Ecological Archives E090-184-D1
Kate E. Jones, Jon Bielby, Marcel Cardillo, Susanne A. Fritz, Justin O'Dell, C. David L. Orme, Kamran Safi, Wes Sechrest, Elizabeth H. Boakes, Chris Carbone, Christina Connolly, Michael J. Cutts, Janine K. Foster, Richard Grenyer, Michael Habib, Christopher A. Plaster, Samantha A. Price, Elizabeth A. Rigby, Janna Rist, Amber Teacher, Olaf R. P. Bininda-Emonds, John L. Gittleman, Georgina M. Mace, and Andy Purvis. 2009. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology 90:2648.
INTRODUCTION
Macroecology and macroevolution are growing research areas (Brown 1995, Gaston and Blackburn 2000), describing and testing hypotheses for many large-scale patterns in biodiversity, such as species richness (Orme et al. 2005, Grenyer et al. 2006); extinction risk (Purvis et al. 2000, Jones et al. 2003, Fisher and Owens 2004, Jetz et al. 2004, Cardillo et al. 2005, Price and Gittleman 2007); evolutionary history (Sechrest et al. 2002, Bininda-Emonds et al. 2007, Davies et al. 2008); geographic range size (Gaston 2003, Orme et al. 2006), and interspecific allometric relationships (Carbone et al. 2007a, Carbone et al. 2007b). Such comparative studies require large amounts of data, often covering a wide range of species or taxonomic groups in a number of geographic regions. Researchers gathering these data face two general problems. First, the amount of time and effort required to collect enough comparable information can be considerable; and second, the coverage of the available data, which determines the feasibility of studying different geographic regions or taxonomic groups, may be very inconsistent.
Here we describe a global species-level data set of key life-history, ecological and geographical traits of all known extant and recently extinct mammals (PanTHERIA) developed for a number of macroecological and macroevolutionary research projects. Additionally, we describe the tools, techniques and protocols developed to minimize errors and biases given the disparate data sources required to generate this data set and the large team of data-gatherers used to collect these data (referred to here as data-miners). We also describe our statistical methods developed to detect and, where possible, eliminate outlying values, and to then derive a single value for each trait for each species.
METADATA
CLASS I. DATA SET DESCRIPTORS
A. Data set identity: PanTHERIA1.0: a species-level data set of life history, ecology, and geography of extant and recently extinct mammals.
B. Data set identification code:
(1) PanTHERIA_1-0_WR93_Aug2008.txt
(2) PanTHERIA_1-0_WR05_Aug2008.txt
C. Data set description:
Principal Investigator(s): Kate E. Jones, Institute of Zoology, Zoological Society of London, Regents Park, London, NW1 4RY, United Kingdom. Olaf R.P. Bininda-Emonds, AG Systematik und Evolutionsbiologie, Carl von Ossietzky Universität Oldenburg, 26111 Oldenburg, Germany. John L. Gittleman, Odum School of Ecology, University of Georgia, Athens, Georgia 22902, USA. Georgina M. Mace, Centre for Population Biology, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, United Kingdom. Andy Purvis, Division of Biology, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, United Kingdom; and Centre for Population Biology, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, United Kingdom.
Abstract: Analyses of life history,
ecological, and geographic trait differences among species, their causes,
correlates, and likely consequences are increasingly important for understanding
and conserving biodiversity in the face of rapid global change. Assembling multispecies
trait data from diverse literature sources into a single comprehensive data set
requires detailed consideration of methods to reliably compile data for
particular species, and to derive single estimates from multiple sources based
on different techniques and definitions. Here we describe PanTHERIA — a species-level
data set compiled for analysis of life history, ecology, and geography of all
known extant and recently extinct mammals. PanTHERIA is derived from a database
capable of holding multiple geo-referenced values for variables within a
species containing 100740 lines of biological data for extant and recently
extinct mammalian species, collected over a period of three years by 20
individuals. PanTHERIA also includes spatial databases of mammalian geographic
ranges and global climatic and anthropogenic variables. Here we detail how the
data fields are extracted and defined for PanTHERIA using a customized data
input format MammalForm; how data were collected from the literature, species
names and sources tracked, error-checking and validation procedures applied, and
how data were consolidated into species-level values for each variable. Tables
of the consolidated species-level values are made available for each of two recent
species-level taxonomic classifications of mammals, as well as associated
taxonomic synonymy conversion and data-input files. This study provides a
useful guide to prospective researchers on how to structure and codify life history,
ecological, geographic, and taxonomic data and methods to extract meaningful
species-level traits. It also provides comprehensive information on traits like
size, diet, environmental conditions, and ecology to permit macroecological and
macroevolutionary analyses of this important clade.
