&EPA
United States
Environmental Protection
Agency
EPA/600/R/12/654 September 2012 www.epa.gov/ord
North Pacific Ocean
User's Guide and Metadata for
the PICES Nonindigenous
Species Information System
?
PICES
Henry Lee II, Deborah Reusser, Katharine Marko, and Maria Ranelletti
Office of
Research and Development
National Health and
Environmental Effects
Research Laboratory
-------
EPA/600/R/12/654
User's Guide and Metadata for the
PICES Nonindigenous Species Information System
Henry Lee II
U.S. Environmental Protection Agency
Office of Research and Development
National Health and Environmental Effects Research Laboratory
Western Ecology Division
Deborah A. Reusser
U.S. Geological Survey
Ecosystems
Western Fisheries Research Center
Katie Marko
U.S. Environmental Protection Agency
Office of Research and Development
National Health and Environmental Effects Research Laboratory
Western Ecology Division
Maria Ranelletti
National Center for Ecological Analysis and Synthesis
Santa Barbara, California
-------
Disclaimer: The information in this document has been funded in part by the U.S.
Environmental Protection Agency (U.S. EPA). The publication was subjected to review by the
National Health and Environmental Effects Research Laboratory's Western Ecology Division
and the U.S. Geological Survey (USGS), and is 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 U.S. Department of Interior, the
USGS, or the EPA of any product or service to the exclusion of others that may be suitable. The
views and terms expressed in the information presented here are those of the contributing scientists
under their responsibilities and do not necessarily represent the views of the North Pacific
Marine Science Organization (PICES). In all cases, scientific content, geographic names and
data were not edited by PICES. Portions of this document were extracted from Lee and Reusser
(2012. Atlas of Nonindigenous Marine and Estuarine Species in the North Pacific).
Acknowledgements: We would like to acknowledge the following funding sources in
supporting the development of the "Atlas of Nonindigenous Marine and Estuarine Species in the
North Pacific.", the "PICES Nonindigenous Species Information System", and the "User's Guide
and Metadata for the PICES Nonindigenous Species Information System": the Japanese Ministry
of Agriculture, Forestry and Fisheries (MAFF), U.S. Geological Survey, U.S. Environmental
Protection Agency, and the Western Regional Panel of the Aquatic Nuisance Species Task
Force. Deborah Reusser was partially funded through a USGS Geography Research Prospectus
and by AMI/GEOSS lAGs #DW-14-92231501-0 and #DW-14-95778101-0 from the U.S.
Environmental Protection Agency. Darlene L. Smith, as chair of Working Group 21 (Non-
indigenous Aquatic Species) of North Pacific Marine Science Organization (PICES), as well as
all the members of Working Group 21, provided support and insights in making the Atlas and
PICES database possible. Special thanks go to Gustav Paulay and Lucius G. Eldredge who
provided detailed reviews of an earlier version of the Atlas and database and to Katie Marko, Lee
McCoy, Gayle Hansen, Jody Stecher, Rebecca Loiselle, Rene Graham, and Chris Janousek for
reviewing the database and User's Guide. In addition, we thank all the people who diligently
provided data entry support for the PICES database, especially Katie Marko, Rene Graham,
Emily Saarinen, Caroline Emch-Wei, Karen Ebert, Stacy Strickland, Jody Stecher, Maria
Ranelletti, Laurel Hillmann, Joan Cabreza, Aaron Norwood, and others. GIS support was
provided by Meredith Payne and Patrick Clinton. Taxonomic assistance was provided by John
Chapman, Kathy Welch, and Gayle Hansen; programming support by Tad Larsen, Rachel
Nehmer and Dustin Wilson; and quality assurance assistance from Melanie Frazier, Rebecca
Loiselle, and Justin Saarinen.
Cover Photos: Green crab holding a CD by Deborah Reusser, U.S. Geological Survey; Map of
the North Pacific and ecoregions of PICES member countries, Patrick Clinton, U.S. EPA;
Yaquina Head Lighthouse and Poole Slough in Yaquina Bay, Newport, OR, USA, Eric Vance,
U.S. EPA.
11
-------
Suggested citations:
Lee II, H., Reusser, D.A., Marko, K.M., and Ranelletti, M. 2012. User's Guide and Metadata for
the PICES Nonindigenous Species Information System. Office of Research and
Development, National Health and Environmental Effects Research Laboratory, EPA
EPA/600/R/12/654.
Lee II, H. and Reusser, D. A., 2012. PICES Nonindigenous Species Information System. Office
of Research and Development, National Health and Environmental Effects Research
Laboratory. Microsoft Access database.
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.
Author Affiliations:
Henry Lee II: Pacific Coast Ecology Branch, Western Ecology Division, National Health and
Environmental Effects Research Laboratory, U.S. Environmental Protection Agency,
Newport OR 97365.
Deborah A. Reusser: Newport Duty Station, Western Fisheries Research Center, Ecosystems,
U.S. Geological Survey, Newport OR 97365.
Katie Marko: Pacific Coast Ecology Branch, Western Ecology Division, National Health and
Environmental Effects Research Laboratory, U.S. Environmental Protection Agency,
Newport OR 97365.
Maria Ranelletti: National Center for Ecological Analysis and Synthesis, 735 State St Suite 300,
Santa Barbara, California 93101, USA (current address)
in
-------
TABLE OF CONTENTS
LIST OF FIGURES VI
LIST OF TABLES VII
1.0 INTRODUCTION TO PICES 1
1.1 INTRODUCTION TO THE PICES "NONINDIGENOUS SPECIES INFORMATION SYSTEM" 1
1.2 DEFINITIONS AND APPROACH TO THE DEVELOPMENT OF PICES 2
1.2.1 Definitions 2
1.2.2 Linking Environmental and Natural History Attributes with Distributions 4
1.2.3 Hierarchical Approach to Environmental and Life History Data 5
1.2.4 Mapping Distributions at Individual Publication and at Master Views 5
1.2.5 Geographic Scope of the Analysis - Marine Ecoregions of the World (MEOW) 5
1.2.6 Inclusion of Nonindigenous Species with an Unknown Population Establishment 7
1.3 OVERVIEW OF THE STRUCTURE OF THE PICES DATABASE 7
2.0 INSTALLING PICES 11
3.0 USING PICES 12
3.1 MAIN MENU 12
3.2 SPECIES INFORMATION AND DISTRIBUTION SEARCH 12
3.3 LOCATIONS SEARCH 13
3.4 PUBLICATIONS SEARCH 13
3.5 SPECIES INFORMATION SCREEN 13
3.5.1 Species Identification 14
3.5.2 Taxonomy and "Also Known As" 15
3.5.3 "SpeciesInformation" Function Buttons 17
3.6 "ENVIRONMENT AND BIOGEOGRAPHY" - BIOGEOGRAPHY SCREENS 20
3.6.1 Opening Environment and Biogeography Screen: Realms 21
3.6.2 Environment and Biogeography Screen: Selecting a Publication for Mapping 22
3.6.3 Environment and Biogeography Screen: Regions 23
3.6.4 Environment and Biogeography Screen: Provinces 25
3.6.5 Environment and Biogeography Screen: Ecoregions 25
3.6.6 Environment and Biogeography: Advanced Function and Master Classifications 26
3.6.7 Environment and Biogeography: Viewing Maps in Advanced Biogeography 29
3.6.8 Environment and Biogeography: Searching for Locations 29
3.6.9 Environment and Biogeography: Classification Function and Master Classification 30
3.6.10 Environment and Biogeography: View Summary & View Comments 33
3.7 ENVIRONMENT AND BIOGEOGRAPHY SCREEN-HABITAT ATTRIBUTE TABS 35
3.7.1 Observed versus Preferred Habitats 35
3.7.2 Regime Tab 35
3.7.3 Ecosystem Tab 36
3.7.4Depth Tab 37
3.7.5. Substrate Tab 38
3.7.6. Energy Tab 39
3.7.7. Temperature Tab 40
3.7.8. Salinity Tab 41
3.8 SPECIES INFORMATION SCREEN - LIFE HISTORY TABS 42
3.8.1 Trophic Level and Feeding Tab 42
3.8.2 Reproduction Tab 43
3.8.3 Development Tab 44
3.8.4 Habitat Association Tab 45
3.8.5 Life Style Tab 46
3.9 SPECIES INFORMATION SCREEN - INVASION BUTTON 47
IV
-------
4.0 PICES DATABASE OUTPUTS 48
4.1. MULTIPLE SPECIES QUERIES-TYPES OF QUERIES 48
4.1.1 Output publication list to (Microsoft) Word 49
4.1.2 Output citation list to (Microsoft) Word 50
4.1.3 Output Short Summary 50
4.1.4. Output Long Summary 57
4.1.5 Output Species Profiles 52
4.2 CREATING A MULTIPLE SPECIES QUERY-NARROWING THE SEARCH 56
4.2.1 Limiting Query to a Specified Taxon 56
4.2.2 Limit Query by Classification and/or Population Status 56
4.2.3 Limit Query by Location 57
4.2.4 Querying All vs. Master Classifications 57
4.2.5 Querying Atlas versus RAS Species 58
4.2.6 Completing the Query. 58
4.2.7 Example Queries 58
4.3 SPECIES DISTRIBUTION SPREADSHEET 59
5.0 PICES TROUBLESHOOTING TIPS 61
5.1. RUNTIME ERRORS 61
5.2. BLACK BOXES 61
6.0 REFERENCES 62
7.0 TABLES 65
8.0 APPENDICES 95
APPENDIX A. MARINE ECOREGIONS OF THE WORLD (MEOW) 95
APPENDIX B: LIST OF PICES TAXA CODES 103
APPENDIX C.. LIST OF COMMONLY USED ABBREVIATIONS FOR MUSEUMS 106
APPENDIX D: INVASION: CRITERIA FOR NONINDIGENOUS CLASSIFICATION 109
APPENDIX E: CRITERIA FOR POPULATION ESTABLISHMENT Ill
-------
LIST OF FIGURES
Figure 1: MEOW ecoregions associated with PICES member countries 6
Figure 2A-C: Flow Diagrams of PICES Menu Options 8
Figure 3: PICES Main Menu 12
Figure 4: Species information and distribution search menu 13
Figure 5: Species Information screen 14
Figure 6: Species Information screen 17
Figure 7: References screen 19
Figure 8: Comments screen 20
Figure 9: Environment and Biogeography home screen 22
Figure 10: Search Publications screen 23
Figure 11: Region level Biogeography Screen 24
Figure 12: Province level Biogeography screen 25
Figure 13: Ecoregion level Biogeography screen 26
Figure 14: Advanced Biogeography menu 27
Figure 15: Map Master Classification view of the Advanced Biogeography Menu 28
Figure 16: Invasion Criteria screen 30
Figure 17: Date of First Record Screen 32
Figure 18: Population Status and Criteria screen 33
Figure 19: View Summary function 34
Figure 20: Regime screen 35
Figure 21: Ecosystem screen 36
Figure 22: Depth screen 37
Figure 23: Substrate screen 38
Figure 24: Energy screen 39
Figure 25: Temperature screen 40
Figure 26: Salinity screen 41
Figure 27: Trophic Level and Feeding screen 42
Figure 28: Reproduction screen 43
Figure 29: Development screen 44
Figure 30: Habitat Association screen 45
Figure 32: Life Style screen 46
Figure 32: Primary Vectors screen 47
Figure 33: Data Output menu 48
Figure 34: Query Species by Distribution menu 49
Figure 35: Output from a Short Summary query 50
Figure 36: Output Long Summary query 51
Figure 37: Species Profile 53
Figure 38A & B: Key to the Species Profiles (Figure 37) 54
Figure 39: Single Species Distribution Spreadsheet menu 59
Figure 40: Output generated by the Single Species Distribution Spreadsheet 60
VI
-------
LIST OF TABLES
Table 1: Definitions for the regime categories 65
Table 2: Definitions for the ecosystem categories 66
Table 3: Definitions for the depth categories for benthic and pelagic habitats 70
Table 4: Definitions for substrate categories 71
Table 5: Definitions for wave energy classes 74
Table 6: Definitions for current energy classes 74
Table 7: Definitions for the physiological temperature classes 74
Table 8: Definitions for the salinity classes 75
Table 9: Definitions for the trophic modes 76
Table 10: Definitions for symbiotic relationships that a species may use to derive energy 77
Table 11: Definitions for the terms describing various reproductive strategies 78
Table 12: Definitions for early development mechanisms 80
Table 13: Definitions for juvenile development and dispersal 80
Table 14: Definition of alternation of generation categories 81
Table 15: Definitions of habitat types 82
Table 16: Definitions of life style (i.e. mobility) terms 86
Table 17: Definitions of terms for primary vectors of invasion 89
Table 18: Tables associated with attributes in the Species Profiles 92
vn
-------
1.0 INTRODUCTION TO PICES
1.1 Introduction to the PICES "Nonindigenous Species Information System"
Welcome to the PICES Nonindigenous Species Information System, a Microsoft Access
database that displays the biogeographic distributions, invasion status, vectors, and key life
history attributes of the approximately 740 reported nonindigenous species (NIS) in the estuarine
and near-coastal habitats of the North Pacific and Hawaii. This database was developed by the
U.S. Environmental Protection Agency and the U.S. Geological Survey under the auspices of
Working Group 21 (Invasive Species) of the North Pacific Marine Science Organization
(PCIES). The PICES database contains the data used to generate the "Atlas of Nonindigenous
Marine and Estuarine Species in the North Pacific" (Lee and Reusser, 2012; herein referred to as
the "Atlas"). The User's Guide provides instructions on how to use the PICES database as well
as metadata for the database and the Atlas. We note that for most users, the Atlas provides a
simpler approach to accessing key information on NIS in the PICES countries than the database,
though the database does provide additional information on species and sources as well as
allowing users to extract information on specific taxa and/or locations (see Section 4).
The PICES database also includes species reported from the PICES Rapid Assessment Surveys
(RAS). PICES sponsored four rapid assessment surveys with the objective of quickly
characterizing the native, non-native, and cryptogenic species present in different locations.
Surveys were sponsored in Dalian, China in 2008, Jeju, Korea in 2009, Newport, Oregon, USA
in 2010, and Peter the Great Bay, near Vladivostok and Nakhodka, Russia in 2011
(http://www.pices.int/publicati ons/pices_press/volumel9/vl9_nl/pp_30-3 l_Kobe-WS_f.pdf,
http://www.pices.int/publications/picesjress/volume20/v20 nl/pp 26-29 RAS-2011.pdf). The
PICES database contains the RAS species that were made available in time for inclusion. Thus,
the database does not capture all the species found in these surveys. In addition, much of the
information on the RAS species was provided by the experts conducting the survey, and their
distributions, environmental requirements, and life history attributes were not evaluated to the
same level of detail by the PICES authors as the North Pacific NIS. In lieu of the more extensive
review as conduced with the Atlas species, the information on the RAS species needs to be
considered preliminary. Additionally, it is important to use the "Map All Distributions" option
(see Section 3.6.6) when mapping their distribution or conducting a query. The general reference
for the RAS surveys in the PICES database is "PICES Working Group 21, YEAR SURVEY".
The overall goal of both the database and Atlas was to simplify and standardize the
dissemination of distributional, habitat, and life history characteristics of near-coastal and
estuarine nonindigenous species. This database provides a means of querying these data and
displaying the information in a consistent format. The specific classes of information the
database captures include:
• Regional and global ranges of native and nonindigenous near-coastal and estuarine
species at different hierarchical spatial scales.
• Habitat and physiological requirements of near-coastal and estuarine species.
• Life history characteristics of near-coastal and estuarine species.
• Invasion history and vectors for nonindigenous species.
-------
This standardized and synthesized data in the database and the Atlas provide the basic
information needed to address a number of managerial and scientific needs. Thus, users will be
able to:
• Create a baseline on the extent of invasion by region in order to assess new invasions.
• Use existing geographical patterns of invasion to gain some insights into potential new
invaders.
• Use existing geographical patters of invasion to gain some insights into mechanisms
affecting relative invasibility of different areas.
• Use life history attributes and environmental requirements of the reported nonindigenous
species to evaluate traits of invaders.
• Understand the potential spread of invaders based on their habitat and environmental
requirements.
• Understand importance of different vectors of introduction of nonindigenous species by
region.
The data in the Atlas of Nonindigenous Marine and Estuarine Species in the North Pacific (Lee
and Reusser, 2012) are up-to-date as of June 2012. Updates to the PICES database were made in
September 2012.
1.2 Definitions and Approach to the Development of PICES
The definitions used for classifying species according to their origins and population status are
provided below. In addition, this section provides an overview of the key approaches used in the
database and Atlas to capturing the distributions and characteristics of NIS.
1.2.1 Definitions
Within the database and Atlas, species are assigned to one of six classifications regarding their
origin - Native, Nonindigenous, Cryptogenic, Transient, Unknown, or Conflict - at any of the
four biogeographic levels (realm to ecoregion). The following definitions were used for these
classifications:
Native: A species that occurs naturally in the area with no human intervention. Native species
have an evolutionary history within the area.
Nonindigenous: A species that has been introduced into an area through human activities,
whether accidently or on purpose. Other terms used include alien, aquatic nuisance species
(ANS), exotic, introduced, non-native, adventive, and naturalized. Use of "invasive" was limited
to invaders that have or are likely to cause adverse ecological, economic, or human health
impacts.
Cryptogenic: Cryptogenic species are not clearly native or introduced based on current
information. As originally defined, this term was to capture uncertainty regarding a species
biogeography and invasion history. However, "cryptogenic" is used increasingly for species with
taxonomic uncertainties, such as sibling or cryptic species or species complexes. To avoid
mixing uncertainty over invasion history with taxonomic uncertainty, we restricted the use of
-------
cryptogenic to locations where there is some evidence for invasion. Cryptogenic species were not
included in the counts of NTS for a location.
Unknown: A species was classified as unknown when there was insufficient information to make
a judgment as to its origin. This was the default classification in the absence of any evidence. In
addition, taxa with an uncertain taxonomy (e.g., species complexes, taxon only identified to
genus) were assigned an unknown classification except in cases when there is evidence that the
taxon was recently introduced into an area (e.g., recent appearance of genus never observed
within a region). Species with uncertain taxonomies have also been classified as "unresolved"
(CANOD, 2009).
Transient: Transient species are those that temporarily migrate into an area as a result of unusual
climatic conditions, such as El Nino. Their movement into the area is via natural mechanisms
rather than mediated through human activities, and they were not included in the counts of NTS
for a location. The terms "vagrant" or "migrant" have been used in a similar fashion.
Conflict: In some cases, invasion experts disagree as to whether a species is nonindigenous
versus native or cryptogenic within a location. If the information was insufficient to make a
decision among the conflicting classifications, the term "conflict" is used. Our use of "conflict"
instead of "cryptogenic" is to highlight the cases where at least some experts believe that there is
sufficient information to consider a species introduced. "Conflict" species were included in the
counts of NIS within a location.
In addition to origin, species were classified in terms of population status:
Established: A species with a self-maintaining, natural population as indicated by its population
size, occurrence over time, wide-spread geographical distribution, presence of juveniles, and/or
presence of reproductive adults. Pragmatically, the occurrence of a species in a probabilistic-
based survey (vs. targeted sampling) is reasonably strong evidence that the species is established
based on the relatively small areas sampled in such random surveys (e.g., tens of square meters
for benthic surveys). Native species are assumed to be established.
Not Established: A species that has been reported from an area but that does not maintain a self-
reproducing population. One indication of non-establishment is not observing the species for
>=25 years, assuming that the appropriate habitat types were surveyed. . Other indications
include lack of juveniles or reproductive adults. By definition, transient species are considered
not established. Nonindigenous species that were classified as not established were not included
in the counts of NIS within a location.
Unknown: Species for which there is insufficient spatial and/or temporal records to assess
population status. Nonindigenous species that were classified with an unknown population status
were included in the counts of NIS within a location (see Section 1.2.6). This is the default
population status at all biogeographic levels.
Stocked: Species maintained through active human intervention, usually for aquaculture. Stocked
species known only to exist in aquaculture facilities were given a population status of not
-------
established and were not included in the counts of NTS. Stocked species that had been reported
from the wild were assigned a population status of established, not established, or unknown, as
appropriate. In many cases it was unclear whether a stocked species occurred in the wild,
especially in Asia. If there was a potential that the species could occur in the wild, the stocked
species was assigned an unknown population status and included in the counts of NIS. Inclusion
of these stocked species in the counts of NIS could potentially overestimate the actual number of
NIS in the region.
Two non-standard taxonomic definitions were used to better reflect the current state of
taxonomic knowledge.
Species Complexes: With increasing scrutiny, including genetic analysis, it becoming apparent
that several previously recognized "species" are composed of a number different, and often
undescribed, species that have been referred to under the same name. Because of their uncertain
taxonomic position, species complexes are generally not classified as nonindigenous. However,
in a few cases, species complexes can be classified as nonindigenous over some portion of their
range based on their recent arrival in an area or by having other attributes of non-native species.
In the PICES database and Atlas, we identify such species complexes by adding the suffix
"Cmplx" to the name of the purported species. Because of the taxonomic uncertainty, synonyms
of species complexes are considered "ambiguous synonyms" (Section 3.5.2).
Provisional Species: Provisional species are "organisms suspected of being new species or whose
identities cannot be determined from available literature" (SCAMIT, 2012). Thus, these species
are considered to be valid species in a particular region even though they cannot be assigned to
an officially recognized species name. As with species complexes, provisional species can be
considered nonindigenous based on their recent arrival in an area or by having other attributes of
non-native species. Our approach to provisional species was to append a citation from a major
publication to the provisional species name. For example, "Bryopsis sp. (Cohen and Carlton,
1995)" is a provisional species from the Cohen and Carlton (1995) report. By appending the
citation to the species, it becomes possible to find one of the major sources for this species.
Appending the citation also avoids the problem of having different provisional species with the
same name from different areas, as can happen when a letter or number is used as a suffix (e.g.,
Bryopsis sp. A). The person originally identifying the provisional species is given as the
taxonomic source, while type locality is used to identify the general geographical area over
which the provisional name is applicable.
1.2.2 Linking Environmental and Natural History Attributes with Distributions
Where and how a species lives can strongly affect both their potential as invaders and their
ecological/economic impacts in invaded habitats. Therefore, we considered it critical to capture
the environmental tolerances and natural history attributes of the existing nonindigenous species.
Such information was gleaned from a variety of sources, including classic natural history and
taxonomic publications and from quantitative surveys. The environmental requirements and
natural history attributes captured in the PICES database are described in Sections 3.3 and 3.7.
-------
1.2.3 Hierarchical Approach to Environmental and Life History Data
Much of the data in the PICES database and the Atlas were captured and displayed in a
hierarchical fashion. As discussed in Reusser and Lee (2011), hierarchical topologies were
developed to synthesize both natural history attributes and species' environmental requirements.
These topologies were developed for both quantitative (e.g., numerical depth ranges) and
qualitative (e.g., depth classes, reproductive type) data. One advantage of hierarchical schemas is
that data of different resolutions can be captured, thus increasing the amount of information that
can be synthesized for a species. For example, with a hierarchical salinity topology, it is possible
to capture detailed salinity ranges as well as a generalized "brackish" class based on a species'
occurrence in estuaries. Another advantage of hierarchical topologies is that the user can use the
information at the level of resolution best suited to the specific question or managerial need.
Besides capturing natural history attributes and environmental requirements in hierarchical
schemas whenever possible, the distributional data were captured in the hierarchical "Marine
Ecoregions of the World" biogeographic schema described below.
