Ecological Archives E092-201-D1

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:

Suggested Data Set Identity Code: Mammal Community Database (MCDB)

C. Data set description:

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 USA

S. K. Morgan Ernest
Department of Biology and the Ecology Center
Utah State University
Logan, Utah, 84322 USA

Abstract: 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 1945–2010. 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; ethan@weecology.org.

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 Jan–Dec 2009
Web of Science Web of Science includes Science Citation Index (1965–present) small mammal* community* abundance* Online; accessed Jan–Dec 2009
BioOne BioOne 1920–present, varies with journal small mammal* community* abundance* Online; accessed May–Dec 2009
UMI ProQuest UMI Dissertations & Theses - Full Text 1861–present small mammal* community* abundance* Online; accessed Sept–Dec 2009
US Gov Pubs MarciveWeb DOCS - Catalog of U.S. Government Publications July 1976–March 2010 mammal, mammal* Online; accessed Jan–Dec 2009
Monthly US Gov Pubs ProQuest - Monthly Catalog of US Government Publications January 1895–June 1976 mammal, mammal* Online; accessed Jan–Dec 2009
Ecological Archives Ecological Society of America Archives 2000–2009 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, 227–237 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, 1478–1512. 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

Blackburn, T. M., O. L. Petchey, P. Cassey, and K. J. Gaston. 2005. Functional diversity of mammalian predators and extinction in island birds. Ecology 86:2916–2923.

Brown, J. H. 1995. Macroecology. University of Chicago Press, Chicago, Illinois, USA.

Firn, J., J. L. Moore, A. S. MacDougall, E. T. Borer, E. W. Seabloom, J. HilleRisLambers, W. S. Harpole, E. E. Cleland, C. S. Brown, J. M. H. Knops, S. M. Prober, D. A. Pyke, K. A. Farrell, J. D. Bakker, L. R. O'Halloran, P. B. Adler, S. L. Collins, C. M. D'Antonio, M. J. Crawley, E. M. Wolkovich, K. J. La Pierre, B. A. Melbourne, Y. Hautier, J. W. Morgan, A. D. B. Leakey, A. Kay, R. McCulley, K. F. Davies, C. J. Stevens, C. Chu, K. D. Holl, J. A. Klein, P. A. Fay, N. Hagenah, K. P. Kirkman, and Y. M. Buckley. 2011. Abundance of introduced species at home predicts abundance away in herbaceous communities. Ecology Letters 14:274–281.

McGill, B. J. 2003. A test of the unified neutral theory of biodiversity. Nature 422:881–885.

Ulrich, W., M. Ollik, and K. I. Ugland. 2010. A meta-analysis of species-abundance distributions. Oikos 119:1149–1155.


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