Katherine M. Thibault, Sarah R. Supp, Mikaelle Giffin, Ethan P. White, and S. K. Morgan Ernest. 2011. Species composition and abundance of mammalian communities. Ecology 92:2316.
Abstract: Ecologists have long sought to understand the mechanisms underlying the assembly and structure of communities. Such understanding is relevant to both basic science and conservation-related issues. The macroecological approach to this problem involves asking scientific questions using a large number of communities in order to elucidate generalities in pattern and process. Such analyses are typically conducted using a substantial amount of data from a particular taxonomic group across a diversity of systems. Large community databases are available for a number of taxa, but no publicly available database exists for mammals. Given the logistical challenges of collecting such data de novo, compiling existing information from the literature provides the best avenue for acquiring the necessary data. Here, we provide a data set that includes species lists for 1000 mammal communities, excluding bats, with species-level abundances available for 940 of these communities. All communities found in the literature that included complete, site-specific sampling data, composed of species lists with or without associated abundances, were included in the data set. Most, but not all, sites are limited to species groups that are sampled using a single technique (e.g., small mammals sampled with Sherman traps). The data set consists of 7977 records from 1000 georeferenced sites encompassing a variety of habitats throughout the world, and it includes data on 660 mammal species with sizes ranging from 2 g to >500 kg.
Key words: abundance; community; community assembly; community structure; composition; mammals.
METADATA
CLASS I. DATA SET DESCRIPTORS
A. Data set identity: Species composition and abundance of mammalian communities compiled from published literature.
B. Data set identification code:
C. Data set description:Suggested Data Set Identity Code: Mammal Community Database (MCDB)
7977 records that indicate the presence and, for a subset of the records, the abundance of mammal species, including representatives across trophic groups and size classes but excluding bats, documented at 1000 sites throughout the world, encompassing a variety of habitats.
Principal Investigators:
Ethan P. White
Department of Biology and the Ecology Center
Utah State University
Logan, Utah, 84322 USAS. K. Morgan Ernest
Department of Biology and the Ecology Center
Utah State University
Logan, Utah, 84322 USAAbstract: as above
D. Key words: as above
CLASS II. RESEARCH ORIGIN DESCRIPTORS
A. Overall project description
Identity: Species composition of mammalian communities compiled from published sources, with abundance data when available.
Originators: Ethan P. White and S. K. Morgan Ernest
Period of Study: Data compiled in this project were published from 19452010. The authors intend to continue adding to the database indefinitely, and encourage others to contribute their data and/or recommendations for additional sources to this effort.
Objectives: To provide data for macroecological analyses of mammalian community assembly and structure.
Taxonomy: Taxonomy follows Wilson, D. E., and D. M. Reeder, editors. 2005. Mammal species of the world, Third Edition. Smithsonian Institution Press, Washington, D.C., USA.
Sources of funding: National Science Foundation DEB-0827826 and DEB-0953694.
CLASS III. DATA SET STATUS AND ACCESSIBILITY
A. Status
Latest update: August 2011 for the final format of all files.
Latest Archive date: August 2011
Metadata status: The metadata are complete and up to date.
Data verification: Data quality has been carefully checked as described in class V, section B, below.
B. Accessibility
Storage location and medium: Copies of the latest version of the data file are being stored on the principal investigator's personal computer, two Weecology servers, and Amazon S3 (via Dropbox) in Microsoft Excel, Text, and MySQL formats.
Contact person: Ethan P. White, Department of Biology and the Ecology Center, Utah State University, Logan, UT, 84322; [email protected].
Copyright restrictions: None.
Proprietary restrictions: None.
Costs: None.
CLASS IV. DATA STRUCTURAL DESCRIPTORS
COMMUNITY DATA
A. Data Set File
Identity: MCDB_communities.csv
Size: 7977 records, not including header row, 207,757 bytes.
Format and storage mode: ASCII text, comma delimited.