1.2.4 Mapping Distributions at Individual Publication and at Master Views
Information on the distribution and classification of species was compiled on a publication by
publication basis, and the PICES database allows the user to view such information by individual
publications. This allows the user to examine the conclusions of specific experts. However, to
provide a consolidated analysis, the database also provides a "Master" view. The Master
classification and population status for a species is the final conclusion by the PICES authors
based on all the available information.
1.2.5 Geographic Scope of the Analysis - Marine Ecoregions of the World (MEOW)
The "Marine Ecoregions of the World" (MEOW) biogeographic schema was used as the
framework for displaying the global distributions of the species (Spalding et al., 2007;
http://www.worldwildlife.org/science/ecoregions/marine/iteml266.html). The MEOW schema is
hierarchical, originally consisting of three levels; from the ocean basins (e.g., Temperate North
Pacific realm) to "ecoregions" at the finest scale. One limitation of the MEOW schema is that it
does not split the Pacific and Atlantic into east/west components, which limits it utility in
evaluating transoceanic invasions. Accordingly, we split the 12 MEOW realms into 19
"regions", thus adding a new level to the MEOW schema between the realm and province levels
to provide east-west breaks in the Pacific and Atlantic Oceans (Reusser and Lee, 2011). Detailed
maps of the MEOW regions and ecoregions are available in the Atlas, and the various MEOW
levels can be viewed in the PICES database. Additionally, a list of all the Realms, Regions,
Provinces, and Ecoregions are given in Appendix A along with their identification numbers.
The MEOW Temperate North Pacific Realm includes most of the shorelines bordering the
Pacific of the PICES countries. As mentioned, this realm was divided into the Northeast Pacific
(NEP) and Northwest Pacific (NWP) regions. The Hawaii Ecoregion in the Eastern Indo-Pacific
Realm was included to provide complete coverage of U.S. Pacific states. For complete coverage
of China and Japan, NIS were also reported from five ecoregions in the Central Indo-Pacific
Realm (Southern China, Gulf of Tonkin, South China Sea Oceanic Islands, South Kuroshio, and
Ogasawara Islands). A map of the 23 ecoregions included in the analysis is shown in Figure 1.
Nonindigenous species found only in the Arctic ecoregions of PICES countries (e.g., Eastern
Bering Sea, Chukchi Sea, Beaufort Sea, Siberian Sea) were not included in the database or Atlas.
-------
120
140'
160'
180r
160'
140
120f
Sea of
Japan
Sea of Kamcnatka^oast and Shelf
Okhotsk
Oyashio Current
Yellow Sea
Gulf of Alaska
North American
Aleutian Islands Pacific Fijordland vPuget Trough/
OR, WA, Vancouver
Coast and Shelf
'$
ITi
Georgia Basin
<
O Q
^
Northeastern Honshu
Central Kuroshio Current
Northern California
East
China Sea
Southern South Ogasawara Islands
China Kuroshio
Gulf of
Tonkin
South China Sea
Oceanic Islands
~ North Pacific Ocean
Southern CA Bight
Magdalena Transition
Cortezian
Figure 1: Twenty-three MEOW ecoregions analyzed for reported near-coastal nonindigenous species. The Northeast Pacific (NEP)
region is defined as the ecoregions from the Cortezian Ecoregion northward through the Aleutian Islands Ecoregion. The Northwest
Pacific (NWP) region is defined as the East China Sea Ecoregion northward through the Kamchatka Coast and Shelf Ecoregion. The
Northern Central Indo-Pacific (NCIP) is defined as the Southern China, Gulf of Tonkin, South China Sea Oceanic Islands, South
Kuroshio, and Ogasawara Island Ecoregions. The Hawaii Ecoregion is contained within the Eastern Indo-Pacific Region.
-------
1.2.6 Inclusion of Nonindigenous Species with an Unknown Population Establishment
In many cases, it is not known whether a particular nonindigenous species has established a
viable population in the wild. This is especially true for many of the non-native aquaculture
species in Asia. To more thoroughly document potential invaders, these species were included as
NTS within the North Pacific both within the PICES database and Atlas with the population
status set to "Unknown" (see Section 3.6.9). Inclusion of these non-native species with an
unknown population status can potentially inflate the number of NIS in the wild. To view only
the nonindigenous species with a known establishment, run Default Query #2 (described in
Section 4.2.7) for a specified location.
1.3 Overview of the Structure of the PICES Database
This section provides a brief overview of the structure of the database (Figures 2A-2C). From
the main menu, the options are to search for information on a single species, search for a
location, search for a publication, or to run queries on single or multiple species. The final
options from the Main Menu include calling up the documentation or acknowledgements.
The Species Search menu (Section 3.2) is the entrance into the suite of menus that provide
details about the global distribution, environmental requirements, life history attributes, and
invasion vectors of a single species. Options within the Species Search menus also allow the user
to view the comments associated with the species or to view/output the publications associated
with the species.
The other noteworthy choice from the opening screen is the Data Output menu (Section 4.0),
which is the entrance to the suite of menus allowing the user to query the data. The Multiple
Species Queries allow the user to run customized queries to output targeted groups of species by
location and to generate the two-page species profiles that are used in the Atlas. There are,
however, limitations to complex queries for species outside the North Pacific and Hawaii and at
biogeographic levels other than ecoregions and regions (see Section 4.2.2). Additionally, the
user can generate a Microsoft Word document of the publications associated with a species or
Microsoft Excel files summarizing the distribution of a set of species at MEOW biogeographic
level or summarizing all the life history and environmental data for a set of species. The Species
Distribution Spreadsheet menu allows the user to generate a Microsoft Excel spreadsheet
summarizing a single species' distribution and classification across MEOW biogeographic
levels.
-------
f
f
Species Search
Sec. 3.2
Species Information
And
Distribution Search
Sec. 3.2
Species Information
Sec 3.5
Main Menu
Sec. 3.1
Locations Search j
Sec. 3.3 I
Publication Search |
Sec. 3.4 j
Data Output
Sec. 4.0
| Documentation and
[ Acknowledgements
Multiple
Species Query
Sec. 4.1 &4,2
See Fig. 2C
-- -X.
Single Species
Distribution
Spreadsheet
Sec. 4.3
References
Sec, 3,5.3
View
Comments
Sec. 3.6,10
View
Images
Environment &
Geography
Sec, 3.6 & 3.7
Life History
Sec. 3.3
Invasion
Sec. 3.9
See Fig. 2B
Figure 2A: Main Menu of the PICES database. From the Main Menu, the user has five options. The Species Search submenus allow
users to view information on a single species, including references, comments, life history attributes, and invasion vectors.
Additionally, the Environment and Biogeography submenu allows users to view maps of the species' distribution (Figure 2B). The
Data Output submenus allow the user to run queries on the data involving multiple species (Figure 2C).
-------
fif
Environment & Biogeography |
H^ Sec. 3.6 & 3. 7 J
Biogeography Maps
(single publication)
Sec.
Comments)
[sec. 3.6.1oJ
---
Tabs
7
O.I
fView Summary^
1 Sec' 3'6-10 J
> --- '
Advanced
Sec 3 6 6
Realm
Sec. 3.6.1
Region
Sec. 3.6.3
I Province |
I^Sec. 3.6.4 J
Ecoregion
Sec. 3.6.5
Select
Publication
Sec. 3.6.2
Ecosystem
f 1 N
Salinity
Depth
"Ect."
( Master |
1 Classification I
>N
Advanced
Biogeography Maps
(all publications)
Sec. 3.6.7
( Date ^1
^ 1st Record j
| Population I
^ Status J
All Classifications
Versus
Master Classification
Sec. 3.6.6 & 3.6.9
Find
Locations
Sec. 3.6.3
Gazetteer
I
,Latitutd^
Longitude
Figure 2B: Environment and Biogeography menu of the PICES database. From this screen, users can view a map of a single species'
distribution based on an individual publication at different MEOW scales, view the Master Classification of the species within a
location as well as the date of first record for a nonindigenous species, or view a summary of the species distribution in a tabular
fashion. Under the Advanced menu, users can view maps of a species' distribution based on all the publications, either unedited or
using the Master Classification (PICES values).
-------
• Multiple Species Query
Sec. 4.1 &4.2
Type of Query
Sec. 4.1
'Define Query Parameters |
Sec. 4.2 J
Short
Summary
Sec. 4.1.3
Long
Summary
Sec. 4.1.4
Publications
Sec. 4.1.1
Citations
By Species
Sec. 4.1.2
Taxon
Sec. 4.2.1
f Location
Sec. 4.2.3
Master Classification
Versus
All Classifications
Sec. 4.2.4
Atlas, RAS,
Or Both
Sec. 4.2.5
Classification
& Population Status
Sec. 4.2.2
Species
Profiles
Sec. 4.1.5
Figure 2C: Multiple Species Query menu of the PICES database. From this menu, users extract information for specified groups of
species and locations. One type of query is the long summary that outputs all the habitat, life history, and vector information on
defined group of species into a Microsoft Excel spreadsheet. The species profile query generates two-page summaries that include a
map of species' distributions and their summarized habitat and life history information. The species profiles can be saved as Adobe
pdf files, which were the basis of the "Atlas of Nonindigenous Marine and Estuarine Species in the North Pacific" (Lee and Reusser,
2012).
10
-------
2.0 INSTALLING PICES
The PICES database is designed to run in Microsoft Access 2003 and Access 2007 under two
operating systems, Windows XP and Windows Vista. Note that all Windows XP and Office 2003
or Office 2007 service packs are required prior to installation of the database. Note the PICES
database will not run under 64 bit operating systems.
The install procedure using PICES_install.exe is as follows:
1. Log on to computer with administrator access
(Neededfor registering the 3rdparty mapping control in the registry)
2. Insert CD or thumb drive and navigate to the drive.
3. Double click the file PICES_install.exe
4. Accept the defaults for install
5. The VB06 runtime dll is required so say yes to installing VB06 runtime dll (unless you
already have Visual Basic on your computer).
6. Click finish on the install program
7. Reboot the computer
8. Log back into the computer with the same log in as in step 1 (required)
9. The post install registers components in the registry. If it finds the component already
registered, it does not register it again, so 1 to 6 message boxes may appear indicating
some dll's did not register. This is normal.
10. Installation is now complete.
11. There will be a new program group added under Start —»• programs -H>PICES_NISIS —»•
PICES_NISIS.mdb
12. The default location of this file is:
a. C:\program files\PICES_NISIS
i. A soft copy of this User's Guide is in this directory
ii. A soft copy of the MEOW Ecoregions publication is in this directory
iii. The data subfolder containing two shape files of geospatial data and an
empty directory called ../images is in this directory and is required for
generating species profiles
Your database should now be installed and ready to run. Navigate to the directory where
the database has been installed and double click on the pices_nisis.mdb.
Tips and Important Notes Regarding Installation:
1. If you are using Access 2003 - each time you open the database it will ask you if you
want to block unsafe expressions; click "No". It will then tell you that there is code in the
database that might be unsafe; click "Open". The database will not function if other
selections are chosen when entering the database.
2. If you are using Access 2007 - each time you open the database you will need to enable
the content of the database for the data entry forms to work. Between the forms window
and the top tool bar there is a windows message and an options button; click on the
options button and select "Enable this content".
3. If you do not have Access 2003 or higher on the computer at all, you will need to install
the Runtime version of Access 2007 before the database will run.
a. Navigate to the CD or thumb drive
b. Double click on the Runtime directory
c. Double click on AccessRuntime.exe - this will install Access 2007 Runtime.
11
-------
3.0 USING PICES
3.1 Main Menu
Once loaded, the PICES database will open to a main menu of choices (Figure 3). Each section
will open to forms that provide corresponding information screens:
Species Search: Allows searches for species within the database and provides a gateway
to menus with data on a single species.
Location Search: Allows searches for a location either by a Gazetteer or by latitude and
longitude.
Publications Search: Allows searches for existing publications within PICES.
Data Output: Provides a gateway to menus to conduct single or multiple species queries
and to export species profiles and publications.
Documentation: Calls up this PICES User Guide.
Acknowledgements: Lists the funding sources and contributors.
Exit: Closes and exits the PICES database.
1 .
2.
3.
4.
5.
6.
7.
PICES
Northpacific^MarineScienceprganizatior
Nonindigenous Species Information System
• Species Search
Locations Search
Publications Search
Data Output
Documentation
Acknowledgements
Henry Lee n
^USGS
Deborah Reusser
Figure 3: PICES Main Menu. See Figure 2A for a flow diagram of the options from
this menu.
3.2 Species Information and Distribution Search
Click on the Species Search button and the Species Information and Distribution Search
menu will be displayed (Figure 4). This screen allows the user to access summarized
information on an individual species. There are three ways to find a species in PICES:
1) Scientific name
2) "Also Known As" name (e.g., synonym, misspelling)
3) Common name
Enter the name of a species in one of the three information fields or begin typing the name and
the program will fill in the rest. If the name of the species is not automatically filled in, click on
12
-------
the small arrow in the right hand corner and a dropdown list will be displayed. This list contains
the names of all the species in the database. Begin typing in the name again until the species you
are looking for is displayed and then select that name (or you determine the species is not
included in the database). Once the name has been entered or selected click on the Find Species
button (Figure 4).
S Main Switchboar g Find Species by Classificati...
Figure 4: Species information and distribution search menu. From this screen, the user
chooses the species to call up in the Species Information screen (Figure 5). Species can
be searched via scientific name, "Also Known As" name (e.g., synonyms, misspellings),
and common name.
3.3 Locations Search
This function allows the user to associate a location with a MEOW Ecoregion either by the
location's name using a Gazetteer or by latitude and longitude. The screens and output are the
same as the search location function in the Advanced Biogeography, which is described in detail
in Section 3.6.8.
3.4 Publications Search
This function searches for a publication in the PICES reference list by citation, title, author, or
PICES ID (an identification number internal to PICES). The screens and output are the same as
the search publication function in the Environment and Biogeography screen (Section 3.6.2).
3.5 Species Information Screen
Once a species is selected from the Species Information and Distribution Search, the Species
Information screen will appear (Figure 5). This screen displays the taxonomic information
regarding the chosen species, and it contains the buttons by which users can access additional
data on a species biogeography, life history, invasion vectors, images, and comments.
13
-------
Corcphium insidtcsum
Corophium caMandense
Mcnocorcphium oaklandense
Figure 5: Species Information screen with colored areas highlighted to explain
functional areas of the screen. The yellow box identifies the chosen species (indicated
by the red arrow). A different species can be chosen by using the dropdown list to the
right of the species name (green circle) starting alphabetically at the chosen species'
name. The orange box summarizes the taxonomy of the species while the green box lists
alternative scientific names and the nature of the alternative name. The blue box gives
the type locality of the species and the location (museum) where the type exists. The
red box lists common names. The buttons on the bottom are explained in Figure 6.
3.5.1 Species Identification
The color coding in Figure 5 highlights the specific areas of functionality on this menu. The
yellow shaded box highlights all the information relating to the species identification:
Species ID: PICES database species identification number. This is a unique number for that
species assigned by the database and is one of two ways of choosing the species of interest
from this screen.
Species Name: displays what species is currently in view (indicated by the red arrow). A
different species can be called-up in this screen by clicking on the small arrow next to the
information screen (circled in green). This will open a drop-down list of all the species in the
PICES database in alphabetical order, starting with the species currently entered.
Author: lists the taxonomic authority for that species. The authority consists of the author
name(s) and date of publication.
14
-------
ITIS Code: acts as an internet link to the Integrated Taxonomic Information System
https://www.itis.gov. The ITIS code is a unique number for species or higher taxonomic
level. When an ITIS code is available, clicking on the ITIS code button will take you to the
ITIS website for that species. When a species does not have an ITIS number, an
identification number starting with "N" was used. Note that the ITIS code is blank for many
species.
TaxaCode: term associated with commonly used groups of organisms (e.g., bivalve,
amphipod, or decapod). See Appendix B for a list of all PICES taxa codes.
Data Source: indicates which publication was originally used when the species was entered
into the PICES database. That is, the Data Source is the first reference that initiated the
inclusion of the species. The Data Source is a quality assurance tool to assist in tracking
down sources for questionable species or name changes, but otherwise does not have special
significance. The Data Source does not change, even if the species name changes. As an
example, the first reference used to enter Monocorophium acherusicum into the PICES
database was TN & Associates, 2002, a report to the U.S. EPA (Figure 5).
3.5.2 Taxonomy and "Also Known As"
Highlighted in the orange box in Figure 5 is the taxonomic hierarchy for the selected species,
from kingdom through tribe. Taxonomy above the level of genus was primarily based on the
World Register of Marine Species (WoRMS; http://www.marinespecies.org/index.php).
WoRMS is an international database with the objective of providing the most authoritative list of
names of all marine species globally. WoRMS was also used for species levels designations in
most cases, though for some taxa regional authoritative taxonomic references were used (e.g.,
Coan et al., 2000 used for bivalves in the NEP). Differences in species designations with
WoRMS are mentioned in the species' comments
Highlighted in the red box in Figure 5 is the list of Common Names. This feature contains the
well-known English common names for the selected species as well as some Japanese or Spanish
common names. When two or more species have the same common name, the scientific name
for the specific species is appended to the common name.
Note 1: The PICES database lists all the common names that have been recorded while the Atlas
is limited to listing Jive common names in the species profiles (see Section 4.1.5).
Note 2: Because common names are not standardized and vary among countries, we caution
about using them as the primary source for identifying a species.
Highlighted in the green box in Figure 5 is the Also Reported As list. This feature lists other
scientific names by which the selected species may also be known. This includes synonyms,
misspellings, alternate spellings, naming conventions, and regional misidentifications. Each
entry is identified as one of the following:
1. Ambiguous synonym: A possible synonym of the species, such as when it is not certain
exactly what species is being referred to (i.e. Polydora nr. cornuta). Ambiguous
15
-------
synonyms are also associated with species complexes; the cases in which a species name
is now thought to consist of more than one valid species but which are not, as yet,
individually named (see Section 1.2.1). Because of the taxonomic uncertainties, all
synonyms of species complexes are referred to as ambiguous, with the exception of
names identifying the taxon as a complex (e.g., complex, hyperspecies, etc.). We classify
pro-parte synonyms as "partial synonyms" rather than as ambiguous.
2. Convention: A different version of the name. Alternates may include the
inclusion/omission of a subgenus or a difference in the gender of the name. Because
subspecies are not recorded in the PICES database, subspecies are also considered
alternatives.
3. Misidentified: An incorrect identification assigned to a species. Misidentifications or
synonyms specific to a publication but not to the original description of a species include
the author names (i.e., "Tellina (Angulus) meropsis of Coan 1971"; "Ensis californicus of
authors not Dall 1899 in part") or region (i.e., "Macoma irus of NEP authors") or a
combination of both (i.e., "Penitella gabbii of NEP authors, not Tryon, 1863"). Inclusion
of the author names keeps the misidentified species name from being incorrectly
considered as a general synonym.
4. Misspelling: An incorrect spelling of a taxon that was erroneously incorporated into the
scientific literature.
5. Nomen nudum: A nomen nudum is an invalid scientific name because the species was
not originally described with sufficient detail, and thus the name is considered "naked"
(see International Commission on Zoological Nomenclature;
http://www.nhm.ac.uk/hosted-Zites/iczn/code/index.jsp?booksection=glossary&nfv=true)
6. Partial Synonym: Partial synonyms are species names that are synonyms of two or more
valid species. Thus, there is not a one-to-one relationship between a partial synonym and
a valid species name. This can happen when an older species is split into two or more
new species. In these cases, the partial synonyms are identified either by 1) including the
taxonomic author's name as part of the partial synonym; 2) including "of authors" as part
of the partial synonym when many authors have used the partial synonym; or 3) including
"in part" as part of the partial synonym. Inclusion of these markers keeps the partial
synonym from being incorrectly considered as a general synonym. These are also
referred to as "pro-parte synonyms".
7. Synonym: A scientific name that applies to a taxon but is no longer "accepted"; such a
species now goes by a different name. As used in PICES, the objective was to limit
synonyms to those with a one-to-one relationship with the current name.
Note 1: The PICES database lists all the Also Known As names that have been recorded while
the Atlas is limited to listing five Also Known As names in the species profiles (see Section
4.1.5).
16
-------
Note 2: The primary purposes in listing the "Also Known As " species names are to assist
invasion biologists track the global distributions and invasion histories of species. There are not
meant for formal taxonomic evaluations, and the users should consult the taxonomic literature
for complete synonymies and references.
Highlighted in the blue box in Figure 5 is the Type Locality, which gives the location from
which a species was initially described and the Location of Type, which displays the location
(typically a museum) where the type specimen for a given species is stored. The Location of
Type is often populated with abbreviated museum names (see Appendix C for museum
abbreviations).
3.5.3 "Species Information" Function Buttons
In addition to the various information fields, the Species Information screen has multiple
function buttons that let a user access additional information on a species (Figure 6). The
descriptions for these buttons are provided below.
31 Species Information Form
Species Informati.
Kingdom
Species ID
: Subkingdom [EUmetazoa
Crustacea
, Superclass
Corophium insidiosum
Corophium oaklandense
Uonocoroptiium osklandense
Figure 6: Species Information screen. The References button (yellow) calls up the
references associated with the species (Figure 7) while the View Comments button
(orange) calls up the comments (Figure 8). The View Images (red) calls up any
associated images (Note: Very few images are associated with species in the PICES
database). The green, blue, and purple boxes highlight the access points to the
Environment and Biogeography, Life History, and Invasion tabs, respectively.
Highlighted in yellow in Figure 6 is the References button. This button brings up a separate
screen (Figure 7) that shows all the publications associated with the selected species. The
publications are arranged by citation in alphabetical order with the exception of the first
17
-------
publication which is the original "data source", the publication initially used when entering the
species into PICES database. Each publication has been assigned a PICES ID number which is
found in the Pub ID field. The full reference for each publication is highlighted in the yellow
box.
Shown to the left within the green box in Figure 7 are the general areas to which each reference
is related. The Biogeographic and Comment fields were filled in automatically, and indicate
whether the reference was used to map the distribution of the species or whether a comment has
been added to the species using this reference, respectively. The Taxonomic, Ecological, and
Other fields were manually filled in, and when checked indicate that the reference relates to the
taxonomy, ecology, or some other aspect of the species, respectively. The Classification,
Population, and First Record checkboxes were filled in automatically, and indicate whether the
reference was used in assigning the Master Classification or Master Population status in any
area, or the date for first record for a nonindigenous species in an ecoregion. Master
Classifications are discussed in Section 3.6.6.
Note 1: Some species may have a "#Master Comment" listed in the References, which refers to a
PICES comment that summarizes key information about the species (see Figure 8). Master
Comments are printed out on the species profiles.
A feature of the References screen is the Export References button (shown in the purple box in
Figure 7). Clicking this button will create a new Microsoft Word document consisting of a
bibliography of all of the references used for a given species.
18
-------
ill View Species Publications
Conen, A.fl. and Lartton, J. .. IsSr. Ncnindigencus aquatic species in a United States estuary: A case
study of the biological invasions of the San Francisco Bay and Delta.. E3.. Washington D.C.: United
States Fish and vVildlife Service ana National Sea Grant College Program (Connecticut Sea Grant':.
pages.
