Sediment habitats not previously
mentioned or not identified in
the literature.
Ecosystem types associated with
hard substrate.
Rocky environments on the
coastal shore periodically
exposed to both air and water.
The zone between the high and
low tide marks.
Pools in the supralittoral zone
maintained by wave splash.
A pool of water left behind by
the receding tide. Commonly
found in the rocky intertidal.
Rocky habitats dominated by
species of surfgrass within the
genus Phyllospadix.
A chamber formed by rocks or
another hard substrate (i.e. lava
tubes) in the intertidal zone.
Species living in the space under
or between rocks in the rocky
intertidal.
88
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Major
Ecosystem Type
Level 1
Ecosystem/Habitat
Class
Level 2
Subtidal Rocky
Coral
Oyster Beds
Ecosystem/Habitat
Class
Level 3
Estuarine
Under Rocks
Estuarine
Coral Reef
Ecosystem
Non-Reef Corals
Crassostrea gigas
Crassostrea
virginica
Ostrea conchaphila
Ecosystem/
Habitat
Class
Level 4
Natural
Artificial
Natural
Artificial
Living Corals
Non-Li ving
Coral Reef
Isolated
Coral Heads
Deep/Cold
Water
Corals
Definition
Rocky intertidal found in
estuaries.
Natural rocks in estuaries.
Rocks placed in estuaries, such
as rip rap.
Rocky environments below the
low tide mark nearly always
submerged by water.
Found in space under or
between rocks in the subtidal.
Rocks found subtidally in
estuaries.
Natural rocks in estuaries.
Rocks placed in estuaries, such
as rip rap.
Areas where the consolidated
substrate is dominated by reef
forming coral animals.
Ecosystem associated with reefs
formed by hermatypic corals.
Ecosystem associated with living
hermatypic coral reefs.
Ecosystem associated with dead
hermatypic coral reefs (e.g.,
coral blocks).
Biotically generated areas of
physical relief other than the
reefs formed by hermatypic
corals.
Solitary heads of living corals;
may be composed of isolated
heads of reef-forming corals or
non-reef forming corals.
Corals found in deep, cold
waters; many are solitary but
some may form "reefs" or
mounds.
Substrate that is covered or
formed by oyster shells.
Area with a dense cover of the
Japanese oyster, C. gigas.
Area with a dense cover of the
Atlantic oyster, C. virginica.
Area with a dense cover of O.
conchaphila, native to the NEP.
89
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Major
Ecosystem Type
Level 1
Ecosystem/Habitat
Class
Level 2
Non-Coral Reefs
Algal Mats
Kelp
Ecosystem/Habitat
Class
Level 3
Ostrea lurida
Other /Unknown
Sabellariid Reef
Serpulid Reef
Vermetid Reef
Sponge Reef
Other/ Unknown
Coralline Algal
Mats
Algal Tuft
Ecosystem/
Habitat
Class
Level 4
Definition
Area with a dense cover of O.
lurida, native to the NEP.
Area with a dense cover of other
or unidentified oyster species.
Hard substrate with substantial
relief that is formed from the
structures of taxa other than
corals or oysters.
Reefs or aggregations composed
of the calcareous tubes of
polychaetes of the family
Sabellariidae.
Reefs or aggregations composed
of the calcareous tubes of
polychaetes of the family
Serpulidae.
Reefs or aggregations composed
of the calcareous tubes of
gastropods of the family
Vermetidae.
Reefs or aggregations composed
of sponges.
Other or unidentified non-coral
taxa that forms reefs.
Hard substrate that is
predominantly covered with
attached algae, including both
macroalgae and encrusting
microalgae.
Hard substrate that is
predominantly covered with a
layer of coralline algae.
Hard substrate that is
predominantly covered by an
aggregation of algae with a more
three-dimensional structure
than a mat. Often consists of
multiple algae taxa.
Hard substrate that supports the
growth of very large brown algae
(Laminariales and/or Fucales).
These habitats tend to be
subtidal and occur in mid to high
latitudes.
90
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Major
Ecosystem Type
Level 1
Pelagic
Ecosystems
Ecosystem/Habitat
Class
Level 2
Fouling
Wood
Mussel Beds
Rhodoliths/Maerl
Bryozoan mats
Solitary Sponge
Other/ Unknown
Water Column
Floating Plants
Ecosystem/Habitat
Class
Level 3
My til us sp.
Musculista
senhousia
Other/ Unknown
Microlayer
Ecosystem/
Habitat
Class
Level 4
Definition
Hard substrate such as piers or
boat hulls that support a
community of organisms of
attached and mobile species.
Hard substrate that is
predominantly composed of
wood, (e.g., drift wood).
Dense aggregations of mussels.
Areas with a dense cover of
mussels of the genus Mytilus.
Areas with a dense cover of the
mussel M. senhousia, a non-
native in the NEP.
Areas with a dense cover of
mussels of other or unidentified
species.
Free-living (unattached) masses
of coralline algae (Order
Corallinales) forming a hard
substrate. Large aggregations of
rhodoliths can form beds
covering hectares. Also referred
to as maerl.
Dense cover of bryozoans
forming a mat on substrate.
Non-reef forming sponges,
including mat-like colonial
species.
Habitats associated with hard
substrates that were not
previously mentioned or that
were not identified.
The ocean water column and
unobstructed surface. Open
water.
Open water habitat where
organisms are completely
surrounded by water; within the
pelagic zone.
The boundary between the
atmosphere and the water,
defined as the surface 1 mm of
the water.
Large mats/rafts of plants or
algae that float unattached on
the water's surface in the open
ocean.
91
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Major
Ecosystem Type
Level 1
Specialized
Systems
Ecosystem/Habitat
Class
Level 2
Floating Debris
Saline lagoons
Seamounts
Cold seeps
Hydrothermal vents
Sea Ice
Whale Falls
Ecosystem/Habitat
Class
Level 3
Ecosystem/
Habitat
Class
Level 4
Definition
Aggregated floating debris in the
open ocean.
Ecosystems composed of benthic
and pelagic habitats with
physical and/or chemical
characteristics distinct from
surrounding ecosystems.
Bodies of saline water wholly or
mostly separated from the sea
by dunes or rock barriers, and
retain water during low tide. Sea
water exchange with the lagoon
can occur through percolation,
channels, or overwash. Salinity
can vary from nearly fresh to
hypersaline.
An ocean mountain that does
not reach the sea surface. Most
are volcanic in origin. Typically
deep but some are located at
<200 m depth.
Areas of the ocean's bottom
where hydrogen sulfide-rich,
methane-rich, or other
hydrocarbon-rich water is
discharged. Food webs around
seeps are often based on
chemosynthetic bacteria. Most
seeps are deep though some are
located at <200 m depth.
Areas of the ocean bottom
located in subduction zones
where heated water is
discharged through fissures in
the ocean crust. Food webs
around seeps are often based on
chemosynthetic bacteria. Most
vents are deep though some are
located at <200 m depth.
Ecosystem formed by sea ice and
ice melt (sympagic).
Micro-ecosystem formed by the
carcasses of whales.
92
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Appendix Table 5: Definitions for the depth classes for the benthic and pelagic
zones (Figure 25).
Benthic/Pelagic
Benthic
Pelagic
Depth Class:
Level 1
Coastal Fringe
Supralittoral
Intertidal (MLLW-
MHHW)
Neritic
Bathyal
Abyssal
Hadal
Epipelagic
Mesopelagic
Bathypelagic
Abyssopelagic
Hadopelagic
Depth Class:
Level 2
Upper Intertidal
Mid Intertidal
Lower Intertidal
Shallow Subtidal
Deep Subtidal
Surface
Shallow
Deep
Definition
Associated with the seafloor.