D. Key words: behavior; biogeography; body size; climatic variables; comparative analyses; conservation; ecology; geographic range; life history; mammals; PanTHERIA; population density.
CLASS II. RESEARCH ORIGIN DESCRIPTORS
A. Overall project description
Identity: Understanding past, present, and future mammalian biodiversity.
Originators: Kate E. Jones, Institute of Zoology, Zoological Society of London, Regents Park, London, NW1 4RY, United Kingdom. Olaf R.P. Bininda-Emonds, AG Systematik und Evolutionsbiologie, Carl von Ossietzky Universität Oldenburg, 26111 Oldenburg, Germany. John L. Gittleman, Odum School of Ecology, University of Georgia, Athens, Georgia 22902, USA. Georgina M. Mace, Centre for Population Biology, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, United Kingdom. Andy Purvis, Division of Biology, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, United Kingdom; and Centre for Population Biology, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, United Kingdom.
Period of study: 2001 – continuing.
Objectives: 1. To understand the patterns of mammalian biodiversity and extinction risk, and the processes behind them. 2. As necessary steps towards objective 1, to assemble comprehensive information on the comparative ecology and life history, the geographic distribution and the phylogeny of extant mammalian species.
Abstract: Species-richness and extinction risk are distributed unevenly among mammalian taxa and among geographic regions. This project aims to document these patterns across the entire class Mammalia and to use phylogenetic comparative analyses to test a wide range of hypotheses for them. Two research grants in particular supported the work, one entitled “Threatening processes and the conservation status of contemporary mammals” (awarded by NERC to G.M. and A.P.) and one entitled “The macroecology and biodiversity of geographic ranges in mammals” (awarded by NSF to J.L.G.). The combination of the different facets of mammalian biodiversity information has permitted large-scale analyses of (among many others) diversification rates through time and correlates of extinction risk, and identification of species particularly vulnerable to rapid decline if threatening processes intensify.
Sources of funding: NERC grant (NER/A/S/2001/00581) to GM and AP, NSF grant (DEB/0129009) to JLG and funding from Conservation International. KEJ was additionally funded through an Earth Institute Fellowship, Columbia University and the University of Virginia. SAF through the European Commission (FP6 Early-Stage Training Network HOTSPOTS) and KS was funded through a Swiss National Science Foundation fellowship.
B. Specific subproject description
Site description: Data collection from all extant and recently extinct mammalian species.
Experimental design: Data were collected from the literature or from the author’s previously collated databases.
Research methods:
Field/Laboratory: n/a
Data sources: Multiple values of biological trait data were gathered with geo-references where available for extant and recently extinct mammalian species from primary and secondary sources. Data gathering was completed until June 2004. Data were initially gathered systematically from the most relevant journals
and secondary sources (e.g., Mammalian Species, Journal of Mammalogy, Mammalia, Journal of Zoology, Hayssen et al. 1993) and the electronic search engine Web of Science (WOS) and Zoological Record were used to locate further sources for particular variables, clades or individual species. We reduced data duplication by developing a dynamic online source reference library that was consulted prior to searching for new sources or new data entry sessions. Additionally, we incorporated previous data compilations held by the authors, i.e., Small Mammal Life History Database (Mace 1979); Bat Life History Database (Jones 1998); Carnivore Body Size and Life History Database (Gittleman 1982, Bininda-Emonds 1998); unpublished Primate Life History Database from (Purvis et al. 2000); unpublished Population Density Database from (Carbone and Gittleman 2002). In total we used data from 3143 sources for the PanTHERIA data set (see Class V, Section F for a full reference list). We also used spatial databases of mammalian geographic ranges and global climatic and anthropogenic variables (see Class V, Section C for a full description).