Header information: The first row of the file contains the variable names. See section B below for detailed descriptions of the column contents.
Alphanumeric attributes: Mixed.
Special characters/fields: If no information is available for a given record, this is indicated by NULL.
Authentication procedures: MD5 Checksum for the file: 79f03946c8ecbfe38ad4c059e07a9742
B. Variable information
Variable name | Variable definition | Units | Storage type | Variable codes and definitions | Missing value codes |
Site_ID | Unique numeric code, starting with 1001, for each site; links to Sites and Trapping tables | N/A | Integer | N/A | N/A |
Initial_year | Initial year of sampling for the associated data; some sites may have several years of data presented separately or in aggregate; with Site_ID, links to Trapping table | N/A | Integer | N/A | NULL |
Species_ID | Unique 4 character identifier for each species, typically derived from the first 2 characters of both the genus and species; links to Species table | N/A | Character | N/A | N/A |
Presence_only | Indicates whether abundance data, regardless of format, is given for the species | N/A | Character | 1 = presence data only; 0 = abundance data given | N/A |
Abundance | Abundance data | N/A | Fixed point | N/A | NULL |
Mass | Average mass of the individuals of a given species captured at the particular site, if provided | grams | Fixed point | N/A | NULL |
SPECIES DATA
A. Data Set File
Identity: MCDB_species.csv
Size: 700 records, not including header row, 26,064 bytes.
Format and storage mode: ASCII text, comma delimited.
Header information: The first row of the file contains the variable names. See section B below for detailed descriptions of the column contents.
Alphanumeric attributes: Mixed.
Special characters/fields: None.
Authentication procedures: MD5 Checksum for the file: c42f8e2c42ecac75f66d54357c876efa
B. Variable information
Variable name | Variable definition | Units | Storage type | Variable codes and definitions | Missing value codes |
Species_ID | Unique 4 character identifier for each species derived from the first 2 characters of both the genus and species; links to Communities table | N/A | Character | N/A | N/A |
Family | Family to which the species listed belongs | N/A | Character | N/A | N/A |
Genus | Genus to which the species listed belongs | N/A | Character | N/A | N/A |
Species | specific epithet | N/A | Character | N/A | N/A |
Species_level | Indicates whether the taxon has been identified to the species-level | N/A | Integer | 0 = not identified to species; 1 = identified to species; 2 = identified to species pair (i.e., either of two possible species) | N/A |
SITES DATA
A. Data Set File
Identity: MCDB_sites.csv
Size: 1000 records, not including header row, 184,649 bytes.
Format and storage mode: ASCII text, comma delimited.
Header information: The first row of the file contains the variable names. See section B below for detailed descriptions of the column contents.
Alphanumeric attributes: Mixed.
Special characters/fields: If no information is available for a given record, this is indicated by NULL.