The terrestrial area immediately surrounding
estuaries and oceans. It is the location of
habitats such as coastal dunes and certain
types of intermittently flooded wetlands (e.g.,
forested wetlands).
Area above the high water level that is
periodically wetted by breaking waves or
during extreme storms. The splash zone.
The zone between the average daily highest
high tide and the average daily lowest low tide.
This zone is periodically submerged by water
and exposed to air. Also referred to as the
littoral zone, though some publications use
littoral to include the shallow subtidal.
Highest intertidal zone, predominantly
exposed to the air.
Between the highest and lowest intertidal
zone, regularly submerged and exposed.
Lowest intertidal zone, predominantly
submerged by water.
>0-200 m. Subtidal zone extending from the
low water mark to the approximate edge of
the continental shelf. Also referred to as the
sublittoral zone.
>0-30 m.
>30-200 m.
>200-2000 m. This benthic zone is below the
euphotic zone and extends down the
continental slope.
>2000-6000 m. This zone has a temperature of
4°C or less. It is the largest benthic ocean zone.
>6000 m. The deepest areas of the ocean,
including ocean trenches.
The estuary or ocean water column and
unobstructed surface. Open water.
0-200 m
0-1 m
>1-30 m
>30-200 m
>200-1000 m
>1000-2000 m
>2000-6000 m
>6000 m
93
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Appendix Table 6: Definitions for the salinity classes in practical salinity units
[psu) (Figure 27)
Salinity Classes:
Level 1
Freshwater
Brackish
Marine/Euhaline
Hypersaline
Venice System:
Level 2
Oligohaline
Mesohaline
Polyhaline
Division of Venice Classes:
Level 3
Beta-oligohaline
Alpha-oligohaline
Beta-mesohaline
Alpha-mesohaline
Beta-polyhaline
Alpha-polyhaline
Beta-euhaline
Alpha-euhaline
Definition
<0.5 psu
0.5 - <30 psu
0.5 -<5 psu
0.5 -<3 psu
3 - <5 psu
5-<18psu
5-<10psu
10-<18 psu
18 - <30 psu
18 - <25 psu
25 - <30 psu
30 - <40 psu
30 - <36 psu
36 - <40 psu
>40 psu
94
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Appendix Table 7: Definitions for substrate classes (Figure 29-30).
Level 1
Consolidated
Level 2
Rock
Hardpan
Biogenic
Artificial
Substrate
Level 3
Boulder
Bedrock
Coral
Oyster
Mussel
Worm Reef
Coralline Algae
Kelp
Rooted Aquatic
Mangrove
Wood
Other/Unknown
Rip Rap
Piling
Definition
Substrates composed of particles >256 mm or
unbroken rock. Substrate not moved by organisms
or tidal or ocean currents except in extreme storms.
Hard mineral substrate >256 mm in size.
Substrates composed of particles >256 mm but not
forming a single unbroken surface.
Unbroken rock. Includes both hard rocks and softer
rocks, such as chalk.
Sand, silt, or clay particles slightly cemented to well
cemented together to form a hard, and often flat,
consolidated surface.
Substrate composed of the surface of living or dead
organisms.
Substrate primarily composed of living or dead
corals. (Coral broken into silt, clay, sand, or cobble-
sized particles are classified as unconsolidated
carbonate sediments.)
Substrate primarily composed of living or dead
oyster shells. (Shells broken into clay, silt, sand, or
cobble-sized particles are classified as
unconsolidated carbonate sediments.)
Substrate primarily composed of living or dead
mussel shells. (Shells broken into clay, silt, sand, or
cobble-sized particles are classified as
unconsolidated carbonate sediments.)
Substrate provided by worms with hard tubes
constructed of sand grains or calcium carbonate
(e.g., Sabellariidae).
Calcareous substrate provided by algae of the Order
Corallinales.
Substrate provided by the fronds and holdfasts of
kelp.
Substrate provided by the leaves of rooted aquatic
vegetation, including emergent vegetation.
Hard substrate provided by mangroves.
Natural drift wood and buried logs.
Other consolidated substrates not included in the list
of biotic substrates or not identified.
Hard substrates placed into estuarine or oceanic
environments.
Hard substrate provided by rocks and concrete used
in break walls, groins, jetties, and shoreline
armoring.
Hard substrate provided by concrete and wood
piling and piers to support docks, bridges, and other
superstructures.
95
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Level 1
Unconsolidated
Level 2
Mud
Sand
Mixed Fines
Level 3
Hulls and Ballast
Tanks
Floating Debris
Artificial Reefs &
Structures
Other/Unknown
Clay
Silt
Mineral
Carbonate
Siliceous Ooze
Fine Sand
Medium Sand
Coarse Sand
Mineral
Carbonate
Siliceous Ooze
Sandy Mud
Muddy Sand
Mineral
Definition
Hard substrate on the exterior or interior of ships
and boats, including derelict or decommissioned
ships.
Hard substrate composed of floating debris,
including derelict ships and docks.
Hard substrate provided by sunken ships and
artificial reefs.
Other artificial hard substrates not listed above or
not identified.
Substrate composed of individual particles <256 mm
that are not cemented together. Substrate that can
be moved by tidal or ocean currents or moved by
larger organisms.
Unconsolidated sediment composed of_>75%, by
weight, particles <0.063 mm in size. The
combination of clay and silt is referred to as "fines".
Unconsolidated sediment composed of_>75%, by
weight, particles in the size range of 0.001-0.004
mm.
Unconsolidated sediment composed of_>75%, by
weight, particles in the size range of 0.004-0.063 mm
Mud primarily composed of rock fragments.
Mud primarily composed of carbonate sediments,
such as muds derived from corals.
Mud composed of >30% siliceous remains from
diatoms, radiolarians, siliceous sponges, and
silicoflagellates.
Unconsolidated sediment composed of >75%, by
weight, particles in the size range of 0.063-2 mm.
Unconsolidated sediment composed of >75%, by
weight, particles in the size range of 0.063-0.25 mm.
Unconsolidated sediment composed of >75%, by
weight, particles in the size range of 0.25-0.5 mm.
Unconsolidated sediment composed of >75%, by
weight, particles in the size range of 0.5-2 mm.
Sand primarily composed of rock fragments.
Sand primarily composed of carbonate sediments,
such as maerl.
Sand composed of >30% siliceous remains from
diatoms, radiolarians, siliceous sponges, and
silicoflagellates.
Combination of mud and sand, where the two
classes constitute >95% of the weight. Do not
confuse with "mixed sediments", a mixture of
mud/sand and cobble/gravel/rock.
Unconsolidated substrate where mud constitutes
25-50% and sand 50-75% of the weight.
Unconsolidated substrate where mud constitutes
<50 to 75% and sand 25-50% of the weight.
Mixed fines primarily composed of rock fragments.
96
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Level 1
Level 2
Gravel
Cobble
Mixed
sediments
Shell Hash/
Bioclastic
Sediments
Organic
Sediment
Level 3
Carbonate
Siliceous Ooze
Clean Gravel
Gravel W/Mud
Gravel W/Sand
Mineral
Carbonate
Clean Cobble
Cobble W/Mud
Cobble W/Sand
Mineral
Carbonate
Gravelly Mud
Muddy Gravel
Gravelly Sand
Sandy Gravel
Definition
Mixed fines primarily composed of carbonate
sediments.
Mixed fines composed of >30% siliceous remains
from diatoms, radiolarians, siliceous sponges, and
silicoflagellates.
Unconsolidated sediment composed of >75%, by
weight, of particles in the range of 2-64 mm.
Gravel substrate with <5% mud and sand intermixed.
Gravel substrate with >5% mud intermixed.