----- HT-^^^^^^^^^
:'> Reference
amada and Hauck 2C01
'Yamada, S.B. and Hauck. L. 2001. Field identification of the European green crab species: Carcinus
maenas and Carcinus aestuarii. Journal of Shellfish Researc
. Taxonomic I
Ecological
j'amada. S.B. and Hunt. C.E.. 2000. .he arrival and spread of the European green crab, Carcinus
maenas. in the Pacific Northwest. Dreissena' 11:1-7.
•/ Filtered Search
Figure 7: References screen for the chosen species, accessed by clicking on the
References button on the Species Information Screen (Figure 6). The red box highlights
the citation for the publication while the yellow box provides the complete reference.
The checkboxes in the green box indicate whether the reference was used in
determining a species' biogeographic distribution, has a comment associated with the
reference (check boxes on the left), or was used in the Master Classification, population
establishment, or date of first record (checkboxes on the right). The reference list for
the species can be exported to a Microsoft Word file (purple box).
The View Comments button (highlighted in orange on Figure 6) enables a user to view all of
the comments associated with a species. Clicking this button will bring up a Species Comments
screen (Figure 8) displaying all of the comments regarding that species. The total number of
comments is displayed at the bottom of the screen (purple box), and if more than two comments
are associated with the species the scroll bar at the right of the screen can be used to view the rest
of the comments (green box). All comments are listed under the citation of the associated
publication. A user can view the full reference for a citation by clicking on the View Reference
function button (blue box). As noted above, some species have "#Master Comments"
summarizing key information about the species. The #Master Comments are printed out on the
species profiles (see Section 4.1.5).
19
-------
Based on the assumption that Polydora cornuta is native to the tlvVA. it is tentatively
classified as HIS in the NEP. N'vVP. Australia, Me;v Zealand, Mediterranean, and South
America. However, further anah/sis is needed because of the presence of cryptic species
(Riceetal, 20CB .
Comment From: CANOD
55 Jes -c .. :::-a co'-jia as c-;, ::;:;;- ;- •; ;. "-;.:.....:T.:
a ft a] TOra v>rifiM re-
•f Filtered Search
Figure 8: Comments screen, accessed by clicking on View Comments button on
Species information screen (Figure 6). The number of comments is given in the purple
box and the slider (green box) can be used to scroll down to view comments off the
screen. All comments are referenced to a source, and the full reference can be viewed
by clicking on the View Reference button (blue box). The #Master Comment (red box)
is the PICES comment that summarizes key information about the species, and is
printed in the species profiles (Figure 37).
The View Images button (highlighted in red on Figure 6) enables a user to view images
associated with a particular species. While this button is functional, few species in the PICES
database have images associated with them.
Clicking on the Environment and Biogeography button (highlighted in green on Figure 6)
calls up a map of the distribution of the species at the MEOW realm level (Figure 9). Additional
tabs on the top of the main map include Regime, Ecosystem, Depth, Substrate, Energy,
Temperature, and Salinity. Details on these options are described in Sections 3.6 and 3.7.
Clicking on the Life History button (highlighted in blue on Figure 6) calls up a screen (Figure
27) with tabs for information on Trophic Level and Feeding, Reproduction, Development,
Habitat Associations, and Life Style. Details on these options are given in Section 3.8.
Clicking on the Invasion button (highlighted in purple on Figure 6) calls up a screen (Figure
32) with information on the Primary Vectors for nonindigenous species. Details on this option
are given in Section 3.9.
3.6 "Environment and Biogeography" - Biogeography Screens
An example of the Environment and Biogeography home screen is shown in Figure 9. A series
of tabs below the species name represent the screens related to the habitat attributes of the
20
-------
species. This section will focus solely on the functions within the first tab, the Biogeography
tab. This tab allows the user to examine a species' distribution, classification and invasion status
using a selected publication as the data source. Section 3.6.2 describes how to select a
publication as the data source.
Note 1: Use the Advanced button at the bottom of the screen to view a species' distribution
based on all available publications (see Section 3.6.6).
Note 2: When biogeographic information was entered from a publication, classifications and
population status were propagated upward to higher biogeographic levels. For example, if a
species was Native in an Ecoregion it was also designated as Native in the corresponding
Province, Region, and Realm (the boxes at these levels will reflect this). This upward
propagation allows multiple classifications at biogeographic levels higher than an Ecoregion.
For example, if a publication classifies a species as native and nonindigenous in two different
ecoregions within the same Province, the Province, Region, and Realm would display both
classifications.
3.6.1 Opening Environment and Biogeography Screen: Realms
The Environment and Biogeography screen opens to the map of the twelve MEOW Realms
(Figure 9). By default, this screen opens up with a screen displaying the global distribution and
classification of the species at the Realm level based on all publications (i.e., Map All
Publications, Section 3.6.6). The reference can be changed from default "#A11 Publications" by
using Select Publication tab (Figure 10, Section 3.6.2) to show the distribution for that
publication. If distributional information has not been entered for the chosen species from the
chosen publication, none of the Realms boxes will be checked. However, if the species has been
reported by this publication, there will be a checkmark in the boxes for the appropriate Realm(s)
(shown in the red oval on Figure 9). The green, red, yellow, blue, and black checkmark boxes
indicate whether the publication reported the species as native, nonindigenous, cryptogenic,
transient, or unknown within the Realm. Definitions for these terms were given in Section 1.2.1
and can be viewed on screen by clicking the Legend button shown on the bottom row of action
buttons on Figure 9.
Note #1: It is possible that multiple classifications (native, nonindigenous, cryptogenic,
unknown, and/or transient) are assigned to a species in an individual Realm from one
publication.
Note #2: Population status, as described below, is not available at the Realm level.
Note 3: The "#AH Publication " will also show the species' distribution and classification at the
Region level, but it does not work at the Province or Ecoregion levels. Use the Advanced
Function to map distributions of species based on all publications at those levels (Section
3.6.6).
21
-------
Species Name
Habitat Attribute Tabs
31 Environment And Biogeograp
Me-rr.enaria mercenaria
Ecosystem Depth Substrate Energy Temperature Salinity
^w&fc--
-nan no
Bottom Action
Buttons
Figure 9: Environment and Biogeography home screen (Realm Level), accessed via the
Environment and Biogeography button on the Species Information screen (Figure 6).
The information shown is for a single publication that is listed in the Select Publication
field. To change the publication, click on the Select Publication button and choose
another reference (Figure 10). Checked boxes on the map (in the red oval) indicate a
species invasion status at the Realm Level according to the selected publication. The
classification of the species is indicated by the color of the checked boxes - green is
native, red is nonindigenous, yellow is cryptogenic, blue is transient, and black is
unclassified. Note that more than one classification box can be checked at the Realm
level. Click on the Legend button for definitions of these terms. The habitat attribute
tabs in the green oval are described in Sections 3.6 and 3.7, and the bottom action
buttons in the blue oval are described in Sections 3.5, 3.6 and 3.8. See Figure 2B for a
flow diagram of the options from this menu. Clicking on the name of the Realm
(indicated by red arrow) will call up the screen with the Regions making up the Realm
(Figure 11)
3.6.2 Environment and Biogeography Screen: Selecting a Publication for Mapping
With the exception of the default opening screen, the distributions and population status shown
on the Environment and Biogeography maps are displayed for a single publication. The chosen
publication is shown in the Select Publication field on the Realm page (Figure 9) and in the
upper right hand corner at the lower MEOW level screens (Figures 11-13). To change the
publication, click on the Select Publication tab in the Realm screen. This will open a Search
Publication menu (Figure 10). From this menu, it is possible to search for a publication by its
22
-------
title or by it citation, or less frequently the authors or PICES publication ID. Selecting a new
publication will open the Realm map showing the distribution of the species according to this
publication. However, none of the checkboxes on the Realm level will be checked if the species
has not been linked to the publication. Note that the selected publication does not affect the
information displayed in the habitat attribute tabs (Figure 9) or the Advanced Biogeography
(Figures 14 and 15).
Note 1: To view species that have been found in one of the RAS surveys, use the following
references: "PICES Working Group 21, 2008 "for the China survey; "PICES Working Group
21, 2009"for the Korea survey; "PICES Working Group 21, 2010"for the Oregon survey; and
"PICES Working Group 21, 2011 "for the Russia survey.
H Environment ^llPublication_Search
Biogeography Regime
Search Publications
Search By Title Search By Author Search By Publication ID Search By Citation
i Start typing the Citation to begin
Search, then hit enter when Citation
located.
100334 X.::j/,J^:;.;;;>.
Carlton and Eldredge. 2009
Carlton, J.T and Eidredge. L.G
HMaffiSL' .^ :- J "'
Marine bioinvasions of Hawaii: The introduced and cryptogenic
marine and estuarine animals and plants of the Hawaiian Archipeligo.
Bishop Museum Bulletin in Cultural and Environmental Studies 4.
Reference:
Carlton. J.T. and Eldredge. L.G.. 2005. Marine bioinvasions of Hawaii: The introduced and
cryptogenic marine and estuarine animals and plants of the Hawaiian Archipeligo. Bishop
Museum Bulletin in Cultural an-d Environmental Studies 4.. Ed.. Honolulu: Bern ice Pauahi Bishop
Museum Press. 2C2 pages.
131
dinci etal. 20071
o
•y Advanced
Figure 10: Search Publications screen, accessed from the Environment and
Biogeography home screen (Figure 9). This screen allows the user to choose the
publication to populate the biogeographic map. Publications can be searched by the full
title or citation, or less frequently, author or PICES publication ID. In this example,
selecting this publication would show the distribution and classification information for
the chosen species according to Carlton and Eldredge (2009).
3.6.3 Environment and Biogeography Screen: Regions
To move to the next lowest biogeographic level, click on the name of the Realm (red arrow
pointing to Temperate Northern Pacific in Figure 9). This brings up the screen showing the
Regions making up that Realm (Figure 11). As at the Realm level, checkmarks indicate the
presence of a species in the Region and its classification according to the chosen publication. To
return to the Species Information Summary screen (Realm), select the Close button at the bottom
of the screen.
23
-------
If a species is indicated as occurring within a Region, then a second row of checkmarks becomes
visible. This additional row of checkboxes indicates the population status of the species
according to the publication (red oval highlighted on Figure 11). A checked green box indicates
that a species is established in the Region, red indicates that the species is not established, black
is unknown population status, and yellow indicates that the population is stocked. To see these
definitions, click on the Legend button at the bottom of the screen. The name of the Realm that
the Region is associated with is displayed at the top of the screen.
Note 1: It is possible that multiple classifications (native, nonindigenous, cryptogenic, unknown,
and/or transient) are assigned to individual Regions from one publication.
Higher MEOW level
t/r
Publication linked
to classifications
31 TemperatNorthern Pacific Realm
Mercenaria mercenaria
Hiwatari and Kohata, 2005
Realm: Temperate Northern Pacific
View Comr
lents
Figure 11: Region level Biogeography Screen, accessed by clicking on the Temperate
North Pacific Realm in Figure 9. The displayed information is from the publication
identified in the upper right hand corner. The upper row of checkmarks in the map
indicates a species' classification. The lower row of buttons (highlighted by red oval)
indicates the species' population status within the Region, where a green checkmark
indicates that a species is established, red indicates not established, black is unknown
establishment, and yellow indicates that the species is stocked. The MEOW link in the
upper right hand corner of the map calls up a pdf of the Spalding et al. (2007) paper on
the MEOW schema. The Realm that the Region is associated with is displayed at the top
left of the screen. Clicking on the name of the Region (indicated by red arrow) will call
up the screen with the Provinces making up the Region (Figure 12).
24
-------
3.6.4 Environment and Biogeography Screen: Provinces
To move to the next lowest biogeographic level, click on a Region name, bringing up the screen
with the Provinces making up that Region. The Region and Realm are displayed at the top of the
screen under the species' name. Figure 12 shows an example of the two Provinces that make up
the Northwest Pacific Region. As with the Regions, the classification and population status of the
species within the Province according to the chosen publication are indicated by the checkmarks.
Click on the Close button to return to the Region level.
Note 1: It is possible that multiple classifications (native, nonindigenous, cryptogenic, unknown,
and/or transient) are assigned to individual Provinces from one publication.
HTemperate Northern Pacific Realm
Mercenaria mercenaria
Hwatari and Kohata, 2005
Realm: Temperate Northern Pacific
Region: Northwest Pacific
MEOW f Scalding etal. 2007)
Figure 12: Province level Biogeography screen, displaying two Provinces (Cold
Temperate Northwest Pacific and Warm Temperate Northwest Pacific) that comprise
the Northwest Pacific Region (Figure 11). The Region and Realm are displayed at the
top of the screen under the species' name. Clicking on the name of the Province
(indicated by red arrow) will call up the screen with the Ecoregions making up the
Province (Figure 12).
3.6.5 Environment and Biogeography Screen: Ecoregions
To move to the lowest biogeographic level, click on a Province name, which brings up the
screen with the Ecoregions making up that Province. Figure 13 shows an example of the two
ecoregions making up the Warm Temperate Northwest Pacific Province. The Province and
Realm are displayed at the top of the screen under the species' name. As with the Regions and
Provinces, the classification and population status of the species within the Ecoregions according
to the chosen publication are indicated by the checkmarks. Click on the Close button to return to
the Province level.
25
-------
Note 1: Only one classification and one population status can be selected at the Ecoregion level
per publication with the exception of "Stocked" which can be selected in addition to other
population status classifications.
Note 2: If the selected publication only provided a species' distribution with no mention of
classification or population status then the record for that publication is Unclassified and
Unknown, respectively, for the area.
Note 3: Ecoregions titles are not active buttons since there are no lower levels.
13Temperate Northern Pacific Realm
Mercenaria mercenaria
Hiwatari and Kohata, 2005
Realm: Temperate Northern Pacific
Province: Warm Temperate Northwest Pacific
r.lEO'.'jfSpaldinci etal, 20071
GQOGQ
Figure 13: Ecoregion level Biogeography screen, displaying the two Ecoregions that
make up the Warm Temperate Northwest Pacific Province (Figure 12). The Province
and Realm are displayed at the top of the screen under the species' name. Clicking on
the Ecoregion name will not do anything since there are no lower biogeographic levels.
3.6.6 Environment and Biogeography: Advanced Function and Master Classifications
The Advanced function enables users to view the global distribution and classification of the
chosen species at any of the biogeographic levels based on the distributional data collected from
every publication. The Advanced function plots species' distributions in a color coded map
format versus the checkbox format used at the Realm level with the Environment and Biography
home screen (Figure 9). This function is called up by clicking the Advanced button on the
bottom right corner of the Environment and Biogeography home screen (Figure 9).
Figure 14 shows the Advanced Biogeography screen with the Map All Classifications chosen.
At the top of the screen, there are two buttons (yellow box: Map Master Classifications and
26
-------
Map All Classifications. The Map All Classification function enables the user to see the
distribution data for a species from all publications as it was entered into the database (i.e.,
unedited). Often times, distributional data were gathered from sources such as GBIF or OBIS,
two geographical databases that provide presence/absence data but not a species invasion status.
Such data were given an unclassified status. In addition to unclassified information, the Map All
Classification view enables a user to view when classifications of a species are in conflict
(shaded brown); meaning that two or more sources gave incongruous information as to the
invasion status of a species (Figure 14).
SI Advanced Biogeography
Feature Type: [bay
Latitude:
Longitude:
Hap Place • Flash Place • Clear Place
Figure 14: Advanced Biogeography screen, which is accessed by clicking the
"Advanced" button on the Environment and Biogeography home screen (Figure 9). The
yellow box highlights two different options for viewing species' distributions based on
all publications. In this example, the Map All Classifications button displays
distributional data from all publications, and may include areas where different sources
gave conflicting information (Ecoregions shaded brown in the Northeast Pacific on
map). In this example, the Gazetteer (in the blue box) was used to find Tokyo Bay. Note
that the Location Search from the Main Menu (Figure 3) has a similar function and
interface. See Figures 2A and 2B for flow diagrams of options from these menus. The
Master Classification view with classifications based on the PICES authors is shown in
Figure 15
Figure 15 shows the Master Classification view of the Advanced Biogeography Menu.
Throughout the database, when information is classified as "Master" that means that the PICES
authors have evaluated all available data for a species and made judgments as to the
classification and/or population status of that species. Often times these assessments were made
on the basis of critical publications and/or taxonomic authorities. For example, Carlton and
27
-------
Eldredge, 2009 is the most comprehensive account of NTS in Hawaii, and therefore was often
used as the "Master" authority when classifying species in this Ecoregion. Master Classifications
also shows the final PICES decision when there were conflicts in any given Ecoregion. The
difference between these two classifications is apparent when comparing Figures 14 and 15; the
Master screen has turned unclassified, conflicted, or cryptogenic areas red based on information
gathered from reliable sources that Polydora cornuta is native to the northwest Atlantic.
Note 1: It is possible to have a conflict classification of a species in the Master Classification if
invasion experts disagree and the authors of PICES were not able to resolve this difference of
opinion. In most cases, the references given conflicting information are noted in the #Master
Comment.
Note 2: The maps in the Atlas were produced using the Master Classifications
HAdvanced Biogeography
Polydora cornuta
Map Place • Flash Place • Clear Place
Figure 15: Map Master Classification view of the Advanced Biogeography screen. The
Master view displays a species' classifications based on all publications using the
PICES author's conclusions. Note that that Northeast Pacific Ecoregions are classified
as nonindigenous versus the conflict in the unedited Map All Classifications (Figure
14). The Master Classifications were used to produce the "Atlas of Nonindigenous
Marine and Estuarine Species in the North Pacific" (Lee and Reusser, 2012). The red
box shows the function used to associate a latitude and longitude with a MEOW
Ecoregion, shown in the green box. The "Convert DD/MM/SS" button opens a function
to convert latitudes and longitudes in degrees/minutes/seconds into deci-degrees. Note
that the Location Search from the Main Menu (Figure 3) has a similar function and
interface. See Figures 2A and 2B for flow diagrams of options from these menus.
28
-------
3.6.7 Environment and Biogeography: Viewing Maps in Advanced Biogeography
The map shown in the Advanced Biogeography (Figure 14 & 15) can be adjusted using the
action buttons directly underneath the map:
Zoom In - the cursor will turn into a magnifying glass when over the map. Click and drag a box
around the area of interest. Release the button and the map will zoom in to the area of interest.
Zoom Out - zooms the map out to approximately twice the extent. This function does not
require clicking on the map.
Pan- the cursor will turn into a hand when over the map. Click and drag the map in the direction
that exposes the area of interest desired. Release the button to repaint the new area of the map.
Pan does not work at the whole world view.
Full Extent - resets the map to the whole world view.
Identify - an "i" inside a black circle should appear next to the cursor when over the map. Click
within an Ecoregion area on the map and a popup will appear with the corresponding
biogeographic information.
3.6.8 Environment and Biogeography: Searching for Locations
The PICES database has a function that enables the user to find specific locations (e.g.,
waterbody, city, etc.) within the Advanced Biogeographic maps (area highlighted in red box on
Figure 15). The first method requires lat/long coordinates. In this case, type in the coordinates in
deci-degrees, making sure to use a minus (-) sign to indicate a latitude in the southern
hemisphere or a longitude in the western hemisphere. Click the Map Place button and a red dot
should appear on the map. If you cannot see the dot, click on the Flash Place button and the dot
will start blinking. Selecting the Clear Place button will clear the map entirely.
Note 1: If only degrees and minutes are available for coordinates, click on the Convert
DD/MM/SS button. This will open a popup that allows the user to type in the lat/long as
degrees, minutes, and seconds. Once entered, click the Calculate and Update Latitude and
Longitude button and PICES will automatically fill in the converted coordinates. Do not use (-)
signs if you are using the converter, rather use the radio buttons (on the left) to indicate whether
the latitude is in the northern or southern hemisphere and whether the longitude is in the eastern
or western hemisphere.
The second method to locate an ecoregion utilizes the Gazetteer tab (see blue box on Figure
14). The user enters the name of the location in the Select a Place box or browses through
almost 40,000 pre-entered locations. Begin typing in the name of a location and the program will
fill in the rest for you. If the full name of the location is not known, click on the small arrow in
the right hand corner and an alphabetical dropdown list will be displayed starting at the character
string you have entered. To limit the number of places in the dropdown, type in the name of a
nation in the Select a Nation drop down list. Once the desired location has been selected, click
on the Map Place button and a red dot will appear on the map. If you cannot see the dot, click on
the Flash Place button and the dot will start blinking. Selecting the Clear Place button will clear
the map entirely.
Note 1: If you do not find the location in the Gazetteer, try alternative versions of the name. For
example, Bahia Magdalena is listed as both Bahia Magdalena andMagdalena Bay.
29
-------
3.6.9 Environment and Biogeography: Classification Function and Master Classification
The Classification button on the Environmental and Biogeography screen (Figure 9) and each
of the subsidiary geographic level screens (Figures 11-13) calls up the Invasion Criteria screen
(Figure 16), with tabs that: 1) documents the Master Classification for the species at the chosen
biogeographic level; 2) provides information on date of first record for a nonindigenous species.
3 Invasion Criteria
Mya arenaria
Select an Ecoregion for criteria information
north American Pacific Fijordland
Puget Trough/Georgia Basin
Oregon. Washington. Vancouver Coast and Shelf
Master Classification and Criteria Date of First Record Population Status and Criteria
Clear Y N
Nonindigenous Q Cryptogenic d Transient Q| Unclassified
Criteria for Nonindigenous Classification
Falls within reported invaded range.
Historical records of introduction.
with human vectors of ii
Absence from fossil records in region.
Insufficient natural dispersal mechanisms to create global distribution.
Recent appearance in region where not found previously.
Discontinuous local distributions relative to similar endemic species.
Recent spread from one or few locations to many locations within the region.
Close associations with other introduced species.
Restriction to new or artificial environments.
Conspecific with geographically isolated populations.
locality is geographically isolated from the local region,
ber of a nonindigenous taxonomic group.
ogical or physiological adaptations dissimilar from endemic species.
entfrom ecosystems with low invasion potential.
Reference of classification:
vVonham and Cartton. 2005
Figure 16: Invasion Criteria screen accessed using the Classification button on the
Environment and Biogeography screens (Figure 9 and 11-13). This screen appears with
the Master Classification and Criteria tab active, which gives the Master Classification
for the species at the particular location and MEOW level and the associated reference
for the classification. Different locations within the specified MEOW level can be
chosen from the list at the top of the screen. This is the classification used in the Map
Master Classification (Figure 15) and was used at the Region levels in the species
profiles (Figure 37). The criteria that can be used to assess a species' classification are
defined in Appendix D. Note that most of the RAS species do not have master
classifications.
and its population status; and 3) lists the criteria used to classify a species as nonindigenous or its
population status. Note that the biogeographic scale at which you are working with the maps
corresponds to the scale called up in the Invasion Criteria screens. For example, if you are
30
-------
looking at the Ecoregion scale, the Invasion Criteria tabs and menu options will apply at the
Ecoregion scale.
The Master Classification and Criteria tab shows a screen (Figure 16) that gives the "Master
Classification" for the species. The Master Classification is the overall, or PICES, classification
given to a species at a particular location and biogeographic level. This overall classification is
either based on a key reference or on the PICES authors weighting all the evidence and
publications. With the former case, the reference is listed. When based on the PICES authors,
"Lee and Reusser (PCEIS), 2012" is listed as the reference.
Note 1: The Master Classification is the classification used in the species profiles and
geographical analysis in the Atlas.