Data collection: Biological trait data were collected by 20 different data miners over a period of 24 months from July 2002 to June 2004, using a standardized data input protocol with a Visual Basic interface programmed within Excel (MammalFormv2.xls see Class V, Section D).
Variables: Data were gathered from the literature for 25 types of ecological and life history information for any extant or recently extinct species within class Mammalia (100740 data lines): 1. Activity Cycle; 2. Age at Eye Opening; 3. Age at First Birth; 4. Average Lifespan; 5. Body Mass; 6. Diet; 7. Dispersal Age; 8. Adult Limb Length; 9. Gestation Length; 10. Group Composition & Size; 11. Growth Data; 12. Habitat Layer; 13. Head-Body Length; 14. Interbirth Interval; 15. Litter size; 16. Litters Per Year; 17. Maximum Longevity; 18. Metabolic Rate; 19. Migratory Behaviour; 20. Mortality Data; 21. Population Density; 22. Ranging Behaviour; 23. Sexual Maturity Age; 24. Teat Number; and 25. Weaning Age. 30 specific variables (see Class IV, Table 1) were extracted from the above data types for PanTHERIA from a total of 94729 data lines (before error checking). Additionally, 4 variables were derived from extracted variables within PanTHERIA and 19 variables were calculated from other spatial data sources (see Class V, Section C).
Taxonomy and systematics: Two species-level data output files were generated each using a different taxonomy: (1) (Wilson and Reeder 1993) (PanTHERIA_1-0_WR93_Aug2008.txt) and (2) (Wilson and Reeder 2005) (PanTHERIA_1-0_WR05_Aug2008.txt). SppSynonymID1.0.txt documents how species names or synonyms given in the original data sources were tracked onto these current taxonomies (see Class V, Section B).
Project personnel: Kate E. Jones, Jon Bielby, Marcel Cardillo, Susanne A. Fritz, Justin O’Dell, C. David L. Orme, Kamran Safi, Wes Sechrest, Elizabeth H. Boakes, Chris Carbone, Christina Connolly, Michael J. Cutts, Janine K. Foster, Richard Grenyer, Michael Habib, Christopher A. Plaster, Samantha A. Price, Elizabeth A. Rigby, Janna Rist, Amber Teacher, Olaf R.P. Bininda-Emonds, John L. Gittleman, Georgina M. Mace, and Andy Purvis.
CLASS III. DATA SET STATUS AND ACCESSIBILITY
A. Status
Latest update: 14th June 2004.
Latest archive date: n/a
Metadata status: 8th Aug 2008, metadata are current.
Data verification: Data were carefully checked for quality and consistency (described in Class V, Section B below).
B. Accessibility
Storage location and medium: The species-level data sheets are included here and the raw data are held in an Access database at The Zoological Society of London.
Contact person: Kate E. Jones, Institute of Zoology, Zoological Society of London, Regents Park, London, NW1 4RY, United Kingdom. E-mail: [email protected].
Copyright restrictions: None.
Proprietary restrictions: None.
Costs: None, the authors believe that scientific data collated using public funds should be free for scientific use. We would appreciate researchers citing this paper if using these data.
CLASS IV. DATA STRUCTURAL DESCRIPTORS
A. Data Set File
Identity: (1) PanTHERIA1.0_WR93_Aug2008.txt and (2) PanTHERIA_WR05_Aug2008.txt.
Size: (1) 4629 records, not including header row; (2) 5416 records, not including header row.
Format and storage mode: ASCII text, tab delimited, not compressed.