Gravel substrate with >5% sand intermixed.
Gravel primarily composed of rock fragments.
Gravel primarily composed of carbonate sediments,
such as maerl or shell hash.
Unconsolidated sediment composed of >75% by
weight of particles in the size range of 64-256 mm. In
some classifications, cobble is considered
consolidated sediment.
Cobble sediment with <5% sand and mud
intermixed.
Cobble sediment with >5% mud intermixed.
Cobble sediment with >5% sand intermixed.
Cobble composed primarily of rock fragments.
Cobble composed primarily of carbonate.
Unconsolidated sediment composed of both sand
and mud with gravel or cobble, where gravel and
cobble constitute >5% but <75% of the sediment
weight. Do not confuse with "mixed fines".
Unconsolidated sediment where gravel >5% but
<30% of the weight and the percentage of mud
exceeds the percentage of sand.
Unconsolidated sediment where gravel >30% but
<75% of the weight and the percentage of mud
exceeds the percentage of sand.
Unconsolidated sediment where gravel >5% but
<30% of the weight and the percentage of sand
exceeds the percentage of mud.
Unconsolidated sediment where gravel >30% but
<75% of the weight and the percentage of sand
exceeds the percentage of mud.
General class for sediments predominately
composed of shells or other biogenic calcium
carbonate particles. Also includes sediments whose
physical structure is strongly modified by the
presence of shells or other carbonate remains.
Proportions of different particle size classes are
given under the other Unconsolidated classes.
Sediment with high proportion of vegetative
detritus. >30% organic matter (>17% organic carbon)
according to Howes and Kenik (1997).
97
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Appendix Table 8: Definitions for the wave energy classes (Figure 31).
Wave energy classes are derived from Howes et al. (1999) based on fetch.
Wave Energy Classes
Exposed
Semi-exposed
Semi-protected
Protected
Very Protected
Definition
"High ambient wave conditions usually prevail within this exposure
category, which is typical of open-ocean type conditions." Max.
fetch distances >500 km.
"Swells, generated in areas distant from the shore unit create
relatively high wave conditions. During storms, extremely large
waves create high wave exposures." Max. fetch distance between
50 and 500 km.
"Waves are low most of the time except during high winds." Fetch
in range of 10-50 km.
"Usually areas of provisional anchorages and low wave exposure
except in extreme winds." Fetch <10 km.
"Usually the location of all-weather anchorages, marinas and
harbors." Max. fetch <1 km.
Appendix Table 9: Definitions for the current energy classes (Figure 31).
Current classes are based on Madden et al. (2005).
Current Energy Classes
High Energy
Moderate Energy
Low Energy
No Energy
Definition
Strong currents (>4 knots or >2.056 m/sec or >7.408 km/hr)
Moderate currents (2-4 knots or 1.028-2.056 m/sec or 3.704-7.408
km/hr)
Weak currents (0-2 knots or 0-1.028 m/sec or 0-3.704 km/hr)
No detectable currents.
Appendix Table 10: Definitions for the physiological temperature classes
(Figure 32).
Physiological Class
Stenothermal
Mesothermal
Eurythermal
Definition
Species with a narrow temperature range, such as
deeper water and Antarctic species.
Species with a moderate temperature range; species
with a moderate temperature tolerance.
Species with a wide temperature range, such as many
intertidal species and species with wide geographic
distributions.
98
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Appendix Table 11: Definitions for the trophic modes (Figure 34).
Level 1
Primary
Producer
Herbivore
Predator
Scavenger
Detritivore
Decomposer
Suspension
Feeder
Deposit
Feeder
Osmotrophy
Other
Level 2
Photosynthetic
Chemosynthetic
Grazer
Folivore
Herbivore -
Other
Active
Passive
Suspension -
Obligate
Suspension -
Facultative
Surface Deposit
Feeder
Subsurface
Deposit Feeder
Deposit -
Obligate
Deposit -
Facultative
Coprophagic
Explanation
Metabolic energy derived from sunlight or chemosynthesis in contrast to
consumption of other organisms.
Metabolic energy derived from photosynthesis.
Metabolic energy derived from oxidation of methane, hydrogen sulfide, or
other reduced molecules.
An organism that feeds on plants. Species feeding on phytoplankton via
suspension feeding are covered under "Suspension Feeders".
An organism that feeds by rasping benthic algae from sediment, rocks, or
leaf surfaces. May consume some smaller benthic organisms, but if animals
are dominant food source, the species is classified as a predator.
An organism that feeds on leaves.
Herbivore feeding mechanism not included in the above list.
Organism that feeds on animals.
Organism that feeds on dead organic material. Usually used for species
feeding on larger particles or animal remains.
In contrast to scavengers, feeds on small detritus (i.e., plant and animal
remains).
Organisms that breakdown and digest dead organisms. Bacteria and fungi
are major decomposer groups.
Organism that feeds on phytoplankton, zooplankton, and/or suspended
particles in the water column.
Captures planktonic particles by pumping or sweeping water past a filter.
Utilizes water currents to transport planktonic particles past a particle-
trapping mechanism, such as a filter or sticky trap.
Organism that feeds only as a suspension feeder.
Switches between suspension feeding and other feeding mechanism(s),
such as deposit feeding.
Ingests sediment particles, feeding on the associated detritus, microflora,
and microorganisms.
Ingests particles at the sediment interface.
Ingests subsurface particles.
Feeds only as a deposit feeder.
Switches between deposit feeding and other feeding modes, such as
suspension feeding.
Consumes feces.
Uptake of dissolved organic matter (DOM) for nutrition.
Feeding mechanism not included in the above list.
99
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Appendix Table 12: Definitions for trophic interactions among symbionts
(Figure 34).
Level 1
Parasite/Disease
Symbiotic Algae
Chemoautotrophic Bacteria
Level 2
Ectoparasite
Endoparasite
Kleptoparasite
Mucus Consumption
Disease
Explanation
Organisms that feed on a host and are usually
physiologically / metabolically dependent upon
the host. Usually smaller than host.
External parasite, including gill parasites.
Internal parasite.
Parasites that feed on the food items that the
host has collected.
Feeding on the mucus produced by another
species, including certain crabs living on corals
and cleaner wrasses feeding on mucus of reef
fish. Considered parasitism because of the
energetic cost to the host of producing mucus.
Does not include the use of mucus by a species as
a feeding mechanism.
Microorganisms living in or on a host and
resulting in deleterious impacts. Also called
pathogens.
Species deriving nutrition from symbiotic
microflora, such as many corals. This classification
is for the host species; the microflora would be
classified as a primary producer.
Chemoautotrophs are organisms, typically
bacteria that derive their energy from inorganic
sources, including sulfides and ferrous iron.
Chemoautotrophic bacteria are known to live
symbiotically with certain clams, such as some
lucinids in reduced sediments, providing nutrients
to their host.
100
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Appendix Table 13: Definitions for the terms describing reproductive classes
(Figure 36).
Level 1
Asexual
reproduction
Sexual
Reproduction
Level 2
Sporogenesis
Binary fission
Budding and
Fragmentation
Parthenogenesis
Agamospermy
Vegetative
Propagation
Hermaphrodite/
Monoecious
Level 3
Heterogamy
Monoecious
(plants)
Synchronous
Hermaphrodite
(animal)
Sequential
Hermaphrodite
(animal)
Level 4
Self-
fertilizing:
Y/N
Self-
fertilizing:
Y/N
P rota n dry
Protogyny
Explanation
Reproduction without the fusion of
gametes.
Reproduction and dispersal through
formation of spores. Spores differ
from seeds in having little food
reserves. Most spores are haploid
and may be part of an alternation
of haploid and diploid life history
stages. Red algae have both diploid
and haploid spores.