Note 2: Multiple classifications at the Realm, Region, and Province levels can indicate that the
species has different classifications at lower levels. For example, the Master Classification of
Mya arenaria is Native and Nonindigenous in the Temperate North Pacific Region, reflecting its
native status in Asian ecoregions and its introduced status in ecoregions on the West coast of
America and Canada. Multiple classifications at the Ecoregion scale indicate a conflict among
experts that cannot be resolved with the available evidence.
Note 3: Unknown was used as the default population establishment. For locations outside the
North Pacific and Hawaii (e.g., Europe), this default was used for many species because of time
limitations.
The Master Classification and Criteria screen also lists the criteria that can be used to assess
the classification status of a species. Discussion of the strengths and limitations of the criteria is
given in Appendix D. These criteria were generally not populated in the PICES database, in part
due to resource limitations. Nonetheless, these criteria will be useful in classifying newly
reported species as native orNIS.
Note 1: The classification criteria were phrased so that "Yes" indicates an introduction.
The Date of First Record tab (Figure 17) lists the date and location of the first record for a NIS,
as well the source for this information. For nearly all species this information was available at
the Region level in the NWP and NEP and for the Hawaii Ecoregion. These are the dates of first
record that are printed in the Atlas. However, this information was not necessarily collected at
other biogeographic levels or for Regions outside the NWP, NEP, and Hawaii. Note that the date
of first record may be years or even decades after the species was first introduced.
The Population Status and Criteria tab (Figure 18) gives a screen with the Master Population
status (established, not established, unknown, or stocked) of a species in a location at a particular
biogeographical level. Definition of the different status types are given in the Legend on the
Environment and Biogeography map (Figure 9), and criteria for assessing status are discussed in
Appendix E. In nearly all cases population status was available and recorded at the Region level
for Atlas species in the NWP and NEP and for the Hawaii Ecoregion. However, this information
was often not collected for other Regions, and the Unknown default was used. The criteria used
31
-------
to assess whether a species is established are shown on this screen, but these criteria are
maintained for informational purposes as they were rarely populated in the PICES database.
Note 1: Establishment of a species at the Region level indicates that the species is established in
at least one lower-level Ecoregion. It does not, however, mean that the species occurs or is
established in all the Ecoregions within the Region.
Note 2: The population status criteria were phrased so that "Yes" indicates an established
species.
Master Classification and Criteria I Date of First Record Population Status and Criteria
31 Invasion Criteria
My a arenaria
Selects Region for criteria information
Northwest Pacific
Figure 17: Date of First Record Screen accessed using the appropriate tab on the
Invasion Criteria screen (Figure 16). This gives the date that a nonindigenous species
was first reported at the particular location and MEOW level chosen, the location where
first reported, and the associated reference. Different locations within the MEOW level
can be chosen from the list at the top of the screen. This example is for the Northeast
Pacific Region, and it is the Region level information that is printed in the species
profiles (Figure 37).
32
-------
3Invasion Criteria
Mya arenaria
Select a Region for criteria information
Northwest Pacific
Master Classification and Criteria Date of First Record Population Status and Criteria
"^rj \ts^-:.r.'~ • •' .'"•'' •":". ': :^rj-VO''i';-'^i
0 Established Q| riot Established FJ Unknown
D Stocked
Clear Y N
Criteria for Population Establishment
Falls within reported range.
Species not directly dependent upon human support.
Population size steady or increasing.
nd in more than one year,
und within the last 20 years within the juveniles and adults.
Mixed population structure with juveniles and adults.
Reproductive females found.
Widespread distribution in region (extent of occurrence).
Found in multiple locations in region (area of occupancy).
Population size>'range>'frequency of occurrence comparable to ecologically
similar native species in region.
Population size'Tange'trequency of occurrence comparable to that for same
species in regions where established.
restricted to spatially limited habitat.
population:
'iVonham and Carltcn. 2CC
View Comments
Figure 18: Population Status and Criteria screen accessed using the appropriate tab on
the Invasion Criteria screen (Figure 16). This gives the Master Population status for the
species at that particular location and MEOW level and the associated reference for the
classification. Different locations within the MEOW level can be chosen from the list at
the top of the screen. This is the population status used in the Map Master
Classification (Figure 15) and at the Region levels in the species profiles (Figure 37).
The criteria that can be used to assess a species' population status are defined in
Appendix E. Note that not all species have a master population status at all MEOW
levels and most of the RAS species do not have a master population status.
3.6.10 Environment and Biogeography: View Summary & View Comments
The View Summary function (accessed from the Environment and Biogeography home
screen, Figure 9) provides a summarized list of all of the geographic areas in which the species
occurs (Figure 19). From this screen, the user has can view all the sources that were used to
place a species in any given Ecoregion, Province, or Realm. To view an alphabetized list of the
publication(s) that were referenced in the geographic area, click on the Realm, Province, or
Ecoregion button of interest and the references will appear in a new screen. To switch between
Realms, click on the tabs located at the top of the screen (Figure 19, highlighted in red box).
33
-------
Note 1: This function was built into the database before the MEOW schema was modified to
include the "Region " level and it is not possible to see a summary of occurrences by Region
using this function.
H species Biogeography Summary Overview
x
Overview Summary and Supporting References for
My a arena/73
. REALF.l: Temperate Northe
ECQREGIQN: North American Pacific Fijordlancf
• ; PROVINCE: Cold Temperate
;,';"'• ECCP.EGIOII: SeaofOkhols
Northwest Pacific
It
i;'? ECCREGICN: Cyashio Current
??f/,i ECOREGION: Sea of Japan
fff}: ECOREGIOH: Yellow Sea
•'$•£ PROVINCE: -=jl
ffe PROVI1ICE: 1
*f$ ECOHEGIoH
'ffSS ECOREGloB
•-••.-• i •
ECOREGION: PugetTroughi'Georgia Basin |
ECOREGION: Oregon. Washington. Vancouver Coast and Shelff
. ECOREGION: Northern Californ:- |
'';•;• f; PROVINCE: Warm Temperate Northeast Pacific |
:??& ECOREGION: Southern California Sight j
Biogeography References for
Northern California Ecoregion
Kimmerer et a I.. 1&S-
QDB
' Kimmerer. vVJ.. Gartside. E. and Orsi. J.J.. 1994. Predatien by an introduced clam as the likely cause of
substantial declines in zooplankton of San Franascc Bay. Marine Ecology Progress Series 113:81-92.
iann. C.. 15B6. Benthic monitoring in the Sacramento-San Jcaquin Delta results from 1975
ircugh 1381. Interagency Ecological Studes Program, "eccnical report 12.. Ed. . Sacramento.
afrfornia: California Department of vVater Resources. EE cages.
aim
' 'er^-31- B..; Cariton. J. .. and '/v'enne. R.. 19S9. Genetic affinities of the bivalve Mace ma bafthica
from the Pacific coast of North America: Evidence for recent introduction and historical distribution.
Marine Btctogv 1C2:23E-2
-------
3.7 Environment and Biogeography Screen - Habitat Attribute Tabs
The habitat attribute screens are accessible via the tabs located at the top of the Environment
and Biogeography home (Realm) screen (Figure 9). These tabs open screens that summarize
key habitat requirements of the chosen species. Unlike the biogeographic data, the habitat data
were not linked to specific publications, though the key publications used to generate these
summaries are included in each species' reference list.
3.7.1 Observed versus Preferred Habitats
Much of the data within these screens is hierarchical. If more detailed information is available at
a lower hierarchical level there is an ellipsis button located next to the category. Additionally,
many of the habitat data screens have red and green boxes for each category. The box bordered
with red is for "Observed" selections and the box bordered with green is for "Preferred"
selections. Observed distributions or habitat characteristics are used to capture the full range of
where a species has been reported, even if the location or habitat is marginal. Preferred is used to
indicate the locations and habitats that the species normally occupies.
Note 1: There are no hard and fast rules for defining Observed versus Preferred habitats. In
general, Preferred habitats are indicated by: 1) species occurring frequently within the habitat
range; 2) species occurring at high densities within the habitat range; 3) presence of breeding
populations within the habitat range, and 4) experts referring to the habitat as preferred.
3.7.2 Regime Tab
HI Environment And Biogeography
eography Regime Ecosystem Depth Substrate Energy Temperature Salinity |'^':^'. .'"••
Figure 20: Regime screen, which is accessed from the Environmental and
Biogeography home screen (Figure 9). Checks in red boxes indicate that a species has
been observed living within that regime; checks in green boxes indicate that it is a
preferred regime for the species. See Table 1 for definitions of each regime category.
35
-------
The Regime tab displays a series of broad physical and environmental divisions based on a
combination of salinity, geomorphology and depth (Madden et al. 2005) (Figure 20). Definitions
for each regime category are provided in Table 1.
3.7.3 Ecosystem Tab
The Ecosystem tab displays generally recognizable ecosystem types that occur within Regimes
(Figure 21). The ecosystem types are separated into three major categories: Unconsolidated,
Consolidated, and Pelagic ecosystems. Multiple selections are allowed on this tab. Definitions
for all classifications shown on this screen are provided in Table 2.
31 Environment And Biogeography
Polydora comma
Biogeography Regime Ecosystem Depth Substrate Energy Temperature Salinity
' sysit-.v/tiv/iis^s;
* Coastal Shore
Unconsolidated
Ecosystems
Consolidated
Ecosystems
Pelagic
Ecosystems
Submerged Aq
• Clastic Sediments
Carbonate Sediment
[... |» • Clastic Sediments
Carbonate Sediment
Figure 21: Ecosystem screen, which is accessed from the appropriate tab on the
Environmental and Biogeography home screen (Figure 9). Checked boxes indicate that
the species has been reported from one or more of these Unconsolidated, consolidated,
or pelagic ecosystems. Click on the boxes with the major ecosystem types on the right
to call up the associated ecosystems. At this lower level, the menu is hierarchical, so
boxes with ellipsis buttons (...) indicate that those boxes can be clicked to bring up
more specific information. See Table 2 for definitions of ecosystem types.
36
-------
3.7.4 Depth Tab
The Depth tab displays the categorical (qualitative) and quantitative depth data that have been
gathered for a species (Figure 22). The 30 m depth threshold for shallow subtidal habitats is
based on Madden et al. (2005), though some other classification systems use 20 m as the
threshold (e.g., BIOTIC - Biological Traits Information Catalogue,
http://www.marlin.ac.uk/biotic). A quantitative depth range was entered when the data were
available, though in most cases the qualitative information on depth classes for a species was
more complete. Definitions for depth classifications are provided in Table 3.
31 Environment And Biogeography
Biogeography Regime Ecosystem Depth Substrate Energy Temperature Salinity
Pelagic
rtidal |
Mld Intertidal
fQ-Q Upper Intertid
Bathypelagic
DF MOOOm -2000m)
: Abyssopelagic
;:; (>2000 - sooom)
Qj O Haiiiopelagic i;>600C'ml
Close
J
Figure 22: Depth screen, which is accessed from the appropriate tab on the
Environmental and Biogeography home screen (Figure 9). The boxes at the top display
the minimum and maximum observed and preferred depths reported for a species.
Qualitative depth classifications are broken into benthic and pelagic depth classes.
Classes with ellipsis buttons (...) indicate that more detailed depth classes exist. Boxes
in red indicate an Observed (OBS) depth while boxes in green indicate a Preferred
(PRE) depth. See Table 3 for definitions of depth classes.
37
-------
3.7.5. Substrate Tab
The Substrate tab displays the various types of substrate in or on which a species lives, as well
as quantitative ranges for key substrate characteristic [Mean Phi, % Fines (silt and clays), and %
TOC (total organic carbon)] (Figure 23). A criterion of 75% silt-clays is used to define muds
while a criterion of 75% sand is used to define sands. Some other classification systems use 80%
as the criteria to separate muds and sands (e.g., BIOTIC-Biological Traits Information
Catalogue; http://www.marlin.ac.uk/biotic). Definitions for all the sediment classifications are
provided in Table 4.
H Environment And Biogeography
Corbula amurensis
Biogeography Regime Ecosystem Depth Substrate Energy Temperature Salinity
Mean Phi
% Fines
•QQ Cobble >=75'.i (64 - 256mm
•* • i Mineral ! Carbonate Siliceous Ooze
—-Q-£jClay>=75'i (0.001 -0.004mm)
Silt »=7S!. (0.004-0.063mm |
•Q-Q Mixed Sed
(Mud'sand W''>5-.s grave I'cobble)
-Q-Q C-garic Seciimen:
Figure 23: Substrate screen, which is accessed from the appropriate tab on the
Environmental and Biogeography home screen (Figure 9). Quantitative ranges are
entered in the boxes on the top for Mean Phi, % Fines (sum of silt and clays), and %
TOC (total organic carbon). Qualitative data are organized by unconsolidated and
consolidated categories, and ellipse buttons (...) indicate that more detailed substrate
classes exist. Boxes in red indicate an Observed (OBS) substrate while boxes in green
indicate a Preferred (PRE) substrate. Definitions for the substrate classes are given in
Table 4
38
-------
3.7.6. Energy Tab
The Energy tab displays information about wave energy and current energy that a species may
encounter in the range of habitats that it occupies (Figure 24). Wave energy classes are from
Howes et al. (1999), and procedures for calculating wave energy based on fetch are given in this
publication. Definitions for wave energy classes are provided in Table 5. Tidal and ocean current
energy classes are based on Madden et al. (2005). Madden et al. (2005) proposed a general
energy intensity classification based on current velocity and wave energy. The values used here
only utilize their classification based on current velocity. Definitions for energy classes are
provided in Table 6.
3 Environment And Biogeography
Ampithoe lacertosa
Biogeography Regime Ecosystem Depth Substrate Energy Temperature Salinity
Wave Energy
Current Energy
Open ocean exposure v/rth
high ambient wave
Low waves exct;:t ey.ti'e'ne
Winds areas of provisional
High Energy Strong curre
•;-^ •-:--.;..-~" ' knots
knots')
'/v'eak currents iC -1
knots'!1
Figure 24: Energy screen, which is accessed from the appropriate tab on the
Environmental and Biogeography home screen (Figure 9). Checked boxes indicate that
the species has been reported from the specific level of wave and/or current energy.
Although brief definitions are given for each selection on this screen, more detailed
definitions are listed in Table 5 for the wave energy classes and Table 6 for the current
energy classes.
39
-------
3.7.7. Temperature Tab
The Temperature screen displays temperature classes based on the annual ranges of the
locations where the selected species occurs (Figure 25), which were adapted from Hall (1964).
These temperature classes are primarily based on mean monthly temperatures in the location.
This screen also indicates whether the species has a narrow (stenothermal), normal
(mesothermal), or wide (eurythermal) temperature tolerance range. Specific temperature
tolerances for adult survival and for reproduction (i.e., temperature range at which reproduction
occurs) were entered as numerical values when available. Temperature ranges for adults are
based on temperatures recorded from species' collection sites or laboratory studies. Temperature
for reproduction is based on the best available data from laboratory tests and/or field
observations. Definitions for the Hall temperature classes are provided on the Temperature
screen (Figure 25), while definitions for physiological temperature classes are listed in Table 7.
Note 1: Use of the Hall temperature system is considered an interim classification schema until
new temperature schema can be developed from more recent sea surface temperature data (e.g.,
Payne etal., 2012). Because of the interim nature of this classification, the temperature
classifications were not populated for most species.
13 Environment And Biogeography
My a arenaria
Biogeography Regime Ecosystem Depth Substrate Energy Temperature salinity
Temperature Class Based On Annual Ranges Physiological Class
Nc months := 1C cegrees Celsius \vith
minimum approaching 0 degrees Celsius
Less than 4 months > 10 degrees Celsius
Nc months cooler than 1C cegrees Celsius
and >= 4 months >= 1S degrees Celsius
Nc months cooler than 1C degrees Celsius
and apprcx. 4 months 20 degrees Celsius
Stenothermal
f" Mesothermal
f*~ Eurythermal
Reproductive
10 (C)
15 (C)
ifl .';'•',•.>7.1 r'-~:
Figure 25: Temperature screen, which is accessed from the appropriate tab on the
Environmental and Biogeography home screen (Figure 9). Checked boxes (on left) indicate that
the species has been reported from that temperature regime based on annual ranges, while a
check in the physiological class indicates that the species has been defined as steno-, meso-, or
eury- thermal. Complete definitions for the temperature classes based on annual ranges are
shown on this screen, while definitions for the physiological classes are given in Table 7. As
discussed in Section 3.7.7, these temperature classes are considered an interim classification.
Quantitative temperature data shows the range from which the adult has been reported, or over
which reproduction has been reported.
40
-------
3.7.8. Salinity Tab
The Salinity tab displays salinity classes that indicate the ranges of salinity at which a species
may be found (Figure 26). The salinity classes derived from the Venice system (Anonymous,
1958); they are given in psu = practical salinity units. Definitions for all classifications shown on
this screen are provided in Table 8.
H Environment And Biogeography
-••
Polydora comma
Biogeography Regime Ecosystem Depth Substrate Energy Temperature Salinity
Freshwater
(<'O.Spsul
210 Brackish
^^ 10.5--OO PSb)
Salinity (PSLI): f 34.9* 32 •'^:'-'-
Oligohaline (0.5 - < 5 psu)
Mesohaiine (5 - < 18 psu)
Polyhaline (1S
Marine >' Euhaline
Hypersaline
( >40psu]
Beta-mesotialine(5-< 10 psu)
Alpha-mesohaline(10 - '- IS psu
Beta-polyhaline(18 -<25psu|
Alpha-polyhaline(26-*30 psui
Alpha-euhaline {36 - < 40 psu)
Figure 26: Salinity screen, which is accessed from the appropriate tab on the
Environmental and Biogeography home screen (Figure 9). The boxes at the top display
the minimum and maximum salinity values reported for a species, with the values
reported in practical salinity units (psu). In addition, species' salinity tolerances are
captured using salinity classes, and classes with ellipsis buttons (...) indicate that more
detailed depth classes exist. Boxes in red indicate an Observed (OBS) salinity while
boxes in green indicate a Preferred (PRE) salinity. Salinity classes are defined in Table
8.
41
-------
3.8 Species Information Screen - Life History Tabs
The Life History button on the bottom of the Species Information screen (blue box on Figure
6) is where the user can access the set of tabs displaying key life history attributes for a selected
species. As with the habitat tabs, the life history information is not linked to specific
publications.
3.8.1 Trophic Level and Feeding Tab
The Trophic Level and Feeding tab gives a screen which identifies the primary trophic level(s)
of the adult stage of the species (Figure 27). Multiple selections are possible. For example,
omnivores are indicated by checking both the "primary consumer" (herbivore) box and the
appropriate secondary consumer (predator) boxes. Definitions for the trophic level classifications
are provided in Table 9. In addition, terms associated with symbiotic trophic relationships are
defined in Table 10.
HI Life History
Polydora comma
Trophic Level And Feeding Reproduction Development Habitat Assoc. Life Style
Trophic Mode (Trophic Level)
, Symbiotic Algae
Figure 27: Trophic Level and Feeding screen, which is accessed from the Life History
button on the Species Information page (Figure 6). All common trophic modes of adult
aquatic species are captured in this hierarchical menu. Checked boxes indicate that a
species uses that given trophic mode, and classes with ellipsis buttons (...) indicate that
more detailed trophic classes exist. The "symbiotic" checkboxes capture organisms that
derive energy either from symbiotic algae or as a parasite. Trophic modes are defined in
Table 9 while symbiotic trophic interactions are defined in Table 10.
42
-------
3.8.2 Reproduction Tab
The Reproduction tab displays a screen with the various reproductive strategies that a given
species may utilize (Figure 28). Definitions for all the classifications are provided in Table 11.
SI Life History
My a arenaria
Trophic Level And Feeding Reproduction Development Habitat Assoc. Life Style ;.. •' .'..-
-"-" "'-•''' ~, ". • ' ' '-'• " J''--'. ' '. '
Asexual Reproduction I
v* Sexual Reproduction r— •
'.'•>"" '.-•,'".> 'A ''•-"r--'--'. ';. -
'-'Hermaphrodite'' [ '~
-:-•;;-,..-; Monoecious I '.'.'..
- Gonochoristic •' [ — ^r ;
^"^. Dioecious \.' '.'.>'
•--.-'• ' '• •'" - -: - " 'Xr;.:'-v";/--';,.. . ; ,
- •\-^-^;;/;,::^7^;^^^;;-_ _..-.;•' / . ' . . .
. — Fertilization External Eggs ^ Broadcast Spawne, . ^
P Fertilization,' [^-, ^^ Freecast Spawner, (animal.) |™>L" Spermcast Spawner [
^"^ Pollination (plants]
Close View Comments .
, ,,P,, , .„.'•••' ' :-'' ,,. ._, . '- ' ',' ~:- ^':v'
Figure 28: Reproduction screen, which is accessed from the Life History button on the
Species Information page (Figure 6). The hierarchical reproductive classification
synthesizes reproductive type by separating asexual vs. monoecious vs. dioecious
species and by fertilization and spawning attributes. Classes with ellipsis buttons (...)
indicate that more detailed reproduction classes exist. Definitions for the reproductive
strategies are given in Table 11.
43
-------
3.8.3 Development Tab
The Development screen displays life history developmental characteristics that a species may
use to produce and/or nurture their young (Figure 29). Multiple selections are allowed on this
tab. Maximum durations of larval phases are recorded along with the appropriate time units
(hours, days, months). These larval durations are the maximum lengths reported for a species,
and actual durations may vary with environmental conditions. Additionally, there is an
Alternations of Generations radio button 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. Definitions for early development mechanisms are provided in Table 12,
definitions for juvenile development/dispersal terms are provided in Table 13, and definitions of
the terms associated with alternation of generations are provided in Table 14.
a Life History
My a arenaria
Trophic Level And Feeding Reproduction Development Habitat Assoc, Life Style
Earfy Development Mecf
Alterations of Generations
Figure 29: Development screen, which is accessed from the Life History button on the
Species Information page (Figure 6). The hierarchical schema separates early
development mode of the adult vs. juvenile development. Classes with ellipsis buttons
(...) indicate that more detailed development classes exist. Larval durations represent
the maximum duration reported, while the Alternations of Generations radio buttons
indicate whether the species has separate sexual and asexual phases. Definitions for the
development classes are given in Tables 12 and 13, while Table 14 gives definitions
for the alternation of generations.
44
-------
3.8.4 Habitat Association Tab
The Habitat Association screen displays a variety of habitat types a species may occupy; the
menu is hierarchical, with more detailed information available as you click the ellipsis buttons
(...) (Figure 30). Habitat associations are classifications of where the species lives in
relationship to the air/water and water/substrate interfaces. It has also been referred to as
"Environmental Position" in the Biological Traits Information Catalogue (BIOTIC,
http://www.marlin.ac.uk/biotic) and is similar to the concept of tiering used by Bush et al.
(2007). Ideally, the classes would only capture the habitat relationships and not mix these with
other traits such as a species' mobility or size. However, some terms that mix concepts, such as
macrofauna, are so commonly used that it was not possible to avoid mixing concepts without
abandoning these standard terms. Definitions of the classifications are provided in Table 15.
31 Life History
Mytilus galloprovincialis
Trophic Level And Feeding Reproduction Development' Habitat Assoc. I Life Style
Pelagic
Epibiotic
*•— ' Ctyptofauna
-' Surficisl (epibenthic
. non-swimmingl
I
Epibenthic -
unconsolidaled
' Epifauna -
. consolidated
" Epiphytes -
• consolidated
r:-~
Primary space
~ Semi-infauna
Close
Figure 30: Habitat Association screen, which is accessed from the Life History button
on the Species Information page (Figure 6). The hierarchical schema breaks out the
habitats a species occupies by three major habitat types - pelagic, benthic, and
epibiotic. Then species are classified according to the specifics of where they live
within these broad habitat types. Classes with ellipsis buttons (...) indicate that more
detailed habitat classes exist. Definitions for the habitat classes are given in Table 15.