Header information: Headers describe the content of each column. We use the following abbreviations: MSW93 – Wilson and Reeder (1993) Mammalian Species of the World 2nd Edition; MSW05 – Wilson and Reeder (2005) Mammalian Species of the World 3rd Edition; AET – Actual Evapotransipration Rate; C – centigrade; d – days; dd – decimal degrees; deg – degrees; EXT – extrapolated; g – grams; GR – geographic range; Grp – Group; HuPopDen – Human Population Density; Indiv – Individual; Isl - Island; Lat – Latitude; Len – Length; Long – Longitude; Max – Maximum; Met – Metabolic; Min – Minimum; mLO2hr – milliliters of O2 per hr; mm – millimeters;n/km2 – Number per km2; PET – Potential Evapotranspiration Rate; Precip – Precipitation; Temp – Temperature; and 5p – 5th percentile. Words and abbreviations are separated by underscores. Numeric values at the start of the entries in the header refer to the data type from which the variable was extracted. For example, “5-1_AdultBodyMass_g”, “5” refers to the data type ‘Body Mass’ and “1” that it is the first variable to be extracted from this data type.
Headers included are as follows: MSW93_Order or MSW05_Order; MSW93_Family or MSW05_Family; MSW93_Genus or MSW05_Genus; MSW93_Species or MSW05_Species; MSW93_Binomial or MSW05_Binomial; 1-1_ActivityCycle; 5-1_AdultBodyMass_g; 8-1_AdultForearmLen_mm; 13-1_AdultHeadBodyLen_mm; 2-1_AgeatEyeOpening_d; 3-1_AgeatFirstBirth_d; 18-1_BasalMetRate_mLO2hr; 5-2_BasalMetRateMass_g; 6-1_DietBreadth; 7-1_DispersalAge_d; 9-1_GestationLen_d; 12-1_HabitatBreadth; 22-1_HomeRange_km2; 22-2_HomeRange_Indiv_km2; 14-1_InterBirthInterval_d; 15-1_LitterSize; 16-1_LittersPerYear; 17-1_MaxLongevity_m; 5-3_NeonateBodyMass_g; 13-2_NeonateHeadBodyLen_mm; 21-1_PopulationDensity_n/km2; 10-1_PopulationGrpSize; 23-1_SexualMaturityAge_d; 10-2_SocialGrpSize; 24-1_TeatNumber; 12-2_Terrestriality; 6-2_TrophicLevel; 25-1_WeaningAge_d; 5-4_WeaningBodyMass_g; 13-3_WeaningHeadBodyLen_mm; References; 5-5_AdultBodyMass_g_EXT; 16-2_LittersPerYear_EXT; 5-6_NeonateBodyMass_g_EXT; 5-7_WeaningBodyMass_g_EXT; 26-1_GR_Area_km2; 26-2_GR_MaxLat_dd; 26-3_GR_MinLat_dd; 26-4_GR_MidRangeLat_dd; 26-5_GR_MaxLong_dd; 26-6_GR_MinLong_dd; 26- 7_GR_MidRangeLong_dd; 27-1_HuPopDen_Min_n/km2; 27-2_HuPopDen_Mean_n/km2; 27-3_HuPopDen_5p_n/km2; 27-4_HuPopDen_Change; 28-1_Precip_Mean_mm; 28-2_Temp_Mean_01degC; 29-1_AET_Mean_mm; and 29-2_PET_Mean_mm.
Alphanumeric attributes: Mixed.
Special characters/fields: If no information is available for a given record, this is indicated by -999.