Splitting into two approximately
equal parts.
Splitting into unequal parts.
Includes mechanical fragmentation
and regeneration such as with
nemertean worms. Buds may form
on the body of the "parent".
In animals, parthenogenesis is the
development of an unfertilized egg.
In plants, agamospermy (apomixes)
is the production of fertile seeds
without pollination.
Alternation between sexual and
asexual reproductive phases.
Formation of new individuals in
plants without the production of
spores or seeds by stolons
(runners) or formation of bulbs.
Forms a plant colony.
Reproduction through the fusion of
gametes (fertilization).
Organisms having both male and
female sexual organs.
Primarily used for plants having
separate male and female flowers
on the same individual plant.
Primarily used for animals having
both male and female sexual
organs at the same time
(=simultaneous hermaphrodite).
Animals that change from one sex
into the other.
Initially a male and changes into a
female.
Initially a female and changes into a
male.
101
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Level 1
Level 2
Gonochoristic/
Dioecious
Fertilization /
Spawning Type
Migratory
Level 3
Copulation
Fertilization
External Eggs
Freecast
Spawners
(animals)
Pollination
(plants)
Anadromous
Catadromous
Level 4
Broadcast
Spawner
Spermcast
Spawner
Explanation
Having separate sexes. In plants,
male and female flowers are
produced on different individuals.
Fertilization with both eggs and
sperm internal.
Female lays egg mass and male
fertilizes externally.
In animals, males and/or females
discharge gametes directly into the
water column.
Both males and females discharge
gametes into the water column.
Only males discharge gametes into
the water column.
In plants, fertilization of female
floral structures by pollen.
Migration is normal part of species'
breeding cycle.
Species that spend most of their
lives in saltwater and migrate to
freshwater to breed.
Species that spend most of their
lives in freshwater and migrate to
saltwater to breed.
Appendix Table 14: Definitions for breeding strategy (Figure 38).
Breeding Strategy
Level 1
Viviparous
Oviparous
Ovoviviparous
Level 2
Eggs Deposited in
Environment
Egg Mass Carried
by Female
Eggs Brooded in
Tube
Level 3
Definition
Development takes place within the
female and embryos derive
nourishment from the mother.
Eggs are laid by the female and
develop outside of either parent.
Eggs are laid directly in the
environment in an egg case, egg
mass, or spawned into the water
column.
Eggs are carried as an external mass
by the female (e.g., berried crab).
Eggs are brooded in the adult's
tube; larvae may or may not be
brooded.
Eggs develop within the female, or
male in some cases, but the
embryo derives no nourishment
from the parent. A brooder.
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Breeding Strategy
Level 1
Egg Size
Breeding Frequency
Level 2
Min./Mean/Max.
Semelparous
Iteroparous
Level 3
Max. # broods per lifetime
Mean/Max. # of broods per
year
Definition
The minimum, mean, and/or
maximum egg size, measured in
mm.
How often a species breeds
(spawns) during its lifetime or
during a year.
Species only reproduces once
during its lifespan (big bang
reproduction).
Species is capable of reproducing
multiple times during its lifespan.
Maximum number of reproductive
events for a female over lifespan.
Mean or maximum number of
reproductive events per year for a
female.
103
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Appendix Table 15: Definitions for juvenile development and dispersal
(Figure 38).
Juvenile Development & Dispersal
Level 1
Direct
development
Larval phase
Level 2
Ametabolous
Hemimetabolous
Holometabolous
Duration of
Larval Phase
Benthic Larvae
Planktonic Larvae
Level 3
Brooded
Free Living
Benthic -
Lecithotrophy
Benthic -
Planktotrophy
Benthic -
Adelphophagy
Planktonic -
Lecithotrophy
Level 4
Definition
Development without a larval phase.
Juvenile development with no major
change in body form.
Juvenile development with
incomplete metamorphosis. In
insects, consisting of an egg, nymph,
and adult stage.
Juvenile development with complete
metamorphosis. In insects, consisting
of an embryo, larvum, pupa, and
imago (adult) stage.
Development with a morphologically
distinct, free-living dispersive stage.
Often occupies a different habitat
than the adult.
Maximum duration of larval phase in
days.
Larvae that remain on the bottom or
within the tubes of adults.
The larval phase is brooded within or
on the adult or in tube of the adult.
The larval phase is totally separated
from the adult.
Benthic larvae that do not capture or
use exogenous food, and derive
nourishment from yolk.
Benthic larvae that derive
nourishment by feeding while free of
the parent.
Benthic larvae that feed on other eggs
or larvae prior to hatching or release
from brood. Includes consumption of
nurse eggs.
Larvae that spend at least part of the
larval phase in the water column.
Planktonic larvae that do not capture
or use exogenous food, and derive
nourishment from yolk.
104
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Juvenile Development & Dispersal
Level 1
Fragments
Seeds
Spores
Settlement
Level 2
Minimum Size at
Settlement
Level 3
Planktonic-
Planktotrophy
Level 4
Definition
Planktonic larvae that derive
nourishment by feeding.
Animals or plants that can disperse
through transport of fragments.
Plants that can disperse through
seeds.
Animals or plants that can disperse
through transport of spores.
Size of juvenile when it settles out of
the plankton, in mm.
Appendix Table 16: Definitions for adult development (Figure 38).
Adult Development
Level 1
Maturation
(1st Reproduction)
Fecundity
Max. Life Span
Max. Size
von Bertalanffy (k)
Level 2
Female/ Male/
Unknown
Female/ Male/
Unknown
Female/ Male/
Unknown
Level 3
Min. Size
Min. Age
Definition
Earliest reproductive stage, measured in age
or size.
Minimum size at reproduction, in mm.
Minimum age at reproduction, in months.
Minimum, mean, and/or maximum number
of eggs produced by a female per brood.
Maximum life span of male or female, in
months.
Maximum size of species based on taxon
appropriate measurement(s), in mm.
"k: This is a parameter of the von Bertalanffy
growth function (also known as growth
coefficient), expressing the rate (I/year) at
which the asymptotic length is approached."
(FishBase, http://www.fishbase.org)
105
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Appendix Table 17: Definition for alternation of generations classes (Figure
38).
Level 1
Haploid/Diploid Phases
Medusa/Polyp Phases
Definition
In plants, fungi, and some microorganisms, an alternation of multicellular haploid
and diploid phases.
In Cnidaria, an alternation between a polypoid benthic stage and a free-living
medusoid stage.
Appendix Table 18: Definitions for habitat-association classes (Figure 40).
Level 1
Pelagic
Benthic
Level 2
Pleuston
Neuston
Pelagic
submerged
Demersal
Level 3
Benthopelagic
Level 4
Permanent
Benthopelagic
Definition
Organisms inhabiting the water column
exclusive of the layer immediately above
the bottom.
Buoyant organisms with part of the body
protruding above the water surface and
often subject to wind drift. Includes
animals, such as the Portuguese Man-of-
War, Velella, and plants floating at the
surface.
Pelagic organisms that float near the
water surface, typically the top 5 cm, but
do not protrude above the sea surface
as do pleuston.
Free-living pelagic organisms that spend
all or the vast majority of their time fully
submerged under the surface, and are
not closely associated with the layer
immediately above the bottom.
Organisms living in, on, or immediately
above a consolidated or unconsolidated
substrate.
Mobile animals living on or near the
bottom that routinely swim as a normal
part of their adult life cycle and not just
in response to disturbance.
Animals living all or part of their adult
life in the water column directly above
but not on the bottom.
Animals that spends all or most of their
adult life living in the water column
within a few meters above the bottom,
such a shiner perch.