45
-------
3.8.5 Life Style Tab
The Life Style screen displays a variety of options describing the mobility of a given species
(Figure 31). The menu is hierarchical, with more detailed information available as you click the
ellipsis buttons (...). Definitions for all classifications shown on this screen are provided in
Table 16
3 Life History
•-
Grandidierellajaponics
Trophic Level And Feeding Reproduction Development Habi:a: Assoc, Life Style
Unattached (-1 f.
I mm obi
•'•
1
Attached
• tf^-, fr Unatl
iTively mobileU .. • I ^.
I— Attac
Unattached
Planktonic
IB
Drift
Actively mobile
ii 'iiV Sedentary
.,^-:^^^«
W—J^ Sv/imming
^—••! Periodic mobility
Q-T
e L:
Cravvling
Yes « No
Close
Figure 31: Life Style screen, which is accessed from the Life History button on the
Species Information page (Figure 6). Checked boxes indicate the life style mode of the
chosen species, which is primarily based on mobility. Definitions for the life style
modes are given in Table 16.
46
-------
3.9 Species Information Screen - Invasion Button
The Invasion button on the Species Information screen (purple box on Figure 6) accesses
information regarding Primary Vectors (Figure 32). Primary vectors are the anthropogenic
dispersal mechanisms by which a nonindigenous species can be transported from its native
region to a non-native region. This is in contrast to secondary invasion vectors by which invaders
can spread locally within an invaded region. For example, a nonindigenous species may have
been introduced into the Great Lakes via ballast water (primary vector) but then spread around
the Great Lakes via live bait (secondary vector). Multiple selections are allowed on this tab.
Definitions for the vectors are provided in Table 17.
Note 1: The primary vectors listed include all those listed for the species in the literature and/or
likely based on the species' life history characteristics. The importance of these vectors is likely
to vary among different locations.
\3 Invasion
Research, Education, and Mitigation
Habitat Restoration and Mitigation I ...
Other •' Unknown
1
.
Close
f~
Figure 32: Primary Vectors screen, which is accessed by clicking on the Invasion
Button on the Species Information Screen (Figure 6). Checked boxes indicate that the
selected vector was a potential means of introduction for a species. Definitions for the
primary vectors are given in Table 17.
47
-------
4.0 PICES DATABASE OUTPUTS
Users have the ability to extract specific types of data from the PICES database using a query
menu. On the Main Menu (Figure 3), select the Data Output function. A new menu box will
open (Figure 33), which has the choice for Multiple Species Queries or to generate a Single
Species Distribution Spreadsheet. We first describe the Multiple Species Query.
North Pacific Marine Science Orqanizatior
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^l^tt^^l^^^^^^^l
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^•^^•^^^^^•^^^^^
Nonindigenous Species Information System
Multiple Species Queries
Single Species Distribution Spreadsheet
Main Menu
IUSGS
science lor a cftj'Hjicrg w&titi
Henry Lee n Deborah Reusser
Figure 33: Data Output menu, which is accessed by clicking on the Data Output button
on the Main Menu (Figure 3). The Multiple Species Queries is primarily used for
querying groups of species (Figure 34) and generates short summaries (Figure 35),
long summaries (Figure 36), and species profiles (Figures 37 and 38A and B). The
Single Species Distribution Spreadsheet generates an Excel spreadsheet of the
distribution of a single species (Figures 39 and 40).
Note 1: There are a number of options associated with the Multiple Species Queries, andit is
important for the user to understand each of them to generate the correct data output.
Note 2: Though referred to as Multiple Species Queries, this function has the capability of
running a query on a single species.
4.1. Multiple Species Queries - Types of Queries
The Multiple Species Queries function (Figure 33) enables the user to extract population and
distribution information and the associated references for groups of species defined by their
taxonomy, location, invasion status, or some combination of these attributes. Clicking on the
Multiple Species Queries button opens the Query Species By Distribution menu (Figure 34).
The two steps in generating a query from this menu are to first decide what information you want
to extract and secondly to narrow the search down to what species, classifications, and locations
are of interest (see Figure 2C). This section first describes the types of queries available
48
-------
(highlighted in the purple box in Figure 34) and then the options in defining the queries
(highlighted in yellow, red, green, black and orange, Figure 34).
13 Distribution of Species
_ D X
9R Classification JHHH Population Sf
a
a
D
D
Q-
dative | 0
Established
Nonindigenous ['•- '''•' '.Q[[ Hot Established
Cryptogenic
Transient
Unclassified
Ml
ul
U n k n own
Stocked
AND * OR
Region
* Atlas RAS Both
Guer/
Output publication list to Word t -
Output citation list to Word h-?-
;
-------
generate a Microsoft Word Document of the references for this group. A query for all the
references used in the Atlas is generated by selecting the Atlas checkbox and Map Master
Classification checkbox, and then running the query.
4.1.2 Output citation list to (Microsoft) Word
This query will produce a list of citations referring to each publication that was used for each
individual taxon in the group of species defined by the query. The output is a list of all the
selected species with the citations of the references listed below each species. This query will
open in a Microsoft Word document. A query to generate all the citations used in the Atlas is
generated by selecting the Atlas checkbox and the Map Master Classification checkbox, and
then running the query. The resulting citations list is the same as that in the Atlas.
4.1.3 Output Short Summary
This Query will generate a list of species that includes the species name, taxonomic group (e.g.,
Polychaete), taxonomic author, and a series of columns displaying invasion status (Native, NTS,
Cryptogenic, Transient, and Unclassified) in the chosen location. At the bottom of that screen is
an Export to spreadsheet button that will export the list to a Microsoft Excel spreadsheet. An
example of this output is shown in Figure 35. As explained in Section 4.2.4, this query can be
run using the All Classifications or the Master Classifications.
FJl Species Changes _ n X
Species Distribution Summary
Hawaii
Species
Alitta succinea
Ampniglena mediterranea
Axictheila quadrimaculata
Branch icmma japcnica
Brevicirrcsyllis v.'eismanni
Caulteriella acicula
Chaetopterus variopedatus Cmplx
Taxon
Polychaete
Pclychaete
Pclychaete
Pclychaete
Polychaete
Polychaete
Polychaete
Taxanomic Author Native MIS Crypto Trans Unclass
(Leuckart, 1847) N M N N
(Leydig, 1851} N N N N
AU gener, 1914 N N N N
(Baird, 1865; N N N N
rLangerhans. 1875; N N ti N
Cay, 19€1 N N tl N
Cuvier, 1 827 N ti tl N
A
n
=
Dipolydora normals
Eumida sanguinea
ExcgcnelcngicornK
Ficcpcmatus enigmaticus
Hesicnura australiensis
Hydroides brachyacantnus
Hydroides cruciger
Hydroides dirampnus
Hydroides elegans
^Native: 0 .HIS
' Total number of species: 43
Polychaete
Polychaete
Polychaete
Pclychaete
Polychaete
Pclychaete
Pclychaete
Pclychaete
Polychaete
43
;,„,>..- ;.,i«;- „. .•;. -
(Day, 1957) N N N N
(Orsted, 1843} N N N N
WesttieWe, 1974 N N M N
(Fauvel. 16:: N M M N
Hartmann-Schrbder and Parker, 1991 N N N N
Rioja. 1941 N M N M
Ubrch. 1863 N M M N
Ubrch, 1863 N II II M
(Haswell, 1883) N M M N
Cryptogenic; 0 ^''.Transient 0 •'•?;?; Unclassified: 0
~± ':-^::: 'Hi Export to :p i-fA •• •
W&iilj'ii spreadsheet && Close
Figure 35: Output from a Short Summary query created using the Query Species by
Distribution menu (Figure 34). These queries can be run on either the "Map All
Classification" (unedited) data or the "Master Classification" (edited PICES data), and
can be limited to Atlas species only, RAS species only, or both. NTS = nonindigenous;
Crypto = Cryptogenic; Trans = transient; Unclass = unclassified. The data can be
exported to a Microsoft Excel spreadsheet (yellow box).
50
-------
Note 1: The short summary is usually used to evaluate a group of species though it works for a
single species. An alternative to determine the distribution of a single species is the "Species
Distribution Spreadsheet" (Figures 39 and 40) or the Species Profile outputs (Figure 37).
Note 2: Depending upon the specifics of the query, species can be listed with multiple
classifications within a particular MEOW level.
Note 3: Short queries are a good way to check the correctness of a query before running a Long
Summary or Species Profiles query.
4.1.4. Output Long Summary
This query will generate a Microsoft Excel spreadsheet displaying all the habitat, life history, and
vector data for a defined set of species. The spreadsheet automatically separates the data into two
worksheets entitled "Environment and Biogeography" and "Life History and Invasion." A total
of 426 columns are generated for each species, and an example of a small portion of the output is
shown in Figure 36. Habitat or life history traits are marked with either an "O" for observed, "P"
for preferred, or with an "X" which indicates that a box has been checked in the database (e.g.,
vectors). Numbers in a column are the values when quantitative data were entered (e.g., min. and
max. depth values). As explained in Section 4.2.4, this query can be run using the All
Classifications or the Master Classifications.
A t, L u t >- t, H , : " -
Regime
Species Name Family Name species ID Taxa Lolic Lentic Terrestrial Estuaries Coastal Bay Coastal Fringe Nearshore Shelf Oceanic Jnvegetated Sediment Coastal Shore
Alittssuccinea Nereididae 1081 Polych ete
Amphiglenamediterranea Sabellidae 101839 Polych e e
Axiothella quadrimaculata Maldanidae 11800 Polych e e
Branchiommajaponica Sabellidae 123390 Polych e e
Brevicirrosylllsweismanni Syllidae 101854 Polych e e
Caulleriellaacicula Cirratulidae 101850 Polych e e
) Chaetopterus variopedatusCmplx Chaetopteridae 7388 Polych ee
L Dipolydora normalis Spionidae 11806 Polych e e
'. Eumlda sanguines Ptiyllodocidae 4604 Polych e e
! Exogone longicornia Syllidae 11809 Polych e e
! Ficopomatus enigmaticus Serpulidae 1078 Polych ee
> Hyboscolex longiseta Scalibregmatidae 222325 Polych e e
7 Hydroides brachy acanthus Serpulidae 15702 Polych e e
i Hydroides cruciger Serpulidae 122S2S Polych ee
i Hydroides diramphus Serpulidae 3544 Polych ee
) Hydroides elegans Serpulidae 2224 Polych ee
L Janua pagenstecheri Serpulidae 8638 Polych e e
> Linopherusmicrocephala Amphinomidae 101852 Polych ee
5 Magelona capensis Magelonidae 11813 Polych e e
I Marphysa conferta iunicidae 7299 Polych e e
5 Microspiogranulata Spionidae 222808 Polych ee
i Myrianidapachycera Syllidae 3545 Polych e e
1 Neanthesarenaceodentata Nereididae 220609 Polych e e
! Ophryotrochaadherens Dorvilleidae 11815 Polych ee
i Ophryotrocha labronica pacifica Dorvilleidae 101S42 Polych e e
) Perkinsyllisspinisetosa Syllidae 11819 Polych ee
L Pileolaria militaris Serpulidae 170071 Polych e e
I Plakosyllis brevipes Syllidae 101855 Polych ee
i Polydora nuchalis Spionidae 693 Polych e e
J Polydora websteri Spionidae 594 Polych ee
i Protodorvillea biarticulata Dorvilleidae 101856 Polych e e
i Protodorvillea egena Dorvilleidae 15736 Polych ee
1 Pseudopolydora antennata Spionidae 222811 Polych e e
\ Pseudowermilia occidental Serpulidae 222843 Polych ete
P
O
P
P
O
O
P
0
O
O
P
P
O
O
O
O
O
P
P
P
O
O
P
P
0
O
P
P
O
P
O
O
0
O
O
P
P
O
P
O
O
O
P
O
O
P
O
P
O
O
P
0
O
0
0
O
0
0
0
O
O
O
O
0
0
O
O
O
0
0
O
O
0
0
O
0
O
O
P
0
O
O
O
0
O
O
O
O
0
0
0
O
O
O
O
O
O
0
0
O
O
O
O
X
X
x
X
x
X
X
X
X
x
X
x
x
x
x
x
x
X
X
X
x
X
X
x
x
X
X
Figure 36: Example of a small portion of the Microsoft Excel output generated by the
Output Long Summary query accessed from the Query Species by Distribution menu
(Figure 34). The query outputs both qualitative information (i.e., classes) and
quantitative values. The complete query consists of two worksheets and a total of 426
columns for each species.
51
-------
Note 1: This query can take up to half an hour to run depending on the number of species.
Note 2: Results from the Long Summary are a good approach to analyzing traits associated with
particular groups of species. It is also a good way to determine data gaps regarding habitat and
life history attributes and to assess data quality (e.g., suspect depth range for a species).
4.1.5 Output Species Profiles
This query will generate a two-page profile displaying a map of the species' global distribution
by ecoregion, dates of first record in the North Pacific or Hawaii, invasion vectors, and a keyed
environmental and life history summary. Species profiles for all the NTS in the North Pacific and
Hawaii are available in the "Atlas of Nonindigenous Marine and Estuarine Species in the North
Pacific" (Lee and Reusser, 2012). An example of a species profile is shown in Figure 37. Table
18 lists which of the tables define the attributes in the profiles and provides a list of the
abbreviations, while Figures 38A and 38B provide a key to the profiles. As with other Atlas
queries, the species profile output can be narrowed by defining the taxon, location, classification,
and/or population status. As explained in Section 4.2.4, this query can be run using the All
Classifications or the Master Classifications, or with the Atlas species or RAS species (Section
4.2.5).
Species profiles are generated as a Microsoft Access report. To save the output as an Adobe pdf,
print the Access report using an Adobe printer by first choosing the Print function from the
Access report page and then choosing the specific Adobe printer. To use an Adobe printer, an
Adobe printer function (e.g., Adobe PDF, PDFCreator) needs to be installed as a printer option.
Alternatively, use the "PDF or XPS" export option on the Access report page (Access version
2003), or the Acrobat tab on the top of the report page (Access Version 2007).
Note 1: It is critical to close all the PICES screens except the Query by Distribution screen
before generating the species profiles. On occasion, when we have had other screens open, the
query would generate the correct name and life history data for the first species in a group but
print an incorrect map. We have not experienced this error when the other PICES screens were
closed. Nonetheless, it is critical that you check the accuracy of the profiles for the first few
species. If this error occurs, close the Query by Distribution screen and then reopen it. Also,
close as many other programs as possible. If this does not fix the problem, exit from Access and
then re-open the PICES database. Make sure to clear the information in the screen between
queries by hitting the Reset button (indicated by the red arrow in Figure 34).
Note 2: We recommend generating species profiles on smaller groups (e.g., a single taxon)
rather than attempting to output a large number of species in a single query.
Note 3: To have the profiles print correctly, set the margins to "narrow " (0.25 " on each edge)
and the page size to "Letter" (8.5" x 11") in the Access report window before printing the
profiles as an Adobe pdf. Note that the margins on alternate pages of the printed version of the
species profiles are slightly offset so as to fit into a three-ring binder (assuming that the first
page of the profile is an odd numbered page).
52
-------
Mya arenaria
Tason: Bivalve
Kingdom: Aninialia
"uht'hyium
Subclsu: .„•. !• i •; ..' i
Order: Myoida
Sujwriiauly: Myoidea
Alao Known As
Subtidjl P
Sub-Shallow
I'
Sub-Deep
O
B:i[hv:il Aln^:il
0
I U.I
Pelagic Depth
Hpipelagic
Epi-Surface
Epi-Shallow
Epl-Deep
Meso
Bathyal
Abyssal
Hadal
I'.NCOXSOLIBATEI) Sl'BSTRATK |<)li> ->, I'm.-.:
ML\. Fines
Gravel
Cobble
Mixed Sediments Organic
CONSOLIDATED SUBSTRATE
SALINITY |Obs: (1.4 -3jpsu| |Prcf: 14
1ROP1IIC I.KVKI. AMI yKKRINCi
KKl'liODI CTION
EARLY DF.VEI.OPMENT
~V | OVI I OVO
Jl'\IENILEDE\'ELOP.VIENT/DISPERSAI.
I.P \
HABITAT ASSOCIATION
| R HP
Biogenic
C
0
M
W
CA
K
RA
MAN
DW
Artincial Substrate
R
P
HtB
Oth
Fresh O
Hrackhli P
Oligohalinc O
Beta
II
.ypha
0
Mcsohalinc P
Beta
0
.-\lpha
P
Polvhalittii P
Beta
P
.•ypha
P
Marine P
Bela
P
Alpha
Hyper
Sexual X Asexual
H
SynH
SeqI-I
G;D
X
SF X BF
11
FEE
FCS
X
P
BUD
PAR.'AGA
VP
SP
Pelagic
PL
NF-.
SU)
Bent hie X
DEM
BP
EPS
SlfR
HPli
KPC
UK
B
N
SF
IN
X
Ejnbiotie
EPP
r:P7
Figure 37: Species profile, which is generated by the Multiple Species Query menu (Figure 34). Profiles summarize the
taxonomy, distribution, invasion patterns and history, environmental requirements, and life history attributes of the
species. Presence of an attribute is indicated by an "X" or by O/P where O indicates an observed environmental range and
P indicates a preferred environmental range. The profiles are the basis of the "Atlas of Nonindigenous Marine and
Estuarine Species in the North Pacific" (Lee and Reusser, 2012). Table 18 defines the abbreviations in the profiles and
lists the tables providing the definitions for each attribute, while a key to the profiles is given in Figures 38A and 38B.
53
-------
#Tesf
Key to Species' Profiles
Species ID: 100828
Taxon: N/A
Kingdom
Sub phylum
Subdue
Oder
Superfamily:
Alio Known At (Name - Type):
Taxonomic Author:
Suhkingdom
Superdaii:
Infradaii:
Suborder:
Family:
Phylum:
dan:
Euperorder
Infiaorder
Subfamily:
Type of "Also Known As"
Synonym
Partial synonym
Misidentified
Misspelling
Convention {eg..subspecies
Type Locality: Location where species first described. For provisional species, general location where species description may apply.
Ecoregion-level distribution
Master Classifications
Print Date: 10/20/2010 9:39:54 AM
Native •• Nonindigenous Cryptogenic
NWP
Date 1st record: G^6 firs1 recordwithin Regcn
LoC 1st record' Location where first recorded within Reg on
NiS pcpdation established anywhere within Regon
Transient •• Uidasgfied
Hawaii
Conflicting Classification jj__ ^ Unidentified
HEP
VECTORS
SH ShiF"'
BW
Wate'r
SB
;„-:,, 1
Ballast
HF
HiJI
Fcultna
MS
Pile'.' able
•itru:tur.
AF ArjjacJturefifishenes
S/R
r-k-.T--
AE
*Escai>
* iAq^culture
AO
PO
IR
1 lega
ID
Irtra -
•|r . ;• ii »:•
RE
Res.
Edu.
Dave! .
AP
A
(qflte
P
Plart
REC
Recre-
ation
SF
Sea
HR
H'dtital
o
Oth*r
Comments:
"Master Comments "-lirnitedtofojr lines
Atlantic
Oyster
Pacific
Oyster
Figure 38A: First page of the key to the species profiles (Figure 37).The full
definitions of the environmental parameters and life history attributes are given in the
text and accompanying tables, with Table 18 defining the abbreviations in the profiles
and listing the tables providing the definitions for each attribute.
54
-------
#7esf
Print Date: 10/20/2010
REGIME General location where species occurs
Hstuarv
Coastal Bav
Semi-enclosed
wffull or close to
Nearshore
0-30m
Shelf
>30 - 200 m
(Oceanic
> 200m
Coastal Fringe
Dunes & semi
terrestrial wetlands
Rivers
Includes
streams
Lakes
Includes
ponds
Terrestrial
i ••/•'/••»*•» •*"!'i '\.I Ecosystem type In which the species occi
ELUbYMEM .. .mbodaed wllhin Regimes.
i-nco,,SOhdat^fni»«™ir'Sr8' consolidated ^rr:r,rrsec
Unvegetaled
uv-cs
Coastal
Shore
UV-TF
Tldal Rat
l>-.r,).if ns.-.j
UV-SUB
Subtidal
(estuartne or
SAV
Sub.
Aqnat
MAR
Marsh
MAN
ram
grove
D RI *~kry SR
Dune
Veg.
TP
Tide
Pool
RI-™ ^r
CR
Coral
Reef
Phytlos-
padjx
O/M
Oyster/
MJX. Reei
F K
Foul- Kelp
Ing 1 Forest
Pelagic
Water
column
DEPTH Observed and preferred numerical depth range.
Bent hie Depth Dep(h classes for benthic, demersal, and hypertjentitle species.
Coastal Fringe
Dunes & semi-
Supra littoral
Splash Zone
Intcrtidal
Between high and
Subtid.1 ,."_•£?„,
Sub-Shallow
>0 - 30 m
Sub-Deep
>30 - 200 m
Bathyal
>200 - 2000 m
Abyssal
>2000 - 6000 m
Hadal
-•MOO m
Pel agk Dept h Depth classes for species living In the water column.
Hpipelagic o - 200 m
H pi- Surface
0-1 m
Iipi-Shallo\v
>1-30m
H pi -Deep
•HO L'tfUrn
Meso
>200 - 1000 m
Bathyal Abyssal
>1000 - 2000 m >2000 - 6000 m
Iladal
> 6000m
Sediments tncludinq cobble & gravel. This Is the actual
UNCONSOLIDATED SUBSTRATE
Mud
Sltts & Clays
Sand
Sands
Mix. Fines
Mixture of silt/days
and sand
Gravel
Unconsolidated
Cobble
Unr Diisolidrttt-d
M- 254 mm
Mixed Sediments
Mixture of mud/sand with
arav el/cobble
Organic
I'miMrilv uinsisttmi
of detritus
^ni\r«nT in ATITI «I m«TU \TU The "lual '""""dated subsume type me organism
COINSOLlDAltJJ SL' HS I K,\ 1 Jl occupl,. ..tfiia, Is embMded In the Ecosysmm.
R Rocky
HP"""
BJOgenic Living or Dead Organisms
c
Com
O
Oyster
M
Missel
W
Worm
Reef
CA K
CorallinJ .
RA
Rooted
Aouatlc
MAN
IVtangrovp
DW
Drift
Wood
Artificial Substrate
R
Riprap
P
1 '
H + B
HuW
Oth
other
SALINITY Observed and pref ernsd numerical depth range.
Fresh ••£?
Brackish 0.5 - L,bUl!-U)-..'<
In Water
SeaSurfaceBelowSea Column
Surfice
IL.nll.i, LlVKj UMlhl '"""^"''rt^' "'
in ""*• Unconsoli dated Substrate
DFMDemerw
XJCJV1 - MobHi
BP
Bentho-
p»lMir -
EPS
EpiberlNc -
Swimmlna
1 <;t "D Surficial t -n
bU1>Non-motlle UK
EPU
Eplbenthic
- Unconsol-
T;^-. Under
h^- Rock*
B
Borer In
Wood or
N
NestJer
• In
SF
Semi-
Infaunal
IN
Infaunal
Epibiotic^'.0,
F.PP
Epiphytic
On Plants
EPZ
Eplzoic -
On Animals
Epibenthtc Rock Crevice
- Consol- ,
Swimming
Above
Bottom
wIContacI
wlSubstrate
Idated
Substrate
idafled
Substrate
Figure 38B: Second page of the key to the species profiles (Figure 37). The full
definitions of the environmental parameters and life history attributes are given in the
text and accompanying tables, with Table 18 defining the abbreviations in the profiles
and listing the tables providing the definitions for each attribute.