Authentication procedures:
Sums of the numeric columns for
PanTHERIA1.0_WR93_Aug2008: (1) 1-1_ActivityCycle = -2977053; (2) 5-1_AdultBodyMass_g = 622610217.539998; (3) 8-1_AdultForearmLen_mm = -3679100.18999997; (4) 13-1_AdultHeadBodyLen_mm = -1646782.58; (5) 2-1_AgeatEyeOpening_d = -4147029.48; (6) 3-1_AgeatFirstBirth_d = -3824836.7; (7) 18-1_BasalMetRate_mLO2hr = -3028141.87; (8) 5-2_BasalMetRateMass_g = 375079.45; (9) 6-1_DietBreadth = -2467939; (10) 7-1_DispersalAge_d = -4421311.55999999; (11) 9-1_GestationLen_d = -3121092.90999998; (12) 12-1_HabitatBreadth = -1864542; (13) 22-1_HomeRange_km2 = -3759464.11216601; (14) 22-2_HomeRange_Indiv_km2 = -3844306.9899835; (15) 14-1_InterBirthInterval_d = -3706000.22; (16) 15-1_LitterSize -2147613.93000001; (17) 16-1_LittersPerYear = -3727577.23; (18) 17-1_MaxLongevity_m = -3419427.87; (19) 5-3_NeonateBodyMass_g = 7897056.36899; (20) 13-2_NeonateHeadBodyLen_mm = -4323358.91; (21) 21-1_PopulationDensity_n/km2 = -2939604.31021; (22) 10-1_PopulationGrpSize = -2882537.57; (23) 23-1_SexualMaturityAge_d = -2988989.75; (24) 10-2_SocialGrpSize = -3933491.88; (25) 24-1_TeatNumber = -3982491.86; (26) 12-2_Terrestriality = -1951847; (27) 6-2_TrophicLevel = -2469332; (28) 25-1_WeaningAge_d = -3343767.53999999; (29) 5-4_WeaningBodyMass_g = 22498611.15; (30) 13-3_WeaningHeadBodyLen_mm = -4533545.76; (31) 5-5_AdultBodyMass_g_EXT = -3175645.3; (32) 16-2_LittersPerYear_EXT -4236199.01000001; (33) 5-6_NeonateBodyMass_g_EXT = -59305.9999999998; (34) 5-7_WeaningBodyMass_g_EXT = 3973958.5; (35) 26-1_GR_Area_km2 = 7866119721; (36) 26-2_GR_MaxLat_dd = -299314.0548; (37) 26-3_GR_MinLat_dd = -359359.625670002; (38) 26-4_GR_MidRangeLat_dd -329337.231889999; (39) 26-5_GR_MaxLong_dd = -213097.97; (40) 26-6_GR_MinLong_dd = -307813.81389; (41) 26-7_GR_MidRangeLong_dd = -260457.328693106; (42) 27-1_HuPopDen_Min_n/km2 = -294370; (43) 27-2_HuPopDen_Mean_n/km2 = -22370.5697; (44) 27-3_HuPopDen_5p_n/km2 = -282940.5; (45) 27-4_HuPopDen_Change = -394196.188091501; (46) 28-1_Precip_Mean_mm = 25792.15; (47) 28-2_Temp_Mean_01degC = 300029.089999999; (48) 29-1_AET_Mean_mm = 3216946.29000001; and (49) 29-2_PET_Mean_mm = 4755394.55. .
Sums of the numeric columns for
PanTHERIA1.0_WR05_Aug2008.txt: (1) 1-1_ActivityCycle = -3750219; (2) 5-1_AdultBodyMass_g = 627931538.920001; (3) 8-1_AdultForearmLen_mm = -4458863.50999997; (4) 13-1_AdultHeadBodyLen_mm = -2390461.5599999900; (5) 2-1_AgeatEyeOpening_d = -4928216.74; (6) 3-1_AgeatFirstBirth_d = -4597710.77999999; (7) 18-1_BasalMetRate_mLO2hr = -3761625.05; (8) 5-2_ BasalMetRateMass_g = -229229.44; (9) 6-1_DietBreadth = -3246141; (10) 7-1_DispersalAge_d = -5208296.92; (11) 9-1_GestationLen_d = -3898706.93999997; (12) 12-1_HabitatBreadth = -2685754; (13) 22-1_HomeRange_km2 = -4538723.81603595; (14) 22-2_HomeRange_Indiv_km2 = -4580748.63033297; (15) 14-1_InterBirthInterval_d = -4481414.57; (16) 15-1_LitterSize = -2905774.13999999; (17) 16-1_LittersPerYear = -4515784.58; (18) 17-1_MaxLongevity_m = -4199598.31; (19) 5-3_NeonateBodyMass_g = 7124135.98899836; (20) 13-2_NeonateHeadBodyLen_mm = -5109030.42; (21) 21-1_PopulationDensity_n/km2 = -3694898.15021332; (22) 10-1_PopulationGrpSize = -3667882.43; (23) 23-1_SexualMaturityAge_d = -3668760.78999999; (24) 10-2_SocialGrpSize = -4699371.08; (25) 24-1_TeatNumber = -4766713; (26) 12-2_Terrestriality = -2773092; (27) 6-2_TrophicLevel = -3247567; (28) 25-1_WeaningAge_d = -4109794.78999999; (29) 