106
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Level 1
Level 2
Surficial
(Epibenthic
Non
swimming)
Level 3
Epibenthic -
Swimming
Epibenthic
Unconsolidated
Epibenthic
Consolidated
Level 4
Hyperbenthos
Epifauna
Unconsolidated
Epiphytos
Unconsolidated
Epifauna
Consolidated
Epiphytos
Consolidated
Primary Space
Holder (Y/N)
Definition
Benthic animals that make periodic
forays from the bottom into the water
column, such as some of the corophiid
amphipods.
Animals living in direct contact with the
sediment that swim as part of their
normal adult behaviour, such as flatfish.
Organisms living on the surface of either
consolidated or Unconsolidated
substrate, including both sessile and
vagile species but not species that
routinely swim.
Organisms living on mud (epipelic) or
sand (epipsammic), including mobile
non-swimming fauna that primarily live
on the surface of the sediment,
macrophytes growing in the sediment,
and microflora living on mud or sand
particles.
Non-swimming mobile animals living on
the surface of Unconsolidated
substrates. Larger surface dwelling
species sampled in trawls, such as sea
cucumbers and scallops, are often
referred to as megabenthos.
Plants, including macrophytes,
macroalgae, and microflora living in or
on the surface of Unconsolidated
substrates, including diatoms attached
to mud or sand particles. Macrophytes
(e.g., Zostera) are included to capture
the primary producers as well as the
soft-bottom fauna.
Sessile (e.g., barnacles, algae) and vagile
(e.g., snails) organisms living on the
surface of rocks (epilithic) or other
inorganic hard substrates including man-
made structures.
Sessile and vagile animals living on the
surface of rocks and other inorganic
hard substrates.
Plants, including macrophytes,
macroalgae and microflora, living on the
surface of rocks and other inorganic
hard substrates.
Organisms directly colonizing the
substrate surface and occupying space
(e.g., barnacles, coralline algae).
107
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Level 1
Level 2
Under Rocks
Cryptofauna
Borer
Nestler
Semi-infauna
Infauna
Level 3
Rock Borer
Clay Borer
Shell and Coral
Borer
Wood Borer
Macrofauna
Level 4
Shallow
Macrofauna
Deep
Macrofauna
Definition
Species that often live beneath rocks or
other hard substrates (e.g., shell rubble,
debris). In terms of habitat associations,
may be associated with unconsolidated
and/or consolidated substrates.
Sessile and vagile organisms living in the
interstices and crevices formed by
epibenthic organisms or their structures,
such as formed by mussel beds, living
corals, and coral rubble.
Organisms that bore into living or dead
consolidated substrate.
Organisms that bore into rocks or
artificial hard substrate. The
endolithobiont of Taylor and Wilson
(2002).
Organisms that bore into hard clays.
Organisms that bore into living and dead
shells, including corals. The
endozoobiont of Taylor and Wilson
(2002).
Organisms that bore into living or dead
wood. The endoxylobiont of Taylor and
Wilson (2002).
Bivalve or other animal living within an
existing crevice in a consolidated
substrate, such as Hiatella. The "WN"
class of Todd (2001).
Animals partially buried in mud or sand
and partially exposed in the water
column, such as the bivalve Modiolus
(see Bush etal., 2007).
Animals living within unconsolidated
sediments.
Animals living within unconsolidated
sediment large enough to displace
sediment particles. Macrofauna can be
operationally defined as animals
retained on 0.5 mm mesh screen.
Macrofauna generally have more direct
contact with overlying water than
meiofauna.
<5 cm deep.
>5 cm deep.
108
-------
Level 1
Epibiotic
Other
Level 2
Epiphytic
Epizoic
Secondary
space holder
(Y/N)
Level 3
Meiofauna
Microfauna
Level 4
Shallow
Meiofauna
Deep
Meiofauna
Shallow
Microfauna
Deep
Microfauna
Definition
Animals living within the interstitial
spaces in unconsolidated sediments.
There is no agreed upon size range, but
they can be operationally defined as
organisms less than 0.5 mm and greater
than 50 microns.
<5 cm deep.
>5 cm deep.
Multicellular and single-celled organisms
living within interstitial spaces in
unconsolidated sediments, and smaller
than meiofauna. Can be operationally
defined as organisms less than 50
microns.
<5 cm deep.
>5 cm deep.
Organisms living on the surface of a
living or dead organism. Relationship
may be mutualistic, parasitic, or
commensal. Classified as pelagic or
benthic depending upon the species it
colonizes.
Living on surface of living or dead plant.
Living on surface of a living or dead
animal.
Facultatively mobile or immobile
epibiotic organisms colonizing the
surface of a primary space holder.
Species living in habitats not captured in
those listed above.
Appendix Table 19: Definitions of mobility classes (Figure 42).
Level 1
Immobile
Level 2
Immobile
Unattached
Level 3
Immobile
Infaunal
Level 4
Free Living
Tubicolous
Explanation
Species with no ability to move as an adult.
Species that spends its adult life unattached to a
substrate.
Soft sediment only.
Immobile infaunal species that do not live in a
tube.
Species living in a mud, sand, organic, or
calcareous tube.
109
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Level 1
Faculta-
tively
Mobile
Passively
mobile
Level 2
Immobile
Attached
Immobile
Rooted
Unattached
Immobile
Attached
Planktonic
Level 3
Reclining
Nestler/ Borer
Immobile
Unattached
Other
Cemented
Immobile
Byssally
Attached
Immobile Other
Adhesion
Facultatively
Mobile Byssally
Attached
Facultatively
Mobile
Attached Other
Holoplankton
Meroplankton
Level 4
Explanation
Brachiopods "floating horizontally on (or partially
within) the sediment with the pedicle valve as the
lower valve."
(http://paleo.cortland.edu/tutorial/Brachiopods/
brachmorph.htm)
Species that live within an existing crevice in a
consolidated substrate (nestler) or a species that
bores into a consolidated substrate (borer).
Immobile unattached species using mechanism
not included in the above list.
Species attached to a consolidated substrate.
Species cemented directly to the substrate, such
as barnacles and serpulid worms.
Species attached to the substrate with byssal
threads (organic filaments), such as many
mussels.
Immobile attached species using mechanism not
included in the above list.
Immobile species that used roots to maintain its
position. Only associated with vascular plants, and
primarily in unconsolidated sediments.
Species with limited mobility, in particular to
repositioning themselves in response to
environmental disturbances (e.g., sea anemones).
Species with no permanent attachment to the
substrate, but which have limited mobility, such
as several larger, deeper burrowing bivalves in
mud or sands.
Hard substrates.
Adheres to substrate by foot or is cemented.
Species attached to the substrate with byssal
threads (organic filaments). Certain mussels and
other bivalves with byssal threads have limited
mobility.
Facultatively mobile species with an attachment
mechanism not included in the above list.
Although may be capable of some limited local
movement, the overall movement in the
environment is due to water currents.
In the water column.
Species that are planktonic for their entire life
cycle.
Species that are planktonic for only part of their
life cycle, usually the larval phase.
110
-------
Level 1
Actively
mobile
Level 2
Drift
Other
Sedentary
Swimming
Periodic
mobility
Level 3
Burrowing
Crawling
Other
Nektonic
Demersal
Y/N
Level 4
Fast
Slow
Fast
Slow
Explanation
Non-planktonic species that passively drift in the
currents. This includes benthic macroalgae and
stands of SAV that drift in the currents as well as
the animals associated with the floating algae
and/or SAV. It also includes plants and animals
associated with drifting debris.
Passively mobile mechanisms not mentioned
above.
Mobility is a normal part of the adult life cycle, at
least in spurts. Not dependent upon distance
traveled.
Limited movement but a normal part of the adult
life.