55
-------
4.2 Creating a Multiple Species Query - Narrowing the Search
The Multiple Species Query can be narrowed based on a specific taxon (yellow box in Figure
34), classification and/or population status (red box), location (green box), whether Atlas and/or
RAS species are chosen (black box), whether the Map All Classifications or Map Master
Classifications is chosen (orange box), or a combination of these five. In all cases, the user must
choose among the Atlas species, RAS species, or a both the Atlas and RAS species.
Note 1: If no constraints are entered, the query will by default output all the Atlas species.
Depending on the type of information the user is seeking this may generate a sizeable amount of
unnecessary data. Conversely, entering too many constraints can result in a more limited output
than desired. It is usually better to start with a few constraints and then add more after checking
the initial queries.
4.2.1 Limiting Query to a Specified Taxon
To limit your query to a selected taxon, check the box "Limit results to specified taxon" in the
Query Species by Distribution menu (yellow box on Figure 34). In the Taxon box, choose the
taxonomic level desired (kingdom to species) and then enter the specific taxon in the "Value"
box. If Species is listed in the Taxon box then the Value box will have a list of all the species
names in the PICES database, if Order is displayed in the Taxon box then the Value box will
have a list of all the Orders in PICES, and so on. The query will report that no species fit the
criteria if either: 1) no species in database meet all the criteria chosen or 2) the taxonomic level
entered is not in PICES (i.e., misspelled, not included, etc.).
4.2.2 Limit Query by Classification and/or Population Status
To limit the query by classification and/or population status, click on one or more of the
Classification and/or Population boxes (red box in Figure 34), which will limit the query to
species possessing that particular attribute(s). (Note that the most species are returned by not
choosing any of the classification and/or population attributes.) In designing queries, it is critical
to note that the Classification and Population attributes can be combined using an "or" or an
"and" logic, which is determined by the "and/or" toggle function at the bottom of the Population
checkboxes (red box in Figure 34). We will first discuss the "or" logic, which is the default. The
"or" logic chooses species with any of the chosen attributes, so that the more attributes chosen
the more species that may be returned in a query. For example, checking the Nonindigenous
classification for bivalves in the Oregon, Washington, Vancouver Coast and Shelf Ecoregion
would output 17 non-native bivalves (with Master Classifications and Atlas species chosen and
no population attribute chosen). Clicking on the both the Nonindigenous and Native
classifications would output 20 bivalves (17 NIS and 3 native). Running the same query but
checking the Established population status would output 18 species (excluding 2 NIS that are not
classified as established). If this query is run with both the Established and Non Established
attributes checked, then the query outputs 20 species again.
Using the "and" logic requires that the species have all of the chosen Classification and/or
Population attributes. The "and" logic will, at most, return the same number, and usually fewer,
species than using the "or" logic, and in some cases no species. For example, checking the
Nonindigenous and Native classification for bivalves in the Oregon, Washington, Vancouver
56
-------
Coast and Shelf Ecoregion would not find any species since there are no bivalves that are
classified as both NTS and native in this ecoregion. However, if this query is run on the Yellow
Sea Ecoregion, the query returns one bivalve (Crassostrea gigas) that is classified as both native
and NTS (=Conflict). Running this query on the entire NWP returns four bivalves; Crassostrea
gigas and three bivalves that have been classified as NTS or native in different ecoregions in the
NWP (Note that this query with the "or" logic returns 35 species).
Note 1: Limitation to queries using classification and population attributes. Because of
resource limitations, not every classification and population attribute was set for every one of
the 1340 taxa in the database at all four biogeographic levels across the globe. This can lead to
inconsistencies in the queries. For example, the classification of a species may have been set to
native at the ecoregion scale and in the corresponding region, but defaulted to Unclassified at
the province and realm scales. The database is most complete for NIS for Atlas species in the
North Pacific and Hawaii at the ecoregion and region levels. It is less complete for these species
in other realms. The RAS species are the least complete in terms of populating classifications
and population attributes or in assessing their global distributions. Steps to mitigate this
limitation include: 1) focusing on the Atlas species at the ecoregion and region scales in the
North Pacific and Hawaii; 2) limiting the use of population attributes in queries outside these
locations; and 3) decomposing queries at higher biogeographic levels (e.g., running queries on
individual ecoregions that make up a province). We note again that the key information on NIS
in the North Pacific and Hawaii has been synthesized in the Atlas (Lee andReusser, 2012),
providing a simple to use summary of individual invaders.
Note 2: If the population status of the species has not been defined in the PICES database, then
the specie swill not be included in the query if any of the population classes are checked. Thus,
the total number of species returned with a query with none of the population classes checked
cases may be larger than if all the population classes were checked. This is particularly true for
the RAS species.
4.2.3 Limit Query by Location
To limit the query by location, decide which Realm, Region, Province, or Ecoregion is of interest
(highlighted in green, Figure 34). Use the dropdown lists on the right hand side of the boxes to
choose the geographic area of interest. When the area of interest is selected, it will be highlighted
on the map so that the user will be able to visually see the geographic area selected.
4.2.4 Querying All vs. Master Classifications
As discussed in Section 3.6.6, the distribution and classification results can be viewed in either
of two categories: Map All Classifications or Map Master Classifications. Similarly, queries
can be limited to one of these categories (see section highlighted in the orange box in Figure 34).
The Map All Classifications function will display the raw information collected from all the
sources, some of which may provide conflicting information. However, information in the
Master Classification category has been reviewed by the authors of the PICES database, and
decisions have been made to resolve conflicts and inconsistencies wherever possible. Users
looking for the most consistent and comprehensive query outputs should use the Map Master
Classification function in queries for the nonindigenous species in the North Pacific when using
the Atlas data. However, with the RAS species the Map All Classifications should be used as the
57
-------
RAS data were not received in time to resolve all potential conflicts, and thus in many cases no
Master Classifications were generated. In such cases, the distribution will be blank or have
missing Ecoregions when the Map Master Classification is used.
4.2.5 Querying Atlas versus RAS Species
The query can be limited to only the 747 nonindigenous species included in the Atlas or only to
the species found in the RAS surveys by checking the "Atlas" or "RAS" boxes, respectively, on
the Query Species by Distribution screen (highlighted in black box in Figure 34). If the RAS
species are desired, make sure to check the Map All Classifications button. If both the Atlas and
RAS species are desired, click the "Both" box and check the Map All Classifications button
(orange box). Failure to check the Map All Classification button when searching for RAS species
will result in the loss of many, if not most, of the RAS species in the queries.
4.2.6 Completing the Query
Once all the selections have been made, click on the Query button (Figure 34) to generate the
query output.
Note 1: We suggest that the user initially limit the query to the Short Summary as a rapid query
to evaluate whether the query was designed correctly.
4.2.7 Example Queries
As an example, to query all of the established NIS polychaetes in the Hawaiian Ecoregion, make
the selections shown in Figure 34. The yellow box highlights where the query has been limited
by the taxonomic level and value (Class Polychaeta). In the red box, the Nonindigenous and
Established boxes are checked. The green box shows the Hawaiian Ecoregion was chosen. The
map confirms that Hawaii has been chosen, and shows that the Map Master Classification
(orange box) has been selected to view the edited results. The purple box shows that the Output
short summary was chosen, which will output the names and taxonomic authority of the species
that are NIS and established in the Hawaii Ecoregion. With these parameters selected, a portion
of the results are in Figure 35. Listed below are some of the standard queries.
PICES query #1: Identify all the species classified as nonindigenous within a location that are
established, have an unknown population establishment, or are stocked. Step 1: Choose the
taxon of interest (or blank for all species); Step 2: Choose the location (or blank to get all
locations); Step 3: Chick the Nonindigenous, Established, Unknown, and Stocked boxes; Step 4:
Click on the "or" radio button; Step 5: Click on Atlas species group; Step 6: Choose the Map
Master Classification; Step 7: Choose the type of query (e.g., short output, species profiles, etc.);
Step 8: Click on Query to run the query. This query was used to generate the species profiles in
the "Atlas of Nonindigenous Marine andEstuarine Species in the North Pacific ".
PICES query #2: Identify all the species classified as nonindigenous within a specific location
that are established. This is the same as query #1 except that only the Established population
status is checked (thus excluding nonindigenous species with an unknown status or are stocked).
PICES query #3: Identify all the RAS species from a location. Step 1: Choose the taxon of
interest (or leave blank for all species); Step 2: Choose the location; Step 3: Do not choose any
58
-------
of the Classification or Population attributes (because they often were not determined for the
RAS species); Step 4: Click on RAS species group; Step 5: Choose the Map All Classifications;
Step 6: Choose the type of query (e.g., short output, Atlas, etc.); Step 7: Click on Query.
4.3 Species Distribution Spreadsheet
The Species Distribution Spreadsheet query function (Figure 33) will generate an Excel
spreadsheet of a single species' invasion and population status for all Ecoregions, Provinces,
Regions, and Realms. This list is populated by All Classification data rather than Master
Classification data. Thus, it returns unedited information from each publication, and in many
cases this will include multiple classifications and/or populations statuses for a species within an
ecoregion. This query was created before the Multiple Species Queries, which generates maps of
the species' distribution. Nonetheless the Species Distribution Spreadsheet is still useful to view
the overall distribution and classification of a species across MEOW biogeographic levels in a
tabular fashion.
In order to generate a query, click on the Single Species Distribution Spreadsheet button
(Figure 33). A menu will appear as shown in Figure 39. Type in the name of the species of
interest (synonyms, misspellings, and common names can also be used), and click the Export
Summary button. A Microsoft Excel file will open up that contains a species distribution list
(Figure 40). No other options are available with this query.
ill] Find Species by Classificati...
Export Species
Distribution Data
Scientific Name
Systei
As:
CoromoftiWrjiHii
^USGS
science to .a c&r/iyimp vutrtM
Deborah Reusser
Figure 39: Single Species Distribution Spreadsheet menu, which is accessed from the
Data Output menu (Figure 33). Select a species by its scientific name, synonym, or
common name to export a Microsoft Excel spreadsheet detailing the geographic
distribution and classification of that species. There are no other options for this query.
An example output is shown in Figure 40.
59
-------
Species = Myo orenorio
Realm Region
Arctic
Temperate Northern Atlantic
Temperate Northern Pacific
Central Indo-Pacific
Eastern Indo-Pacific
Temperate South America
Arctic Arctic
Temperate Northern Atlantic Northwest Atlantic
Temperate Northern Atlantic Mediterranean Sea
Temperate Northern Atlantic Northeast Atlantic
Temperate Northern Atlantic Ponto-Caspian
Temperate Northern Pacific Northeast Pacific
Temperate Northern Pacific Northwest Pacific
Central Indo-Pacific Central Indo-Pacific
Eastern Indo-Pacific Eastern fndo-Pacific
Temperate South America Magellanic
Arctic Arctic
Temperate Northern Atlantic Northeast Atlantic
Temperate Northern Atlantic Northeast Atlantic
Temperate Northern Atlantic Mediterranean Sea
Temperate Northern Atlantic Northwest Atlantic
Temperate Northern Atlantic Northwest Atlantic
Temperate Northern Atlantic Ponto-Caspian
Temperate Northern Pacific Northwest Pacific
Temperate Northern Pacific Northwest Pacific
Temperate Northern Pacific Northeast Pacific
Temperate Northern Pacific Northeast Pacific
Central Indo-Pacific Central Indo-Pacific
Central Indo-Pacific Central Indo-Pacific
Eastern Indo-Pacific Eastern Indo-Pacific
Temperate South America Magellanic
Arctic Arctic
Arctic Arctic
Province
Arctic
Northern European Seas
Lusitanian
Mediterranean Sea
Cold Temperate Northwest Atlantic
Warm Temperate Northwest Atlantic
Black Sea
Cold Temperate Northwest Pacific
Warm Temperate Northwest Pacific
Cold Temperate Northeast Pacific
Warm Temperate Northeast Pacific
South China Sea
South Kuroshio
Hawaii
Magellanic
Arctic
Arctic
Ecoregion
Northern Labrador
Chukchi Sea
Native NIS
X
X X
X x
X
X
X
X
X
x
X X
X
X
X
X
X
X
X
X
X
x x
X X
X
Crypto
Transient
Unclass
x
X
x
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
Established
X
X
X
x
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
NotEstablished
x
X
X
Unknown
x
X
x
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
Stocked
Figure 40: Example of a portion of the output generated by the Single Species Distribution Spreadsheet output (Figure
39). The query summarizes a single species' distribution for all the MEOW levels. Additionally, it summarizes the
classification and population status of the species at each of those levels. The output is based on the All Classifications
using the unedited information from all publications, thus in many cases there will be multiple classifications for a
species at a given biogeographic level. NIS = nonindigenous; Crypto = cryptogenic; Unclass = unclassified.
60
-------
5.0 PICES TROUBLESHOOTING TIPS
5.1. Runtime Errors
Occasionally, when using the database, a runtime error message will appear. When this occurs,
click the End button and shut any open database windows and restart the database.
5.2. Black Boxes
Occasionally, when using the database, the checkboxes on the Realm map on the Environment
and Biogeography screen (Figure 9) turn black. When this occurs, the database has become
non-responsive, and it is necessary to shut any open database windows and restart the PICES
database.
61
-------
6.0 REFERENCES
Anonymous. 1958. The Venice system for the classification of marine waters according to
salinity. 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.
CANOD (California Aquatic Non-Native Organism Database). 2009. California Aquatic Non-
Native Organism Database (CANOD) (updated 4-30-09). California Department of Fish
and Game, Office of Spill Prevention and Response. Source:
http://www.dfg.ca.gov/ospr/Science/invasive species.aspx.
Carlton, J.T. and Eldredge, L.G. 2009. Marine bioinvasions of Hawaii: The introduced and
cryptogenic marine and estuarine animals and plants of the Hawaiian Archipelago.
Bishop Museum Bulletin in Cultural and Environmental Studies 4. 230p.
Chapman, J.W. 1988. Invasion of the Northeast Pacific by Asian and Atlantic gammaridean
amphipod crustaceans, including a new species of Corophium. Journal of Crustacean
Biology 8:364-382.
Chapman, J.W. and Carlton, J.T. 1991. A test of criteria for introduced species: The global
invasion by the isopod Synidotea laevidorsalis (Miers, 1881). Journal of Crustacean
Biology 11:386-400.
Chapman, J.W. and Carlton, J.T. 1994. Predicted discoveries of the introduced isopod Synidotea
laevidorsalis (Miers, 1881). Journal of Crustacean Biology 14: 700-714.
Coan, E.V., Scott, P.V., and Bernard, F.R. 2000. Bivalve Seashells of Western North America:
Marine Bivalve Mollusks from Arctic Alaska to Baja California. Santa Barbara, CA:
Santa Barbara Museum of Natural History. 764 pages.
Cohen, A.N. 2004. An Exotic Species Detection Program for Tillamook Bay. Prepared for the
Tillamook Estuaries Partnership Garibaldi, Oregon, (available at
http ://www. sfei. org/bioinvasions/bireports.htm)
Cohen, A.N. and Carlton, J.T. 1995. Nonindigenous aquatic species in a United States estuary: A
case study of the biological invasions of the San Francisco Bay and Delta. Ed. .
Washington D.C.: United States Fish and Wildlife Service and National Sea Grant
College Program (Connecticut Sea Grant). 246 pages.
Cohen, A.N., Harris, L.H., Bingham, B.L., Carlton, J.T., Chapman, J.W., Lambert, C.C.,
Lambert, G., Ljubenkov, J.C., Murray, S.N., Rao, L.C., Reardon, K. and Schwindt, E.
2005. Rapid Assessment Survey for exotic organisms in southern California bays and
harbors, and abundance in port and non-port areas. Biological Invasions 7:995-1002.
62
-------
Hall, C.A. 1964. Shallow-water marine climates and molluscan provinces. Ecology 45:226-234.
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/cove 1 .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/estuary/assets/estuary.pdf)
IUCN. (2001). IUCN Red List Categories and Criteria: Version 3.1. IUCN Species Survival
Commission. IUCN, Gland, Switzerland and Cambridge, UK. ii + 30 pp. (available at
http://intranet.iucn.org/webfiles/doc/SSC/RedList/redlistcatsenglish.pdf).
IUCN. (2003). Guidelines for Application of IUCN Red List Criteria at Regional Levels: Version
3.0. IUCN Species Survival Commission. IUCN, Gland, Switzerland and Cambridge,
UK. ii + 26 pp. (available at
http://intranet.iucn.org/webfiles/doc/SSC/SSCwebsite/Red List/regional guidelinesEn.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/ 12/63 1 .
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).
Morris, W. and Doak, D. 2002. Quantitative Conservation Biology: Theory and Practice of
Population Viability Analysis. Sinauer Associates, Inc. Sunderland, MA.
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%3 Adoi%2F 10.1371 %2Fj ournal .pone .003 0 105)
Poore, G.C.B. 1996. Species differentiation in Synidotea (Isopoda: Idoteidae) and recognition of
introduced marine species: A reply to Chapman and Carlton. Journal of Crustacean
Biology 16:384-394.
Reusser, D.A. and Lee II, H. 201 1. Evolution of natural history information in the 21st century -
developing an integrated framework for biological and geographical data. Journal of
Biogeography 38:1225-1239.
63
-------
Ruiz, G.M., Fofonoff, P.W., Carlton, J.T., Wonham, M.J., and Hines, A.H. 2000. Invasion of
coastal marine communities in North America: Apparent patterns, processes, and biases.
Annual Review Ecology and Systematics 31:481-531.
SCAMIT (Southern California Association of Marine Invertebrate Taxonomists). 2012. A
Taxonomic Listing of Macro- and Megainvertebrates from Infaunal and Epifaunal
Monitoring Programs in the Southern California Bight, Vol. 7, ed. Cadien, D.B. and
Lovell, L.L. Los Angeles, CA: SCAMIT. 137 pages.
Spalding, M.D., Fox, H.E., Allen, G.R., Davidson, N., Ferdana, Z.A., Finlayson, M., Halpern,
B.S., Jorge, M.A., Lonbana, 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.
Sytsma, M.D., Cordell, J.R., Chapman, J.W., and Draheim, R.C. 2004. Lower Columbia River
Aquatic Nonindigenous Species Survey 2001-2004. Final Technical Report. Prepared For
The United States Coast Guard and The United States Fish and Wildlife Service. 69
pages. Available at http://www.clr.pdx.edu/docs/LCRANSFinalReport.pdf
Taylor, P.D. and Wilson, M. A. 2002. A new terminology for marine organisms inhabiting hard
substrates. PALAIOS 17:522-525.
Todd, J.A. 2001. Molluscan life habits databases. In Neogene marine biota of tropical America.
See http://porites.uiowa.edu/database/mollusc/mollusclifestyles.htm.
64
-------
7.0 TABLES
Table 1: Definitions for the regime categories (Figure 20, Section 3.7.2). Regimes are the broad
physical and environmental divisions based on a combination of salinity, geomorphology, and
depth (see Madden et al., 2005).
Regime Class
Terrestrial
Lakes and Ponds (Lentic)
Rivers, Streams, and Creeks (Lotic)
Estuaries and Lagoons
Coastal Fringe
Coastal Bay
Nearshore
Shelf
Oceanic
Definition
Land areas not directly impinging upon aquatic ecosystems.
Body of standing fresh water, including 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.
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.
0 - 30m. The outer coast; from the intertidal to 3 Om bathymetric isopleth.
30 - 200m bathymetric isopleths. The benthos and water above that
borders the continent and extends out to where there is an increased slope
of the seafloor, approximately 200m depth.
> 200m bathymetric isopleths. Includes the benthos and water above the
continental slope and ocean floor.
65
-------
Table 2: Definitions for the ecosystem categories (Figure 21, Section 3.7.3). Ecosystems are broad ecosystem types located within
the regimes.
Major Habitat Type:
Level 1
Unconsolidated
Ecosystems
Ecosystem Class:
Level 2
Unvegetated
Sediment
Submerged Aquatic
Vegetation (SAV)
Ecosystem Class:
Level 3
Coastal Shore
Tide Flats
Subtidal
Zostera
Ecosystem Class:
Level 4
Clastic Sediments
Carbonate Sediment
Burrowing Shrimp
Clastic Sediments
Carbonate Sediment
Clastic Sediments
Carbonate Sediment
Zostera marina
Zostera japonica
Definition
Ecosystem types associated with sediment.
Sediment environments where plants or algae do not
dominate. Exposed sediment.
Sediment environments along the coast that are affected by
the tides and water activity (shore waves), i.e. sandy beaches
A sediment environment (beach) composed of rock fragments.
A sediment environment (beach) composed of calcium
carbonate, including shells, calcified algae, and coral
skeletons.
Relatively flat, sediment areas that are submerged or exposed
by the changing tides. Includes mud flats.
Sediment environments that are 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 coral
skeletons.
Sediment that is covered by a body of water at all times,
without exposure to air due to tides.
Sandy subtidal where the sediment is composed of rock
fragments.
Sandy subtidal where the sediment is composed of calcium
carbonate. Sources include shells, calcified algae, and coral
skeletons.
Sediment environments that include and are dominated by
aquatic plants that are covered by water, i.e. seagrasses.
SAV environments dominated by the seagrass Zostera.
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).
66
-------
Major Habitat Type:
Level 1
Ecosystem Class:
Level 2
Macroalgal Beds
Emergent Marsh
Mangrove
Ecosystem Class:
Level 3
Posidonia
Halodule
Cymodocea
Syringodium
Thalassia
Ruppia
Halophila
Other
Distichlis
Spartina
Salicornia/
Sarcocornia
Juncus
Other
Rhizophora
Ecosystem Class:
Level 4
Definition
SAV environments dominated by plant species within the
genus Posidonia.
SAV environments dominated by plant species within the
genus Halodule (specific manatee grasses or seagrasses).
SAV environments dominated by plant species within the
genus Cymodocea (manatee grasses).
SAV environments dominated by plant species within the
genus Syringodium (manatee grasses).
SAV environments dominated by plant species within the
genus Thalassia (turtle grasses).
SAV environments dominated by plant species within the
genus Ruppia (widgeonweed or widgeon grass).
SAV environments dominated by plant species within the
genus Halophila.
Sediment environments that are dominated by an aquatic plant
that is not included in the provided SAV choices.
Sediment environments where macroalgae are dominant and
shape the habitat characteristics (e.g., algal mats of Ulva,
Porphyra).
Intertidal sediment environments dominated by vegetation that
is rooted in the soil. i.e. marsh grasses and salt tolerant
succulents.
Marshes that are dominated by plant species within the genus
Distichlis.
Marshes that are dominated by plant species within the genus
Spartina (cord grasses)
Marshes that are dominated by plant species within the genus
Salicornia (glasswort, pickleweed). Note that some species of
Salicornia are now referred to Sarcocornia.
Marshes that are dominated by plant species within the genus
Juncus.
Marshes that are dominated by an aquatic plant that is not
included in the provided marsh plant choices.
Intertidal sediment environments dominated by salt-tolerant
trees and shrubs. Found in tropical and subtropical areas.