Authentication procedures: MD5 Checksum for the file: 4064d7d46f6aea130fae44643a940851
B. Variable information
Variable name | Variable definition | Units | Storage type | Variable codes and definitions | Missing value codes |
Site_ID | Unique numeric code for each site; links to Trapping and Communities tables | N/A | Integer | N/A | N/A |
Reference_ID | Unique code for the associated reference; links to the References table | N/A | Character | N/A | N/A |
Location | Details of the site location | N/A | Character | N/A | N/A |
Country | Country in which the site is located | N/A | Character | Full names used except for the United States (USA) | N/A |
State | State/province where the site is located | N/A | Character | Full names used except for the United States (USA), for which standard state abbreviations are used | NULL |
Latitude | Latitude where the site is located | decimal degrees, WGS84 | Fixed point | N/A | NULL |
Longitude | Longitude where the site is located | decimal degrees, WGS84 | Fixed point | N/A | NULL |
Uncertainty_radius | The approximate radius of uncertainty for the given coordinates | kilometers | Integer | N/A | NULL |
Elevation_low | The minimum elevation of the study area | meters | Integer | N/A | NULL |
Elevation_high | The maximum elevation of the study area | meters | Integer | N/A | NULL |
Habitat_description | Brief description of habitat(s) sampled | N/A | Character | N/A | N/A |
Habitat_code | Two-character key indicating general habitat category | N/A | Character | AG = Agricultural, cropland; CF = Coniferous Forest; CLF = cloud forest; D = desert (shrubland vs. grassland not specified); DF = Deciduous forest; DG = desert grassland; DS = desert scrub; GL = grassland; MF = Mixed temperate forest; MX = mixed habitats; SD = sand dunes; SH = Shrubland; TF = tropical forest; W = wetland | N/A |
Abundance_data_present | Indicates whether abundance data are given | N/A | Character | none = no abundance data given for the site; some = abundance data provided for some, but not all, of the species; all = abundance data given for all species reported at the site | N/A |
Abundance_data_format | Indicates the format in which the abundance data are given | N/A | Character | none = no abundance data given for the site, raw = raw abundance data given, estimate = density estimate given in lieu of raw abundances, relative = relative abundances (proportions of total abundance) given | N/A |
Spatial_extent | Approximate spatial extent of trapping grids/transects/webs | square meters | Integer | N/A | NULL |
Study_duration | The number of months between the first sampling efforts and the last | months | Integer | N/A | NULL |
Time_series | Indicates whether temporal data are available | N/A | Integer | 1 = data are presented for more than one time period; 0 = data are aggregated for the entire period of study | N/A |
N_years | Approximate number of years of data | years | Integer | N/A | NULL |
Notes | Miscellaneous notes about the site data | N/A | Character | N/A | NULL |
TRAPPING DATA
A. Data Set File
Identity: MCDB_trapping.csv
Size: 1169 records, not including header row, 75,365 bytes.
Format and storage mode: ASCII text, comma delimited.
Header information: The first row of the file contains the variable names. See section B below for detailed descriptions of the column contents.
Alphanumeric attributes: Mixed.
Special characters/fields: If no information is available for a given record, this is indicated by NULL.
Authentication procedures: MD5 Checksum for the file: 5ca1dd47cc7b095d850a24bb8ed69c7c
B. Variable information
Variable name | Variable definition | Units | Storage type | Variable codes and definitions | Missing value codes |
Site_ID | Unique numeric code for each site; links to Sites and Communities tables; for sites for which time series data are provided, there will be multiple records associated with the Site_ID | N/A | Integer | N/A | N/A |
Initial_year | The first year during which sampling occurred; links to Communities table; | N/A | Integer | N/A | NULL |
Final_year | The final year during which sampling occurred | N/A | Integer | N/A | NULL |
N_sampling_months | The total number of months during which sampling occurred | months | Integer | N/A | NULL |
Trap_nights | Total number of trap nights | nights | Integer | N/A | NULL |
Months_of_sampling | The months (full names) during which sampling occurred | N/A | Character | N/A< | NULL |
Pitfall_traps | Indicates whether pitfall traps were used | N/A | Integer | 1 = pitfall traps used; 0 = no pitfall traps used | N/A |
Small_traps | Indicates whether small live traps (Sherman, Elliott, or Havahart size 0) were used | N/A | Integer | 1 = small traps used; 0 = no small traps used | N/A |
Large_traps | Indicates whether large (larger than the small traps listed above) traps were used | N/A | Integer | 1 = large traps used; 0 = no large traps used | N/A |
Snap_traps | Indicates whether snap traps were used | N/A | Integer | 1 = snap traps used; 0 = no snap traps used | N/A |
Notes | Miscellaneous notes about the trapping data | N/A | Character | N/A | NULL |
REFERENCES DATA
A. Data Set File
Identity: MCDB_references.csv
Size: 186 records, not including header row, 38,610 bytes.
Format and storage mode: ASCII text, comma delimited.
Header information: The first row of the file contains the variable names. See section B below for detailed descriptions of the column contents.