Through sediment.
On sediment or rock. Nereis in mussel beds.
Other sedentary movement not mentioned
above.
Active movement through the water column,
normal part of adult behaviour.
Swims against current in the water column.
A general term for nektonic species that swim at a
high velocity, such as tuna, mackerel, and certain
squid.
A general term for nektonic species that normally
swim at a low velocity, such as ocean sunfish and
sea horses. Such species may be capable of short
bursts of fast swimming.
Swimming on or near the bottom.
A general term for demersal species that swim at
a high velocity.
A general term for demersal species that normally
swim at a low velocity, such as most flatfish and
crabs. Such species may be capable of short
bursts of fast swimming.
Species that show intermittent periods of no or
limited mobility coupled with periods of active
mobility. This includes many of the hyperbenthic
species.
Ill
-------
Appendix Table 20. Taxa codes used to identify major taxonomic groups.
Taxa codes are short-hand abbreviations to identify major taxonomic levels. "Group" is a code to link
species that display generally similar taxonomic levels, sizes and/or body types. However, "Groups" have
no taxonomic standing.
TAXA CODE
ACEL
ACT
AM
AMB
AMP
AN
ANN
AP
APIC
AR
ART
ASCO
AST
AVE
B
BACT
BR
BRCH
BRN
BRY
CAUD
CC
CE
CENT
CEP
CEPH
CERC
CEST
CHAR/STRE
CHIM
CHL
CHR
CHT
CIL
CIR
CN
COP
CR
CRUS
CRY
CT
CU
CUB
CYB
NAME
Acoelomorpha
Actinopterygii
Amphipoda
Amoebozoa
Amphibia
Anthozoa
Annelida
Aplacophora
Apicomplexa
Arachnida
Arthropoda
Ascothoracida
Asteroidea
Aves
Bivalvia
Bacteria
Brachiopoda
Branchiura
Branchiopoda
Bryozoa
Caudofoveata
Cephalocarida
Cephalopoda
Chilopoda
Cephalochordata
Cephalaspidomorphi
Cercozoa
Cestoda
Charophyta /Streptophyta
Holocephali
Chlorophyta
Chrysophyceae
Chaetognatha
Ciliophora
Cirripedia
Cnidaria
Copepoda
Crinoidea
Crustacea
Cryptophyta
Ctenophora
Cumacea
Cubozoa
Cyanobacteria
COMMON NAME
ray-finned fish
amphipod
amoeba
amphibian
anthozoan
annelid
arachnid
sea star
bird
bivalve
bacterium
brachiopod
fish louse
fairy shrimp
moss animal
cephalpod
centipede
lancelet
lamprey
tapeworm
rat fish
green alga
golden alga
arrow worm
ciliate
barnacle
copepod
sea lily/
feather star
crustacean
cryptomonad
comb jelly
hooded shrimp
box jellyfish
blue-green bacterium
GROUP
Invertebrate
Fish
Invertebrate
Protist
Vertebrate
Invertebrate
Invertebrate
Invertebrate
Protist
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Vertebrate
Invertebrate
Bacteria
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Fish
Protist
Invertebrate
Macroalgae
Fish
Macroalgae
Microalgae
Invertebrate
Protist
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Microalgae
Invertebrate
Invertebrate
Invertebrate
Microalgae
112
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TAXA CODE
DEC
DIA
DINO
EC
ECH
ECHN
ELAS
ENT
EQUI
EU
FACE
FECA
FORM
FUNG
G
CAST
GNAT
HAG
HEMI
HI
HO
HPT
HY
IN
ISO
KINO
LE
LOPH
LOR
LYCO
MAG
MAM
MER
MILL
MOL
MONG
MONO
MY
MYST
MYX
NE
NEM
NEMA
O
OP
ORTH
OS
P
PAUR
NAME
Decapoda
Bacillariophyceae
Dinozoa
Echinoidea
Echiura
Echinodermata
Elasmobranchii
Entoprocta
Equisetophyta
Euphausiacea
Facetotecta
Fecampiida
Foraminifera
Fungi
Gastropoda
Gastrotricha
Gnathostomulida
Myxini
Hemichordata
Hirudinea
Holothuroidea
Haptophyta
Hydrozoa
Insecta
Isopoda
Kinorhyncha
Leptostraca
Lophogastrida
Loricifera
Lycopodiophyta
Magnoliophyta
Mammalia
Merostomata
Diplopoda
Mollusca
Monogenea
Monoplacophora
Mysida
Mystacocaridida
Myxozoa
Nemertea
Nematoda
Nematomorpha
Oligochaeta
Ophiuroidea
Orthonectida
Ostracoda
Polychaeta
Pauropoda
COMMON NAME
decapod
diatom
dinoflagellate
sea urchin
spoon worm
echinoderm
cartilaginous fish
horsetail
krill
foram
fungi
snail
hagfish
leech
sea cucumber
hydrozoan
insect
isopod
club moss
flowering plant
mammal
horseshoe crab
millipede
mollusk
mysid
myxozoan
nemertean
nematode
horsehair worm
oligochaete
brittle star
ostracod
polychaete
GROUP
Invertebrate
Microalgae
Microalgae
Invertebrate
Invertebrate
Invertebrate
Fish
Invertebrate
Plant
Invertebrate
Invertebrate
Invertebrate
Protist
Fungi
Invertebrate
Invertebrate
Invertebrate
Fish
Invertebrate
Invertebrate
Invertebrate
Microalgae
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Plant
Plant
Vertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
113
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TAXA CODE
PENT
PER
PFUN
PH
PHA
PL
PLAC
PO
PP
PRI
PTER
PY
RAD
RAP
REM
REP
RHD
RHIZ
RHOM
ROT
SCA
SCY
SI
SOL
STAUR
STO
SYMP
SYNC
TA
TANT
TAR
TREM
TU
TURB
VIR
XAN
NAME
Pentastomida
Pericarida
Oomycota
Phoronida
Phaeophyceae
Platyhelminthes
Placozoa
Porifera
Polyplacophora
Priapulida
Pteridophyta
Pycnogonida
Radiozoa
Raphidophyceae
Remipedia
Reptilia
Rhodophyta
Rhizopoda
Rhombozoa
Rotifera
Scaphopoda
Scyphozoa
Sipuncula
Solenogastres
Staurozoa
Stomatopoda
Symphyla
Syncarida
Tanaidacea
Tantulocarida
Tardigrada
Trematoda
Tunicata
Turbellaria
Viruses
Xanthophyceae
COMMON NAME
tongue worms
pseudofungi /
water mold
horseshoe worm
brown alga
flatworm
sponge
chiton
priapulid worms
fern
sea spider
radiolarian
reptile
red alga
amoeba
rotifer
tusk shell
jellyfish
peanut worm
stalked jellyfish
mantis shrimp
pseudocentipedes
water bear
fluke
sea squirt
flatworm
virus
yellow-green alga
GROUP
Invertebrate
Invertebrate
Pseudofungi
Invertebrate
Macroalgae
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Plant
Invertebrate
Protist
Microalgae
Invertebrate
Vertebrate
Macroalgae
Protist
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Invertebrate
Viruses
Microalgae
114
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Appendix Table 21: List of the MEOW ecoregions classified as tropical.
In general, species occurring in one or more tropical ecoregions are considered less vulnerable to
temperature increases in temperate ecoregions.