Mangrove forests that are dominated by plant species within
the genus Rhizophora.
67
-------
Major Habitat Type:
Level 1
Consolidated Ecosystem
Ecosystem Class:
Level 2
Dune
Wrack
Other
Rocky Intertidal
Subtidal Rocky
Coral Reef
Oyster/ Mussel
Reef
Worm Reef
Coralline Algae
Reef or Habitat
Kelp forest
Fouling
Ecosystem Class:
Level 3
Avicennia
Languncularia
Other
Tide Pool
Phyllospadix
Caves
Ecosystem Class:
Level 4
Definition
Mangrove forests that are dominated by plant species within
the genus Avicennia (includes black mangroves).
Mangrove forests that are dominated by plant species within
the genus Languncularia.
Mangrove forests that are dominated by an aquatic plant that
is not included in the provided marsh plant choices.
Sand hills or ridges on land that are be created by wind.
Dried vegetation and associated debris usually left behind by
the receding tide.
Sediment habitats not previously mentioned.
Ecosystem types associated with hard substrate.
Rocky environments on the coastal shore that are periodically
exposed to both air and water. The zone between the high and
low tide marks.
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.
Rocky environments below low tide mark that are always
submerged by water.
Areas where the rocky substrate is dominated by reef forming
coral animals.
Hard substrate that is covered or formed by bivalve shells.
Hard substrate that is predominantly composed of worm
tubes.
Hard substrate that is predominantly composed of calcified
algae. The algae can either be the encrusting form or the
unattached rhodolith form.
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 and high latitudes.
Hard substrate such as a boat hull that supports a community
of organisms.
68
-------
Major Habitat Type:
Level 1
Pelagic Ecosystem
Ecosystem Class:
Level 2
Other
Water
Column
Floating Vascular
Plants or
Macroalgae
Flotsam
Ecosystem Class:
Level 3
Ecosystem Class:
Level 4
Definition
Habitats associated with hard substrates that were not
previously mentioned.
The ocean water column and unobstructed surface. Open
water.
Open water habitat where organisms are completely
surrounded by water (no surfaces, sides, or floors); within the
pelagic zone.
Large mats/rafts of plants or algae that float unattached on the
water's surface in the open ocean.
Aggregated floating debris in the open ocean.
69
-------
Table 3: Definitions for the depth categories for benthic and pelagic habitats (Figure
22, Section 3.7.4)
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 or
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.
Lowest intertidal zone, predominantly submerged
by water.
> 0 - 200m. Subtidal zone extending from the
low water mark to the approximate edge of the
continental shelf. Also referred to as the
sublittoral zone.
> 0 - 30m
>30 - 200m
>200 - 2000m. This benthic zone is below the
euphotic zone and extends down the continental
slope.
>2000 - 6000m. This zone has a temperature of
4°C or less. It is the largest benthic ocean zone.
> 6000m. The deepest areas of the sea, including
ocean trenches.
The estuary or ocean water column and
unobstructed surface. Open water.
0 - 200m
0-lm
> 1 - 30m
> 30 - 200m
>200 - 1000m
> 1000 - 2000m
> 2000 - 6000m
> 6000m
70
-------
Table 4: Definitions for substrate categories (Figure 23, Section 3.7.5).
Level 1
Unconsolidated
Level 2
Mud
Sand
Mixed fines
Level 3
Clay
Silt
Mineral
Carbonate
Siliceous ooze
Fine sand
Medium sand
Coarse sand
Mineral
Carbonate
Siliceous ooze
Sandy mud
Muddy sand
Mineral
Carbonate
Siliceous ooze
Definition
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
O.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.
Mixed fines primarily composed of carbonate sediments.
Mixed fines composed of > 30%_siliceous remains from diatoms,
71
-------
Level 1
Consolidated
Level 2
Gravel
Cobble
Mixed sediments
Organic Sediment
Rock
Level 3
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
Boulder
Bedrock
Definition
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.
Unconsolidated sediment composed of >75%by weight of particles in
the size range of 64-256 mm. In some classifications, cobble is
considered a 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.
Sediment with high proportion of vegetative detritus. >30% organic
matter (> 17% organic carbon) according to Howes and Kenik (1997).
Substrates composed of particles >256 mm or of unbroken rock.
Substrate not moved by organisms or tidal or ocean currents except in
extreme storms.
Substrates composed of particles >256 mm but not forming a single
unbroken surface.
Unbroken rock. Includes both hard rocks and softer rocks, such as
72
-------
Level 1
Level 2
Hardpan
Biogenic
Artificial Substrate
Level 3
Coral
Oyster
Mussel
Worm reef
Coralline algae
Kelp
Rooted Aquatic
Mangrove
Drift wood
Other
Rip rap
Piling
Hulls & Ballast tanks
Other
Definition
chalk.
Sand, silt, or clay particles that are 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.
Other consolidated substrates not included in the list of biotic substrates.
Hard substrates placed into estuarine or oceanic environments.
Hard substrate provided by rocks and concrete used in breakwalls,
groins, jetties, and shoreline armoring.
Hard substrate provided by concrete and wood piling and piers to
support docks, bridges, and other superstructures.
Hard substrate on the exterior or interior of ships and boats, including
derelict or decommissioned ships.
Other artificial substrates not listed above.
73
-------
Table 5: Definitions for wave energy classes (Figure 24, Section 3.7.6).
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.
Table 6: Definitions for current energy classes (Figure 24, Section 3.7.6).
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.
Table 7: Definitions for the physiological temperature classes (Figure 25, Section
3.7.7).
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 "normal" temperature tolerance.
Species with a wide temperature range, such as many
intertidal species and species with wide geographic
distributions.
74
-------
Table 8: Definitions for the salinity classes (Figure 26, Section 3.7.8).
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-poly haline
Alpha-poly haline
Beta-euhaline
Alpha-euhaline
Definition
< 0.5 psu
0.5 - < 30 psu
0.5 - < 5 psu
0.5 - < 3 psu
3 - < 5 psu
5 - < 18 psu
5 - < 10 psu
10 - < 18 psu
18 - < 30 psu
18 -< 25 psu
25 - < 30 psu
30 - < 40 psu
30 - < 36 psu
36 - < 40 psu
> 40 psu
75
-------
Table 9: Definitions for the trophic modes (Figure 27, Section 3.8.1).
Level 1
Primary
Producer
Herbivore
Predator
Scavenger
Detritovore
Decomposer
Suspension
Feeder
Level 2
Photosynthetic
Chemosynthetic
Grazer
Folivore
Other
Secondary
Consumer
Tertiary Consumer
Quaternary
Consumer
Quinary Consumer
Active
Passive
Obligate
Facultative
Level 3
Level 4
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.
Feeds on leaves.
Herbivore feeding mechanism not included in the above list.
Feeds on animals.
Predator feeding primarily on herbivores. Also called a Primary
predator.
Predator feeding primarily on secondary consumers. Also called a
Secondary predator.
Predator feeding primarily on tertiary consumers. Also called a
Tertiary predator.
Predator feeding primarily on quaternary consumers. Also called a
Quaternary predator.
Feeds on dead organic material. Usually used for species feeding on
larger particles or animal remains
In contrast to scavengers, feed on small detritus (i.e. plant and animal
remains).
Organisms that breakdown and digest dead organisms. Bacteria and
fungi are major decomposer groups.
Feeds on phytoplankton, zooplankton, and/or suspended particles in
the water column.
Captures planktonic particles by pumping or sweeping water past a
filter.
Utilizes ocean currents to transport planktonic particles past a
particle-trapping mechanism, such a filter or sticky trap.
Feeds only as a suspension feeder.
Switches between suspension feeding and other feeding mechanism,
such as deposit feeding.
76
-------
Level 1
Deposit Feeder
Other
Level 2
Surface Deposit
Feeder
Subsurface Deposit
Feeder
Obligate
Facultative
Level 3
Level 4
Explanation
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.
Feeding mechanism not included in the above list.
Table 10: Definitions for symbiotic relationships that a species may use to derive energy (Figure 27, Section 3.8.1).
Level 1
Parasite/Disease
Symbiotic Algae
Level 2
Ectoparasite
Endoparasite
Disease
Explanation
Organisms that feed on host and are physiologically
/ metabolically dependent upon host. Usually
smaller than host.
External parasite, including gill parasites.
Internal parasite.
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.
77
-------
Table 11: Definitions for the terms describing various reproductive strategies (Figure 28, Section 3.8.2).
Level 1
Asexual
reproduction
Sexual
Reproduction
Level 2
Binary fission
Budding and fragmentation
Parthenogenesis
Agamospermy
Vegetative propagation
Sporogenesis
Hermaphrodite/Monoecious
Gonochoristic / Dioecious
Level 3
Heterogamy
Monoecious
(plants)
Synchronous
Hermaphrodite
(animal)
Sequential
Hermaphrodite
(animal)
Migratory
Level 4
Self fertilizing:
Y/N
Self fertilizing:
Y/N
Protandry
Protogyny
Anadromous
Explanation
Reproduction without the fusion of gametes.
Splitting into two approximately equal parts.
Splitting into unequal parts. 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 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.
Reproduction through the fusion of gametes (fertilization).
Plants having separate male and female flowers on the same
individual plant.
Animals having both male and female sexual organs at the same
time (= simultaneous hermaphrodites).
Animals that change from one sex to the other.
Initially a male and changes to a female.
Initially a female and changes to a male.
Having separate sexes. In plants, male and female flowers are
produced on different individuals
Fish that spend most of their lives in saltwater and migrate to
78
-------
Level 1
Level 2
Fertilization / Spawning
Type
Level 3
Internal
fertilization
Fertilization
External Eggs
Freecast
spawners
Pollination
Level 4
Catadromous
Broadcast
spawner
Spermcast
spawner
Explanation
freshwater to breed
Fish that spend most of their lives in freshwater and migrate to
saltwater to breed
Copulation 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 male discharges gametes into the water column.
In plants, fertilization of female floral structures by pollen.
79
-------
Table 12: Definitions for early development mechanisms (Figure 29, Section 3.8.3).
Early Development Mechanism
Level 1
Viviparous
Oviparous
Ovoviviparous (brooder)
Level 2
External eggs
Egg mass carried by female
Definition
Development takes place within the
female and embryo derives
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 egg
mass by the female, such as by many
crabs (e.g., berried crab).
Eggs develop within the female, or
male in some cases, but the embryo
derives no nourishment from the
parent. A brooder.
Table 13: Definitions for juvenile development and dispersal (Figure 29, Section
3.8.3).
Juvenile Development/Dispersal
Level 1
Direct
development
Larval phase
Level 2
Ametabolous
Hemimetabolous
Holometabolous
Benthic larvae
Level 3
Lecithotrophy
Planktotrophy
Brooded
Free living
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.
Larvae that remain on the bottom or
within the tubes of adults.
Benthic larvae that derive nourishment
from yolk.
Benthic larvae that derive nourishment
by feeding.
The larval phase is brooded within the
adult or tube of the adult.
The larval phase is totally separated
from the adult.
80
-------
Juvenile Development/Dispersal
Level 1
Fragments
Seeds
Spores
Level 2
Planktonic larvae
Level 3
Duration of
larval phase
Lecithotrophy
Planktotrophy
Teleplanic
Duration of
larval phase
Level 4
Units
Units
Definition
Maximum duration of larval phase and
units (hours, days, months).
Larvae that spend at least part of the
larval phase in the water column.
Planktonic larvae that derive
nourishment from yolk.
Planktonic larvae that derive
nourishment by feeding.
Larvae with an extended planktonic
phase and a corresponding capacity for
long-distance dispersal.
Maximum duration of larval phase and
units (hours, days, months).
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.
Table 14: Definition of alternation of generation categories (Figure 29, Section 3.8.3).
Alternations of Generations
Level 1
Y/N
Level 2
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.
81
-------
Table 15: Definitions of habitat types (Figure 30, Section 3.8.4).
Level 1
Pelagic
Benthic
Level 2
Pleuston
Neuston
Pelagic
submerged
Demersal
Surficial
(Epibenthic Non
swimming)
Level 3
Benthopelagic
Epibenthic -
swimming
Level 4
Permanent
benthopelagic
Hyperbenthos
Definition
Organisms inhabiting the water column exclusive of the
layer immediately above the bottom.
Buoyant organisms with part of the body protruding above
the sea surface and often subject to wind drift. Includes both
animals, such as the Portuguese Man-of-War and Velella
and plants floating at the surface.
Pelagic organisms that float at the water surface 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 and that swim
as a normal part of their routine and not just in response to
disturbance.
Animals living all or part of their 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 above the bottom.
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 are
able to swim as part of its normal adult life cycle, 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.
82
-------
Level 1
Level 2
Under rock
Cryptofauna
Borer
Level 3
Epibenthic
unconsolidated
Epibenthic
consolidated
Rock
Clay
Level 4
Epifauna
unconsolidated
Epiphytes
unconsolidated
Epifauna
consolidated
Epiphytes
consolidated
Primary space
holder (Y/N)
Definition
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 species sampled in trawls,
such as sea cucumbers and scallops, are 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 so as to capture
the primary producers as well 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.
Facultative mobile or non-mobile organisms directly
colonizing the substrate surface and occupying space.
Species that live beneath rock or other hard substrates (e.g.,
shell rubble, debris).
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.
83
-------
Level 1
Epibiotic
Level 2
Nestler
Semi-infauna
Infauna
Level 3
Shell & Coral
Wood
Macrofauna
Meiofauna
Microfauna
Level 4
Shallow
Deep
Shallow
Deep
Shallow
Deep
Definition
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
ofTodd(2001).
Animals partially buried in mud or sand and partially
exposed in the water column, such as the bivalve Modiolus
(see Bush et al., 2007).
Animals living within unconsolidated sediment.
Animals living within unconsolidated sediment that are
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
Animals living within the interstitial spaces in
unconsolidated sediments. There is not 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 surface of a living or dead organism.
Relationship may be mutualistic, parasitic, or commensal.
Classified as pelagic or benthic depending upon species it
colonizes.
84
-------
Level 1
Other
Level 2
Epiphytic
Epizoic
Secondary
space holder
(Y/N)
Level 3
Level 4
Definition
Living on surface of living or dead plant.
Living on surface of a living or dead animal.
Facultative mobile or non-mobile epibiotic organisms
colonizing the surface of a primary space holder.
Species living in habitats not captured in those listed above.
85
-------
Table 16: Definitions of life style (i.e. mobility) terms (Figure 31, Section 3.8.5).
Level 1
Immobile
Facultatively
mobile
Level 2
Unattached
Attached
Rooted
Unattached
Attached
Level 3
Infaunal -
Immobile
Reclining
Nestler/Borer
Other
Cemented
Byssally attached
Other
Adhesion
Byssally attached
Level 4
Free living
Tubicolous
Explanation
Species with no ability to move as an adult.
Species that spends its adult life not attached to substrate
Soft sediment only.
Infaunal species that does not live in a tube.
Species living in a mud, sand, organic, or calcareous tube.
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 lives within an existing crevice in a consolidated substrate
(nestler) or a species that bores into a consolidated substrate (borer).
Unattached mechanism not included in the above list.
Species attached to or bores into 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.
Attachment mechanism not included in the above list.
Vascular Plants
Species with limited mobility, in particular to repositioning themselves
in response to environmental disturbances (e.g., sea anemones)
Species with no permanent attached to the substrate, and 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.
86
-------
Level 1
Passively
mobile
Actively
mobile
Level 2
Planktonic
Drift
Other
Sedentary
Swimming
Level 3
Other
Holoplankton
Meroplankton
Burrowing
Crawling
Other
Nektonic
Demersal
Level 4
Fast
Slow
Fast
Slow
Explanation
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 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.
Non-planktonic species that passively drift in the currents. This includes
bentltic 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 at least 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
Swims against current in 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.
87
-------
Level 1
Level 2
Periodic
mobility
Level 3
Y/N
Level 4
Explanation
Species that show intermittent periods of no or limited mobility coupled
with periods of active mobility. This includes many of the hyperbenthic
species.
-------
Table 17: Definitions of terms for primary vectors of invasion (Figure 32, Section 3.9).
Level 1
Ships and Boats
Moveable Structures
Aquaculture and
Fisheries
Level 2
Commercial
Recreational
Drilling Platforms
Dry Docks
Buoys
Other
Intentional
Stocking/Release
Aquaculture Escapees
Aquaculture
Associated Species
Level 3
Ballast Water
Solid Ballast
Hull Fouling
Other
Ballast Water
Solid Ballast
Hull Fouling
Other
Atlantic oysters
Pacific oysters
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.
Transport of organisms associated with the movement of buoys.
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
89
-------
Level 1
Infrastructure
Development
Research and
Education
Aquarium and Plant
Trade
Recreation
Live Seafood
Level 2
Intentional Illegal
Release
Other
Canals
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
Navigation
Canals
Irrigation
Canals
Definition
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.
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.
90
-------
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
91
-------
Table 18: Tables associated with attributes in the species profiles (Figure 37) and list
of abbreviations used in the Key to the Species Profiles (Figures 38A and 38B).
Attribute /
Level in Species Profile
Date of 1st Record
Vectors - Level 1
Vectors - Level 2
Vectors - Level 3
Regime
Ecosystem - Level 2
Ecosystem - Level 3
Depth
Unconsolidated Substrate
Consolidated Substrate -
Level 1
Abbreviations
NWP
NEP
SH
MS
AF
ID
RE
AP
REC
SF
HR
O
BW
SB
HF
S/R
AE
AA
IR
A
P
AO
PO
SAV
MAR
MAN
D
RI
SR
CR
O/M
F
K
UV-CS
UV-TF
UV-SUB
TP
RI-PH
R
Meaning
Northwest Pacific
Northeast Pacific
Ships
Moveable structures
Aquaculture and fisheries
Infrastructure development
Research and education
Aquarium and plant trade
Recreation
Seafood
Habitat restoration and migration
Other
Ballast water
Solid ballast
Hull fouling
Stocking and release
Aquaculture escape
Aquaculture associated
Illegal release
Aquarium
Plant
Atlantic oyster
Pacific oyster
Submerged aquatic vegetation
Marsh
Mangrove
Dunes
Rocky intertidal
Subtidal rocky
Coral reef
Oyster/mussel reef
Fouling assemblage
Kelp forest
Coastal shore
Tidal flat (estuaries)
Subtidal (estuaries and oceanic)
Tide pool
Rocky intertidal - Phyllospadix
Rocky
Table / Figure
Figure 1
"
Table 17
"
"
"
"
"
"
"
"
"
"
"
"
"
"
"
"
"
"
"
"
Table 1
Table 2
"
"
"
"
"
"
"
"
"
"
"
"
"
"
"
"
Table 3
Table 4
Table 4
"
92
-------
Attribute /
Level in Species Profile
Consolidated Substrate -
Level 2
Salinity
Trophic Level and Feeding
- Level 1
Trophic Level and Feeding
- Level 2
Reproduction - Level 2
Early Development -
Level 1
Juvenile development and
dispersal - Level 1
Abbreviations
HP
C
0
M
W
CA
K
RA
MAN
DW
R
P
H + B
Oth
PAR
SA
PP
H
P
S
DET
DEC
SF
DF
DF-SUR
DF-SUB
H
G/D
SF
BF
BUD
PAR/AGA
VP
SP
V
OVI
OVO
LP
FR
SD
Meaning
Hard pan
Coral
Oyster
Mussel
Worm Reef
Coralline Algae
Kelp
Rooted aquatics
Mangrove
Drift wood
Rip-Rap
Pilings
Hull/Ballast
Other
Parasite
Symbiotic algae
Primary producer
Herbivore
Predator
Scavenger
Detritivore
Decomposer
Suspension feeder
Deposit feeder
Surface deposit feeder
Subsurface deposit feeder
Hermaphrodite
Gonochoristic/Dioecious
Spawning/Fertilization Type
Binary fission
Budding
Parthenogenic/Agamospermy
Vegetative propagation
Sporogenesis
Viviparous
Oviparous
Ovoviviparous
Larval phase
Fragments
Seeds
Table / Figure
"
"
"
"
"
"
"
"
"
"
"
"
"
"
Table 8
Table 9
66
66
66
66
66
66
66
66
66
66
66
66
66
Table 11
"
"
"
"
"
"
"
"
Table 12
"
"
"
Table 13
"
"
"
93
-------
Attribute /
Level in Species Profile
Juvenile development and
dispersal - Level 2
Habitat Association -
Level 2
Habitat Association -
Level 3
Abbreviations
SP
LP-B
LP-P
PL
NE
SUB
DEM
SUR
UR
B
N
SF
IN
EPP
EPZ
BP
EPS
EPU
EPC
Meaning
Spores
Benthic larvae
Planktonic larvae
Pleuston
Neuston
Submerged in water column
Demersal - motile
Surficial - non-motile
Under rocks
Borer
Nestler
Semi-infaunal
Infaunal
Epiphytic
Epizoic
Benthopelagic
Epibenthic - swimming
Epibenthic - unconsolidated
Epibenthic - consolidated
Table / Figure
"
"
"
Table 15
"
"
"
"
"
"
"
"
"
"
"
"
"
"
"
"
94
-------
8.0 APPENDICES
Appendix A. Marine Ecoregions of the World (MEOW).
A list of the biogeographic Realms, Regions, Provinces, and Ecoregions based on The Nature
Conservancy (TNC) "Marine Ecoregions of the World" (MEOW, Spalding et al 2007) and
modified to include Regions (Reusser and Lee, 2011). MEOW_ID, RegionID, ProvincelD, and
RealmID are identifiers used in the PICES database. The TNC Codes have been used in all cases
unless it created a duplicate MEOW_ID. To resolve duplication of numbers all Provinces have
had 1000 added to the number. We added the Caspian Sea and Aral Sea to the original MEOW
ecoregions.