Alphanumeric attributes: Mixed.
Special characters/fields: If no information is available for a given record, this is indicated by NULL.
Authentication procedures: MD5 Checksum for the file: 71f1194939852571b0a409bfa1fe092d
B. Variable information
Variable name | Variable definition | Storage type | Missing value codes |
Reference_ID | Unique identifier for each reference; links to Sites table | Character | N/A |
Reference_Source | Source ID indicating where reference was found; linked to ID in Table 1 (below) or Reference ID | Character | N/A |
Authors | Names of the authors, in the order given | Character | N/A |
Year_published | Year of publication, if published, otherwise null | Integer | NULL |
Title | Title of the publication, if published, otherwise, "unpublished" | Character | N/A |
Source | Journal, government agency, or university that published the reference, if published | Character | NULL |
Volume | Volume number of source, if applicable | Integer | NULL |
First_page | First page number | Integer | NULL |
Last_page | Last page number | Integer | NULL |
N_pages | Total number of pages | Integer | NULL |
SUDOCS | Number from the cataloging system used for government publications, where applicable | Character | NULL |
N_sites | Total number of sites in reference for which data are included | Integer | N/A |
CLASS V. SUPPLEMENTAL DESCRIPTORS
A. Data Acquisition
The published literature was searched using the databases and keywords listed in the following table:
Table 1. Details of searches and sources of references included in the data set.
ID Database Content Keywords Access JSTOR JSTOR accessed via Utah State University library small mammal* community* abundance* Online; accessed JanDec 2009 Web of Science Web of Science includes Science Citation Index (1965present) small mammal* community* abundance* Online; accessed JanDec 2009 BioOne BioOne 1920present, varies with journal small mammal* community* abundance* Online; accessed MayDec 2009 UMI ProQuest UMI Dissertations & Theses - Full Text 1861present small mammal* community* abundance* Online; accessed SeptDec 2009 US Gov Pubs MarciveWeb DOCS - Catalog of U.S. Government Publications July 1976March 2010 mammal, mammal* Online; accessed JanDec 2009 Monthly US Gov Pubs ProQuest - Monthly Catalog of US Government Publications January 1895June 1976 mammal, mammal* Online; accessed JanDec 2009 Ecological Archives Ecological Society of America Archives 20002009 N/A Online; accessed Dec 2009 Brown & Kurzius 1987 Brown J. H. & Kurzius M. (1987) Composition of desert rodent faunas: combinations of coexisting species. Annales Zoologici Fennici, 24, 227237 Abundance data from 201 small mammal communities compiled from the literature, including some unpublished field data N/A Acquired data from J. H. Brown and original references Brown & Nicoletto 1991 Brown J. H. & Nicoletto P. F. (1991) Spatial scaling of species assemblages: body masses of North American land mammals. American Naturalist, 138, 14781512. Presence/absence data for mammal communities compiled from the literature, plus some unpublished field data N/A Available as an appendix in the original publication
B. Quality assurance/quality control procedures
Each record was entered by one of the authors, and then carefully double-checked by another against the original reference.
C. Related material: N/A
D. Computer programs and data processing algorithms: N/A
E. Archiving: Data files and metadata have been archived at Ecological Data (http://www.ecologicaldata.org/).F. Literature Cited: Contained in the References table.
G. History of data set usage
Data set update history: N/A
Review history: N/A
Questions and comments from secondary users: N/A
ACKNOWLEDGMENTS
This research was funded by two grants from the National Science Foundation to E.P.W. (DEB-0827826 and DEB-0953694). We thank all of the investigators who collected and published these data, especially Jim Brown, who also provided the Brown and Kurzius 1987 data.
LITERATURE CITED
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McGill, B. J. 2003. A test of the unified neutral theory of biodiversity. Nature 422:881885.
Ulrich, W., M. Ollik, and K. I. Ugland. 2010. A meta-analysis of species-abundance distributions. Oikos 119:11491155.