MEOW Ecoregion
Amazonia
Andaman and Nicobar Islands
Andaman Sea Coral Coast
Angolan
Arafura Sea
Araucanian
Arnhem Coast to Gulf of Carpenteria
Bahamian
Banda Sea
Bight of Sofala/Swamp Coast
Bismarck Sea
Bonaparte Coast
Cape Verde
Cargados Carajos/Tromelin Island
Central and Southern Great Barrier Reef
Central Chile
Central Peru
Central Somali Coast
Chagos
Chiapas-Nicaragua
Clipperton
Cocos-Keeling/Christmas Island
Cocos Islands
Coral Sea
Delagoa
East African Coral Coast
East Caroline Islands
Eastern Brazil
Eastern Caribbean
Eastern Galapagos Islands
Eastern India
Eastern Philippines
Exmouth to Broome
Fernando de Naronha and Atoll das Rocas
Fiji Islands
Floridian
Gilbert/Ellis Islands
Greater Antilles
Guayaquil
MEOW Province
North Brazil Shelf
Andaman
Andaman
Gulf of Guinea
Sahul Shelf
Warm Temperate Southeastern Pacific
Sahul Shelf
Tropical Northwestern Atlantic
Western Coral Triangle
Western Indian Ocean
Eastern Coral Triangle
Sahul Shelf
West African Transition
Western Indian Ocean
Northeast Australian Shelf
Warm Temperate Southeastern Pacific
Warm Temperate Southeastern Pacific
Somali/Arabian
Central Indian Ocean Islands
Tropical East Pacific
Tropical East Pacific
Java Transitional
Tropical East Pacific
Tropical Southwestern Pacific
Western Indian Ocean
Western Indian Ocean
Tropical Northwestern Pacific
Tropical Southwestern Atlantic
Tropical Northwestern Atlantic
Galapagos
Bay of Bengal
Western Coral Triangle
Northwest Australian Shelf
Tropical Southwestern Atlantic
Tropical Southwestern Pacific
Tropical Northwestern Atlantic
Marshall, Gilbert and Ellis Islands
Tropical Northwestern Atlantic
Tropical East Pacific
115
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MEOW Ecoregion
Guianan
Gulf of Aden
Gulf of Guinea Central
Gulf of Guinea Islands
Gulf of Guinea South
Gulf of Guinea Upwelling
Gulf of Guinea West
Gulf of Papua
Gulf of Thailand
Gulf of Tonkin
Halmahera
Hawaii
Humboldtian
Lesser Sunda
Line Islands
Lord Howe and Norfolk Islands
Malacca Strait
Maldives
Mariana Islands
Marquesas
Marshall Islands
Mascarene Islands
Mexican Tropical Pacific
New Caledonia
Nicoya
Ningaloo
Northeast Sulawesi
Northeastern Brazil
Northern Bay of Bengal
Northern Galapagos Islands
Northern Monsoon Current Coast
Ogasawara Islands
Palawan/North Borneo
Panama Bight
Papua
Phoenix/Tokelau/Northern Cook Islands
Rapa-Pitcairn
Revillagigedos
Sahelian Upwelling
Samoa Islands
Sao Pedro and Sao Paulo Islands
Seychelles
Society Islands
MEOW Province
North Brazil Shelf
Red Sea and Gulf of Aden
Gulf of Guinea
Gulf of Guinea
Gulf of Guinea
Gulf of Guinea
Gulf of Guinea
Sahul Shelf
Sunda Shelf
South China Sea
Western Coral Triangle
Hawaii
Warm Temperate Southeastern Pacific
Western Coral Triangle
Central Polynesia
Lord Howe and Norfolk Islands
Sunda Shelf
Central Indian Ocean Islands
Tropical Northwestern Pacific
Marquesas
Marshall, Gilbert and Ellis Islands
Western Indian Ocean
Tropical East Pacific
Tropical Southwestern Pacific
Tropical East Pacific
Northwest Australian Shelf
Western Coral Triangle
Tropical Southwestern Atlantic
Bay of Bengal
Galapagos
Western Indian Ocean
Tropical Northwestern Pacific
Western Coral Triangle
Tropical East Pacific
Western Coral Triangle
Central Polynesia
Southeast Polynesia
Tropical East Pacific
West African Transition
Central Polynesia
Tropical Southwestern Atlantic
Western Indian Ocean
Southeast Polynesia
116
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MEOW Ecoregion
Solomon Archipelago
Solomon Sea
South China Sea Oceanic Islands
South India and Sri Lanka
South Kuroshio
Southeast Madagascar
Southeast Papua New Guinea
Southeastern Brazil
Southern Caribbean
Southern China
Southern Cook/Austral Islands
Southern Gulf of Mexico
Southern Java
Southern Red Sea
Southern Vietnam
Southwestern Caribbean
St. Helena and Ascension Islands
Sulawesi Sea/Makassar Strait
Sunda Shelf/Java Sea
Tonga Islands
Torres Strait Northern Great Barrier Reef
Trindade and Martin Vaz Islands
Tuamotus
Vanuatu
West Caroline Islands
Western and Northern Madagascar
Western Arabian Sea
Western Caribbean
Western Galapagos Islands
Western India
Western Sumatra
MEOW Province
Eastern Coral Triangle
Eastern Coral Triangle
South China Sea
West and South Indian Shelf
South Kuroshio
Western Indian Ocean
Eastern Coral Triangle
Warm Temperate Southwestern Atlantic
Tropical Northwestern Atlantic
South China Sea
Southeast Polynesia
Tropical Northwestern Atlantic
Java Transitional
Red Sea and Gulf of Aden
Sunda Shelf
Tropical Northwestern Atlantic
St. Helena and Ascension Islands
Western Coral Triangle
Sunda Shelf
Tropical Southwestern Pacific
Northeast Australian Shelf
Tropical Southwestern Atlantic
Southeast Polynesia
Tropical Southwestern Pacific
Tropical Northwestern Pacific
Western Indian Ocean
Somali/Arabian
Tropical Northwestern Atlantic
Galapagos
West and South Indian Shelf
Andaman
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Appendix Table 22: List of small island MEOW ecoregions.
Small was defined as having an area less than the Hawaii Ecoregion and not abutting the mainland.
Maintenance of a population on a small island ecoregion is an indicator that the species is both a good
colonizer and can maintain a small population size.