REALM REGION PROVINCE ECOREGION
1 Arctic
101 Arctic
1001 Arctic
25007 Baffin Bay - Davis Strait
20012 Beaufort Sea - continental coast and shelf
20011 Beaufort-Amundsen-Viscount Melville-Queen Maud
20013 Chukchi Sea
20003 East Greenland Shelf
20015 East Siberian Sea
25014 Eastern Bering Sea
25010 High Arctic Archipelago
20008 Hudson Complex
20017 Kara Sea
25009 Lancaster Sound
20016 Laptev Sea
20018 North and East Barents Sea
20002 North and East Iceland
20001 North Greenland
20005 Northern Grand Banks - Southern Labrador
20006 Northern Labrador
20004 West Greenland Shelf
20019 White Sea
120 High Arctic
1063 High Arctic
30120 High Arctic
6 Central Indo-Pacific
111 Central Indo-Pacific
1031 Eastern Coral Triangle
20134 Bismarck Sea
20135 Solomon Archipelago
20136 Solomon Sea
20137 Southeast Papua New Guinea
1027 lava Transitional
20120 Cocos-Keeling/Christmas Island
20119 Southern lava
95
-------
1036 Lord Howe and Norfolk Islands
20151 Lord Howe and Norfolk Islands
1033 Northeast Australian Shelf
20143 Central and Southern Great Barrier Reef
20142 Torres Strait Northern Great Barrier Reef
1034 Northwest Australian Shelf
20144 Exmouth to Broome
20145 Ningaloo
1032 Sahul Shelf
20139 ArafuraSea
20140 Arnhem Coast to Gulf of Carpenteria
20141 Bonaparte Coast
20138 Gulf of Papua
1025 South China Sea
20112 Gulf of Tonkin
20114 South China Sea Oceanic Islands
20113 Southern China
1028 South Kuroshio
20121 South Kuroshio
1026 Sunda Shelf
20115 Gulf of Thailand
20118 Malacca Strait
20116 Southern Vietnam
20117 Sunda Shelf/Java Sea
1029 Tropical Northwestern Pacific
20124 East Caroline Islands
20123 Mariana Islands
20122 Ogasawara Islands
20125 West Caroline Islands
1035 Tropical Southwestern Pacific
20150 Coral Sea
25147 Fiji Islands
20149 New Caledonia
20146 Tonga Islands
20148 Vanuatu
1030 Western Coral Triangle
20131 BandaSea
20127 Eastern Philippines
20129 Halmahera
20132 Lesser Sunda
20133 Northeast Sulawesi
20126 Palawan/North Borneo
20130 Papua
20128 Sulawesi Sea/Makassar Strait
7 Eastern Indo-Pacific
112 Eastern Indo-Pacific
1039 Central Polynesia
20155 Line Islands
20156 Phoenix/Tokelau/Northern Cook Islands
96
-------
20157 Samoa Islands
1042 Easter Island
20163 Easter Island
1037 Hawaii
25152 Hawaii
1041 Marquesas
20162 Marquesas
1038 Marshall, Gilbert and Ellis Islands
25154 Gilbert/Ellis Islands
20153 Marshall Islands
1040 Southeast Polynesia
20159 Rapa-Pitcairn
20161 Society Islands
20160 Southern Cook/Austral Islands
20158 Tuamotus
12 Southern Ocean
119 Antarctica
1061 Continental High Antarctic
20228 Amundsen/Bellingshausen Sea
20225 East Antarctic Enderby Land
20224 East Antarctic Wilkes Land
20226 East Antarctica Dronning Maud Land
20229 Ross Sea
20227 Weddell Sea
1060 Scotia Sea
20223 Antarctic Peninsula
20220 South Georgia
20221 South Orkney Islands
20219 South Sandwich Islands
20222 South Shetland Islands
1059 Subantarctic Islands
20217 Bouvet Island
20215 Crozet Islands
20213 Heard and Macdonald Islands
20214 Kerguelen Islands
20212 Macquarie Island
20218 Peter the First Island
20216 Prince Edward Islands
1062 Subantarctic New Zealand
20232 Auckland Island
25230 Bounty and Antipodes Islands
20231 Campbell Island
11 Temperate Australasia
118 Southern Australia and New Zealand
1055 East Central Australian Shelf
20203 Manning-Hawkesbury
20202 Tweed-Moreton
97
-------
1053 Northern New Zealand
25195 Kermadec Island
25196 Northeastern New Zealand
20197 Three Kings-North Cape
1056 Southeast Australian Shelf
20205 Bassian
20204 Cape Howe
20206 Western Bassian
1054 Southern New Zealand
25199 Central New Zealand
25198 Chatham Island
20201 Snares Island
20200 Southern New Zealand
1057 Southwest Australian Shelf
20208 Great Australian Bight
20209 Leeuwin
20207 South Australian Gulfs
1058 West Central Australian Shelf
20211 Houtman
20210 Shark Bay
2 Temperate Northern Atlantic
103 Mediterranean Sea
1004 Mediterranean Sea
20030 Adriatic Sea
25031 Aegean Sea
25036 AlboranSea
25034 Ionian Sea
25032 Levantine Sea
25033 Tunisian Plateau/Gulf of Sidra
25035 Western Mediterranean
104 Northeast Atlantic
1003 Lusitanian
20029 Azores Canaries Madeira
20028 Saharan Upwelling
20027 South European Atlantic Shelf
1002 Northern European Seas
20024 Baltic Sea
20026 Celtic Seas
20021 Faroe Plateau
20025 North Sea
20023 Northern Norway and Finnmark
20020 South and West Iceland
20022 Southern Norway
102 Northwest Atlantic
1005 Cold Temperate Northwest Atlantic
25040 Gulf of Maine/Bay of Fundy
20037 Gulf of St. Lawrence - Eastern Scotian Shelf
20039 Scotian Shelf
20038 Southern Grand Banks - South Newfoundland
98
-------
20041 Virginian
1006 Warm Temperate Northwest Atlantic
25042 Carolinian
20043 Northern Gulf of Mexico
105 Ponto-Caspian
1007 Black Sea
20044 Black Sea
1007 Ponto-Caspian
30100 Aral Sea
30000 Caspian Sea
30101 Sea of Azov
3 Temperate Northern Pacific
106 Northeast Pacific
1010 Cold Temperate Northeast Pacific
20053 Aleutian Islands
20054 Gulf of Alaska
25055 North American Pacific Fijordland
25058 Northern California
25057 Oregon, Washington, Vancouver Coast and Shelf
25056 Puget Trough/Georgia Basin
1011 Warm Temperate Northeast Pacific
20060 Cortezian
20061 Magdalena Transition
25059 Southern California Bight
107 Northwest Pacific
1008 Cold Temperate Northwest Pacific
25046 Kamchatka Shelf and Coast
20048 Northeastern Honshu
20047 Oyashio Current
20049 Sea of Japan
20045 Sea of Okhotsk
20050 Yellow Sea
1009 Warm Temperate Northwest Pacific
20051 Central Kuroshio Current
20052 East China Sea
9 Temperate South America
116 Magellanic
1048 Magellanic
20187 Channels and Fjords of Southern Chile
20188 Chiloense
20186 Malvinas/Falklands
25184 North Patagonian Gulfs
25185 Patagonian Shelf
99
-------
114 Southeast Pacific
1046 Juan Fernandez and Desventuradas
20179 Juan Fernandez and Desventuradas
1045 Warm Temperate Southeastern Pacific
20178 Araucanian
20177 Central Chile
20175 Central Peru
20176 Humboldtian
115 Southwest Atlantic
1049 Tristan Gough
20189 Tristan Gough
1047 Warm Temperate Southwestern Atlantic
20182 Rio de la Plata
20181 Rio Grande
20180 Southeastern Brazil
20183 Uruguay-Buenos Aires Shelf
10 Temperate Southern Africa
117 South Africa
1051 Agulhas
20192 Agulhas Bank
20193 Natal
1052 Amsterdam-St Paul
20194 Amsterdam-St Paul
1050 Benguela
20191 Namaqua
25190 Namib
4 Tropical Atlantic
108 East Tropical Atlantic
1017 Gulf of Guinea
25086 Angolan
20083 Gulf of Guinea Central
20084 Gulf of Guinea Islands
25085 Gulf of Guinea South
20082 Gulf of Guinea Upwelling
25081 Gulf of Guinea West
1015 St. Helena and Ascension Islands
20078 St. Helena and Ascension Islands
1016 West African Transition
20079 Cape Verde
25080 Sahelian Upwelling
109 West Tropical Atlantic
1013 North Brazil Shelf
20072 Amazonia
20071 Guianan
1012 Tropical Northwe stern Atlantic
20063 Bahamian
20062 Bermuda
100
-------
20064 Eastern Caribbean
20070 Floridian
20065 Greater Antilles
20066 Southern Caribbean
20069 Southern Gulf of Mexico
20067 Southwestern Caribbean
20068 Western Caribbean
1014 Tropical Southwestern Atlantic
20076 Eastern Brazil
20074 Fernando de Naronha and Atoll das Rocas
20075 Northeastern Brazil
20073 Sao Pedro and Sao Paulo Islands
20077 Trindade and Martin Vaz Islands
8 Tropical Eastern Pacific
113 Tropical Eastern Pacific
1044 Galapagos
20173 Eastern Galapagos Islands
20172 Northern Galapagos Islands
20174 Western Galapagos Islands
1043 Tropical East Pacific
20167 Chiapas-Nicaragua
20165 Clipperton
20169 Cocos Islands
20171 Guayaquil
20166 Mexican Tropical Pacific
20168 Nicoya
20170 Panama Bight
20164 Revillagigedos
5 Western Indo-Pacific
110 Indian Ocean
1024 Andaman
20109 Andaman and Nicobar Islands
20110 Andaman Sea Coral Coast
20111 Western Sumatra
1023 Bay of Bengal
20107 Eastern India
20108 Northern Bay of Bengal
1022 Central Indian Ocean Islands
20106 Chagos
20105 Maldives
1018 Red Sea and Gulf of Aden
20089 Gulf of Aden
20087 Northern and Central Red Sea
20088 Southern Red Sea
1019 Somali/Arabian
20090 Arabian (Persian) Gulf
20093 Central Somali Coast
101
-------
20091 Gulf of Oman
20092 Western Arabian Sea
1021 West and South Indian Shelf
20104 South India and Sri Lanka
20103 Western India
1020 Western Indian Ocean
20101 Bight of Sofala/Swamp Coast
20097 Cargados Carajos/Tromelin Island
20102 Delagoa
20095 East African Coral Coast
20098 Mascarene Islands
20094 Northern Monsoon Current Coast
20096 Seychelles
20099 Southeast Madagascar
20100 Western and Northern Madagascar
102
-------
Appendix B: List of PICES taxa codes.
The taxa codes identify commonly used taxonomic groups, such a bivalves or amphipods (see
Figure 5). "Group" is a code to link species that display generally similar taxonomic levels
and/or body types. However, Groups have no taxonomic standing.
TAXA CODE
ACEL
ACT
AM
AMB
AMP
AN
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
NAME
Acoelomorpha
Ray -finned fish
Amphipod
Amoeboid
Amphibian
Anthozoan
Aplacorphoran
Apicomplexa
Arachnid
Arthropod
Ascothoracid
Sea star
Bird
Bivalve
Bacterium
Brachiopod
Fish louse
Branchipod
Bryozoan
Caudofoveata
Cephalocarid
Cephalopod
Centipede
Cephalochordate
Lamprey
Cercozoan
Tapeworm
Charophyta /Streptophyta
Chimaeras
Green alga
Golden alga
Chaetognath
Ciliate
Barnacle
Cnidarian
Copepod
Crinoid
Crustacean
Cryptomonad
Ctenophore
Cumacean
GROUP
Invertebrate
Fish
Invertebrate
Protist
Vertebrate
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
103
-------
CUB
CYB
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
MONO
MONO
MY
MYST
MYX
NE
NEM
NEMA
0
OP
Cubozoan
Blue-green bacterium
Decapod
Diatom
Dinoflagellate
Echinoid
Echiurid
Echinoderm
Cartilaginous fish
Entoproct
Horsetail
Euphausid
Facetotecta
Fecampiida
Foram
Fungi
Gastropod
Gastrotricha
Gnathostomulid
Hagfish
Hemichordata
Leach
Sea cucumber
Haptophyte
Hydrozoan
Insects
Isopod
Kinorhyncha
Lepostracean
Lophogastrida
Loricifera
Club moss
Angiosperms
Mammalia
Horseshoe crab
Millipede
Mollusc
Monogenean
Monoplacophoran
Mysid
Mystacocarid
Myxozoan
Nemertine
Nematode
Horsehair worm
Oligochaete
Ophiuroid
Invertebrate
Microalgae
Invertebrate
Microalgae
Microalgae
Invertebrate
Invertebrate
Invertebrate
Fish
Invertebrate
Plant
Invertebrate
Invertebrate
Fecampiida
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
104
-------
ORTH
OS
P
PAUR
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
Orthonectid
Ostracod
Polychaete
Pauropod
Pentastomes
Pericaridan
Pseudofungi
Phoronid
Brown alga
Platyhelminthe
Placozoan
Sponge
Chiton
Priapulids
Fern
Pycnogonid
Radiolarians
Raphidophyceae
Remipedian
Reptilia
Red alga
Rhizopodan
Rhombozoan
Rotifer
Scaphopod
Scyphozoan
Sipunculid
Solenogastres
Stauromedusan
Stomatopod
Symphylan
Syncarid
Tanaid
Tantulocarid
Tardigrad
Fluke
Tunicate
Flatworm
Virus
Yellow-green alga
Invertebrate
Invertebrate
Invertebrate
Invertebrate
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
105
-------
Appendix C. List of commonly used abbreviations for museums listed in the Location of Type field (Figure 5). See The Registry
of Biological Repositories (http://www.biorepositories.org) for additional locations of voucher specimens.
Museum Name
Academy of Natural Sciences, Philadelphia's Natural History Museum, Philadelphia, Pennsylvania, USA
American Museum of Natural History New York City, New York, USA
Australian Museum, Sydney, Australia
Berlin Museum, Berlin, Germany
Bishop Museum Honolulu, Hawaii, USA
British Museum Natural History, London, UK
California Academy of Science, San Francisco, California, USA
Canadian Museum of Nature, Ottawa, Ontario, Canada
Deutsches Entomologisches Institut, Germany
Flordia Marine Research Institute Invertebrate Collection, St. Petersburg, Florida, USA
Hancock Museum, Newcastle-upon-Tyne, Scotland
Institute of Taxonomic Zoology Amsterdam, Netherlands
Institute de Ciencias del Mar y Limnologia, Univ. Nacional Autonoma de Mexico, Mexico
Invertebrates reference Coll., Mazatlan Marine Station, Univ. Nacional Autonoma de Mexica (UNAM), Mexico
Kamchatka Institute of the Ecology and Environment, Russia
Linnean Society of London, U.K.
Manchester Museum, Waters Collection, U.K.
Musee National d'Histoire Naturelle, Paris, France
Museo Civico di Storia Naturale di Geneva "Giacomo Doria", Geneva, Italy.
Museo de Zoologia, Universidad de Costa Rica, Costa Rica
Museu Nacional, Univ. Federal do Rio de Janeiro, Brazil
Common
Abbreviations
ANSP
AMNH
AM
AMS
BNM
BERL
BPBM
BMNH
BM
Brit Mus Nat Hist
Brit Mus Nat Hist, London
British Museum
The Natural History Museum, London
NHM
CASIZ
CAS
NMC
CMN
DEI
FSBC
HMN
ITZ
UNAM
EMU
KIE
KE
LSL
MM
MNHN
MSNG
UCR
MNRJ
106
-------
Museum Name
Museum Godeffroy, Hamburg, Germany
Museum of Comparative Zoology, Harvard University, Massachusetts, USA
Museum of Vertebrate Zoology at University of California, Berkeley, CA, USA
National Museum of Natural Science, Taiwan
National Museum of Nature and Science, Tokyo, Japan
National Museum of Victoria, Melbourne Australia
Natural History Museum of Los Angeles County, California, USA
National Museum of Natural History (Naturalis), The Netherlands
Naturhistorisches Museum Wien (Museum of Natural History of Vienna), Austria
Queensland Museum, Brisbane, Australia
Rijksmuseum van Natural History, Amsterdam, Netherlands
Royal British Columbia Museum, Victoria, British Columbia, Canada
Rutgers University, Dept. of Plant Pathology Mycological Herbarium, New Jersey, USA
San Diego Natural History Museum, California, USA
Scripps Institute of Oceanography, La Jolla, California, USA
Senckenberg Research Institute and Natural History Museum, Frankfurt, Germany
Seto Marine Biological Laboratory, Field Science Education and Research Center, Kyoto University, Japan
Smithsonian Institute National Museum of Natural History, Washington D.C., USA
South Australian Museum, Adelaide, Australia
Stanford Natural History Museum, USA
Swedish Museum of Natural History, Stockholm (Naturhistoriska Rijsmuseet), Sweden
Trinity College Dublin, Ireland
United States National Museum, Washington D.C., USA
Univ. Nacional Autonoma de Mexico, Col. Nacional de Crustaceos; Instituto de Biologia, Mexico City, Mexico
Univ. of Washington, Burke Museum of Natural History and Culture, Seattle, Washington, USA
University Museum The University of Tokyo, Japan
University of Colorado Museum of Natural History, Colorado, USA
University of Trondheim, Dept. of Natural History Museum, Trongheim, Norway
Uppsala University, Museum of Evolution, Sweden
Common
Abbreviations
MGH
MCZ
MVZ
NMNS
NSMT
NMV
LACM
NHMLAC
NNM
RMNH
NHMW
NMW
QM
RMNH
RBCM
RUTPP
SDNHM
SIO
SMF
SMBL
NMNH
USNM
SAM
SNHM
NRM
SSM
SMNH
TCD
USNM
CNCR
UW
UMUT
UCM
CUMNH
NTNU
UUZM
107
-------
Museum Name
Utah Museum of Natural History, Utah, USA
Yale Peabody Museum of Natural History New Haven, Connecticut, USA
Zoological Institute of China, Shanghai, China
Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russia
Zoological Museum Hamburg, Germany
Zoologisch Museum, Universitest Van Amsterdam, Netherlands
Zoologisches Museum der Humboldt-Universitat, Berlin, Germany
Zoologisk Museum, University of Copenhagen, Copenhagen, Denmark
Common
Abbreviations
UMNH
YPM
ZICS
ZIAP
ZIAS
ZIN
HZM
ZMH
ZMA
ZMHU
ZMB
ZMUC
ZMC
108
-------
Appendix D: Invasion: Criteria for Nonindigenous Classification.
Criteria used to evaluate whether a species is nonindigenous or native. Criteria modified from Chapman and Carlton (1991, 1994),
Cohen et al. (2005), and Sytsma et al. (2004). See Poore (1996) for disagreement on the application of the criteria to the isopod
Synidotea. In all cases, the application of the criteria requires high quality taxonomy so as not to confuse distributions of closely
related but different species. The comments on the discriminatory power of the various criteria are our evaluations unless otherwise
noted. Except in cases with historical records of introduction, a weight of evidence approach using multiple criteria should be used in
determining a species' classification, and we recommend against simply summing the number of criteria. The criteria are phrased so
that "Yes" indicates an introduction.
Criteria for Nonindigenous Classification
Historical records of introduction.
Association with human vectors of introduction.
Absence from fossil records in region.
Insufficient natural dispersal mechanisms to create
global distribution.
Recent appearance in region where not found
previously.
Discontinuous local distributions relative to similar
endemic species.
Recent spread from one or few locations to many
locations within region.
Close associations with other introduced species.
Restriction to new or artificial environments.
Definition
Strongest evidence especially for stocked species.
Does not have high discriminatory power since species with a wide variety of reproductive
types and life histories are considered to have successfully invaded new regions.
Utility depends upon whether species is likely to leave a fossil and the completeness of fossil
and midden records. Most useful for mollusks.
Useful to exclude native species that are likely to be widespread due to either active dispersal
mechanisms (e.g., tuna) or passive dispersal mechanisms (e.g., many microbes, pelagic
copepods). However, does not have high discriminatory power to identify a species as non-
native per se.
Reasonably strong evidence depending upon completeness of previous records and collections.
Stronger evidence for larger, more charismatic species (e.g., fish, crabs) that are likely to have
been recorded than the less well studied taxonomic groups.
Reasonably strong evidence depending upon completeness of previous records and collections.
Also requires sufficient understanding of the natural history of the species to assess that the
discontinuous distribution is not due to specific habitat or physiological limitations.
Moderately strong evidence depending upon completeness of previous records and collections.
Need to evaluate whether spread is related to recent environmental conditions (e.g., El Nino)
and whether ecologically similar native species are also showing a similar spread.
Cohen et al. (2005) only used this criterion as evidence if the "association or dependency
appeared to be obligate or near-obligate."
Does not have high discriminatory power and was excluded by Cohen et al. (2005).
109
-------
Criteria for Nonindigenous Classification
Conspecific with geographically isolated populations.
Type locality is geographically isolated from the local
region.
Member of a nonindigenous taxonomic group.
Ecological or physiological adaptations dissimilar from
endemic species.
Absent from ecosystems with low invasion potential.
Definition
Globally disjunct distributions, as indicated by isolated populations in geographically
separated oceans or on different continents, is suggestive that one of the populations was
introduced. An alternative is the vicariance hypotheses that the disjunct distributions result
from the breakup of a previously continuous population due to plate tectonics or other
geographical barrier. Another alternative is that the two populations represent sibling species
that have yet to be recognized.
Added here as a new criterion. The location of the type specimen in a geographically isolated
area is essentially an application of the "Conspecific with geographically isolated populations"
criterion. We suggest that the location of the type specimen can be used as a simple filter to
help identify possible non-native species for more detailed analysis.
Membership in a family or genus that is only found in areas geographically remote from the
local region is suggestive that one of the populations has been introduced (see Chapman,
1988).
"Many introduced species are from climates were temperature ranges exceed those in the new
location or where they escape parasites or diseases. Some introduced species tolerate
temperatures, for instance, that do no exist in the new locations." (Sytsma et al., 2004). While
these differences in adaptation may help explain why a particular species is a successful
invader, they do not have high discriminatory power to separate native vs. non-native species.
Current evidence indicates that certain ecosystems do not contain many nonindigenous
species, such as deep water (>200 m) habitats. Occurrence of a species in such ecosystems is
suggestive of a native origin, while absence of the species from such ecosystems in itself has
little discriminatory power.
110
-------
Appendix E: Criteria for Population Establishment.
Criteria used to evaluate whether the population of a nonindigenous or native species is established within an ecoregion or specific
waterbody. Some of the criteria are drawn from the IUCN Red List guidelines for evaluating the extinction risk of native species at
global (IUCN, 2001) and regional (IUCN, 2003) scales, based on the assumption that the criteria for establishment are basically the
opposite of those that put a species at risk of extinction. Other criteria are based on those proposed for nonindigenous species by Ruiz
et al. (2000) and Cohen (2004) as well as general population and conservation biology (e.g., Morris and Doak, 2002). Except in cases
with multiple years of records of a population, multiple criteria should be used in determining a species' population status. The
population status criteria are phrased so that "Yes" indicates an established species.
Criteria for Population Establishment
Species not directly dependent upon human support.
Population size steady or increasing.
Found in more than one year.
Found within the last 20 years within the region or water
body.
Mixed population structure with juveniles and adults.
Reproductive females found.
Widespread distribution in region
(extent of occurrence).
Found in multiple locations in region
(area of occupancy).
Population size/range/frequency of occurrence comparable
to ecologically similar native species in region.
Definition
Species dependent upon human support, such several non-native oysters, would not be
considered established.
Strong evidence of population establishment, especially if the population has been steady or
increasing for several generations.
While not as strong evidence as a population trend, finding a species in two or more years is
suggestive that the species can survive and perhaps reproduce within the region.
Ruiz et al. (2000) considered that records older than 20-30 years were insufficient to classify a
species as established.
Occurrence of both adults and juveniles indicates that the species can reproduce within the
region.
Presence of reproductive females indicates that environmental conditions are suitable for
reproduction.
Species occupying a wide geographical area within the invaded region. See IUCN (2001, 2003).
Found at multiple locations within its range (extent of occurrence) within the invaded range. See
IUCN (2001, 2003).
Population characteristics of the invader are comparable to those of ecologically similar native
species established within the region or waterbody.
Ill
-------
Criteria for Population Establishment
Population size/range/frequency of occurrence comparable
to that for same species in regions where established.
Not restricted to spatially limited habitat.
Definition
Population characteristics in the invaded region are similar to those in the native re|
invaded areas where the species is considered established.
lion or other
Species with wide habitat requirements are less likely to go extinct.
112
-------
&EPA
United States
Environmental Protection
Agency
PRESORTED STANDARD
POSTAGE & FEES PAID
EPA
PERMIT NO. G-35
Office of Research and Development (8101R)
Washington, DC 20460
Official Business
Penalty for Private Use
$300
Recycled/Recyclable Printed on paper that contains a minimum of
50% postconsumer fiber content processed chlorine free
------- |