MEOW Ecoregion
Aleutian Islands
Amsterdam-St Paul
Andaman and Nicobar Islands
Auckland Island
Azores Canaries Madeira
Bahamian
Bermuda
Bounty and Antipodes Islands
Bouvet Island
Campbell Island
Cape Verde
Cargados Carajos/Tromelin Island
Chagos
Chatham Island
Clipperton
Cocos-Keeling/Christmas Island
Cocos Islands
Coral Sea
Crozet Islands
East Caroline Islands
Easter Island
Eastern Caribbean
Eastern Galapagos Islands
Faroe Plateau
Fernando de Naronha and Atoll das Rocas
Gilbert/Ellis Islands
Gulf of Guinea Islands
Heard and Macdonald Islands
Juan Fernandez and Desventuradas
Kerguelen Islands
Kermadec Island
Line Islands
Lord Howe and Norfolk Islands
Macquarie Island
Maldives
Malvinas/Falklands
Mariana Islands
Marquesas
MEOW Province
Cold Temperate Northeast Pacific
Amsterdam-St Paul
Andaman
Subantarctic New Zealand
Lusitanian
Tropical Northwestern Atlantic
Tropical Northwestern Atlantic
Subantarctic New Zealand
Subantarctic Islands
Subantarctic New Zealand
West African Transition
Western Indian Ocean
Central Indian Ocean Islands
Southern New Zealand
Tropical East Pacific
Java Transitional
Tropical East Pacific
Tropical Southwestern Pacific
Subantarctic Islands
Tropical Northwestern Pacific
Easter Island
Tropical Northwestern Atlantic
Galapagos
Northern European Seas
Tropical Southwestern Atlantic
Marshall, Gilbert and Ellis Islands
Gulf of Guinea
Subantarctic Islands
Juan Fernandez and Desventuradas
Subantarctic Islands
Northern New Zealand
Central Polynesia
Lord Howe and Norfolk Islands
Subantarctic Islands
Central Indian Ocean Islands
Magellanic
Tropical Northwestern Pacific
Marquesas
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MEOW Ecoregion
Marshall Islands
Mascarene Islands
Northern Galapagos Islands
Ogasawara Islands
Peter the First Island
Phoenix/Tokelau/Northern Cook Islands
Prince Edward Islands
Rapa-Pitcairn
Revillagigedos
Samoa Islands
Sao Pedro and Sao Paulo Islands
Seychelles
Snares Island
Society Islands
South China Sea Oceanic Islands
South Georgia
South Orkney Islands
South Sandwich Islands
South Shetland Islands
Southern Cook/Austral Islands
St. Helena and Ascension Islands
Three Kings-North Cape
Tonga Islands
Trindade and Martin Vaz Islands
Tristan Gough
Tuamotus
Vanuatu
West Caroline Islands
Western Galapagos Islands
| MEOW Province
Marshall, Gilbert and Ellis Islands
Western Indian Ocean
Galapagos
Tropical Northwestern Pacific
Subantarctic Islands
Central Polynesia
Subantarctic Islands
Southeast Polynesia
Tropical East Pacific
Central Polynesia
Tropical Southwestern Atlantic
Western Indian Ocean
Southern New Zealand
Southeast Polynesia
South China Sea
Scotia Sea
Scotia Sea
Scotia Sea
Scotia Sea
Southeast Polynesia
St. Helena and Ascension Islands
Northern New Zealand
Tropical Southwestern Pacific
Tropical Southwestern Atlantic
Tristan Gough
Southeast Polynesia
Tropical Southwestern Pacific
Tropical Northwestern Pacific
Galapagos
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Appendix Table 23: Primary invasion vectors (Figure 51).
Hierarchical classification of the anthropogenic mechanisms (vectors) by which species can be transported from their native ecoregion to a
non-native ecoregion. Species can be transported by multiple vectors.
Level 1
Ships and Boats
Moveable
Structures
Level 2
Commercial
Recreational
Drilling
Platforms
Dry Docks
Level 3
Ballast Water
Solid Ballast
Hull Fouling
Other
Ballast Water
Solid Ballast
Hull Fouling
Other
Definition
Transport associated with commercial vessels and recreational boats.
Transport associated with commercial vessels including cruise ships and fishing boats.
Transport of organisms in ballast water, including species growing on the interior of ballast water
tanks and in the sediment in the bottom of ballast tanks.
Transport of organisms living on or associated with solid ballast such as rocks. More important
historically.
Transport of organisms living on or associated with the hulls of commercial vessels, including
organisms ensnared on propellers.
Transport associated with other mechanisms on commercial vessels, including bilge water and
anchor chains.
Transport of organisms associated with recreational boats, including boats limited to coastal/inland
use and ocean-going yachts.
Transport of organisms in ballast water, including species growing on the interior of ballast water
tanks and in the sediment in the bottom of ballast tanks. Usually not a major vector in recreational
boats.
Transport of organisms living on or associated with solid ballast such as rocks. More important
historically.
Transport of organisms living on or associated with the hulls of recreational boats, including
organisms ensnared on propellers.
Transport associated with other mechanisms on recreational boats.
Transport of organisms on mobile seagoing structures other than ships and boats.
Transport of organisms associated with the movement of drilling platforms or oil rigs.
Transport of organisms associated with the movement of floating dry docks.
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Level 1
Aquaculture
and Fisheries
Infrastructure
Development
Level 2
Buoys
Floating Debris
Other
Drilling
Platforms
Dry Docks
Buoys
Floating Debris
Other
Intentional
Stocking/Release
Aquaculture
Escapees
Aquaculture
Associated
Species
Intentional
Illegal Release
Other
Canals
Level 3
Atlantic Oysters
Pacific Oysters
Navigation
Canals
Definition
Transport of organisms associated with the movement of buoys.
Transport of organisms on or in debris, including derelict boats and docks.
Transport of organisms associated with other moveable structures.
Transport of organisms associated with the movement of drilling platforms or oil rigs.
Transport of organisms associated with the movement of floating dry docks.
Transport of organisms associated with the movement of buoys.
Transport of organisms on or in debris, including derelict boats and docks.
Transport of organisms associated with other moveable structures.
Transport of target species and "hitchhikers" associated with enhancement of wild fisheries stocks
or aquaculture.
Intentional release of a non-native species usually a fishery or recreational species.
Target aquaculture species escaping into the wild.
Nonindigenous species associated with target aquaculture species (hitchhikers) escaping into the
wild.
Transport of species associated with Atlantic oysters, including Crassostrea virginica.
Transport of species associated with Pacific oysters, including Crassostrea gigas and C. ariakensis.
The intentional illegal release of non-native species by the public, often to establish a game
population.
Other transport mechanisms associated with fisheries and aquaculture.
Transport of organisms associated with activities related to the development and maintenance of
water ways, agriculture, transportation, or forms of commerce.
Transport associated with construction of a canal between water bodies that were unconnected or
had only limited connection.
Transport associated with canals constructed to allow navigation of ships and barges.
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Level 1
Research and
Education
Aquarium and
Plant Trade
Recreational
Boating and
Fishing
Live Seafood
Level 2
Dredging
Other
Public Aquaria
Research
Other
Aquarium
Escapees and
Hitchhikers
Ornamental
Plant Escapees
and Hitchhikers
Other
Live Bait and
Packing
Other
Processing
Release
Packing
Level 3
Irrigation
Canals
Definition
Transport associated with canals constructed to transport irrigation water, more important for
freshwater organisms.
Transport associated with either the disposal of dredge materials or on the dredgers and their
equipment.
Other transport mechanisms associated with infrastructure development.
Accidental releases from facilities related to research or education.
Accidental releases from public aquaria.
Accidental releases from academic, governmental, or private research facilities.
Accidental releases from other types of research and education facilities.
Transport of organisms associated with the importation, culture, selling, and personal
culture/release of aquarium species or ornamental plants.
Transport and subsequent escape of aquarium fish/plants or of the flora and fauna associated with
the aquarium fish/plants and associated packing material.
Transport and subsequent escape of ornamental plants or of the flora and fauna associated with
ornamental plants and their soil and packing material.
Other transport mechanisms related to the aquarium or plant trade.
Transport associated with outdoor recreational activities (other than gardening).
Transport associated with release of live bait or the packing material, including water, used in live
bait.
Other transport mechanisms associated with recreational water activities.
Transport associated with live seafood trade.
Transport associated with the processing phase of the live seafood trade.
Purposeful or accidental release of live seafood.
Transport of "hitchhikers" associated with the packing material used with live seafood.
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Level 1
Habitat
Restoration and
Mitigation
Other/Unknown
Level 2
Habitat
Restoration
Biocontrol
Other
Unknown
Level 3
Definition
Transport associated with activities related to the creation or restoration of habitats including
control of invasive pests.
Transport associated with habitat restoration such as wetland creation. Includes both the species
used in habitat restoration and any "hitchhikers" associated species, soil, or packing material.
Introduction through non-native biocontrol species becoming established.
Vector either not included in above list or unknown.
Vector not captured in above list.
Unknown vector.
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Cover Photo Credits:
Paul Valentich-Scott (Bivalves); Leslie Harris (Polychaetes and Amphipod);
https://www.flickr.com/photos/noaaphotolib/11468790483/in/album-72157638865533095/(Rockfish);
all other photos: http://www.freeimages.com
\ Jr.
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