5-4_WeaningBodyMass_g = 21720528.5299999; (30) 13-3_WeaningHeadBodyLen_mm = -5319075.47; (31) 5-5_AdultBodyMass_g_EXT = -3579884.12; (32) 16-2_LittersPerYear_EXT = -5016415.79; (33) 5-6_NeonateBodyMass_g_EXT = -948179.94; (34) 5-7_WeaningBodyMass_g_EXT = 3344775.98; (35) 26-1_GR_Area_km2 = 7755657748.19744; (36) 26-2_GR_MaxLat_dd = -687919.002494141; (37) 26-3_GR_MinLat_dd = -748817.5456675; (38) 26-4_GR_MidRangeLat_dd = -718368.751886152; (39) 26-5_GR_MaxLong_dd = -581739.880000002; (40) 26-6_GR_MinLong_dd = -676884.413893151; (41) 26-7_GR_MidRangeLong_dd = -629313.481315651; (42) 27-1_HuPopDen_Min_n/km2 = -675228; (43) 27-2_HuPopDen_Mean_n/km2 = -378781.01794477; (44) 27-3_HuPopDen_5p_n/km2 = -662777; (45) 27-4_HuPopDen_Change = -789755.285668012; (46) 28-1_Precip_Mean_mm = -334931.200000001; (47) 28-2_Temp_Mean_01degC = -35609.3699999999; (48) 30-1_AET_Mean_mm = 3142189.33; and (49) 30-2_PET_Mean_mm = 4795170.44.
B. Variable definitions
30 specific variables were extracted for PanTHERIA (1–30). See Table 1 for definitions, total number of data lines (before error checking), and species coverage (after error checking) according to the classifications of Wilson and Reeder (1993) (NSpp MSW93) and Wilson and Reeder (2005) (NSpp MSW05). 23 variables (31–53) were derived from these variables or other data sources and are described in Class V, Section C.
TABLE 1. Variable definitions.
Variable: Variable Definition |
Units |
Data lines |
NSpp MSW93 |
NSpp MSW05 |
(1) 1-1_ActivityCycle: Activity cycle of each species measured for non-captive populations; adult or age unspecified individuals, male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. Species were defined as (1) nocturnal only, (2) nocturnal/crepuscular, cathemeral, crepuscular or diurnal/crepuscular and (3) diurnal only. |
NA |
2724 |
1646 |
1659 |
(2) 5-1_AdultBodyMass_g: Mass of adult (or age unspecified) live or freshly-killed specimens (excluding pregnant females) using captive, wild, provisioned, or unspecified populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. |
grams |
17528 |
3473 |
3542 |
(3) 8-1_AdultForearmLen_mm: Total length from elbow to wrist of adult (or age unspecified) live, freshly-killed, or museum specimens using captive, wild, provisioned, or unspecified populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. |
mm |
1952 |
897 |
903 |
(4) 13-1_AdultHeadBodyLen_mm: Total length from tip of nose to anus or base of tail of adult (or age unspecified) live, freshly-killed, or museum specimens using captive, wild, provisioned, or unspecified populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. |
mm |
4941 |
1907 |
1941 |
(5) 2-1_AgeatEyeOpening_d: Age at which both eyes are fully open after birth using captive, wild, provisioned, or unspecified populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities |
days |
710 |
471 |
476 |
(6) 3-1_AgeatFirstBirth_d: Age at which females give birth to their first litter (eutherians), or their young attach to teats (metatherians) or hatch out (monotremes), using non-captive, wild, provisioned, or unspecified populations; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. |
days |
780 |
440 |
445 |
(7) 18-1_BasalMetRate_mLO2hr: Basal metabolic rate of adult (or age unspecified) individual(s) using captive, wild, provisioned, or unspecified populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. Metabolic rate was measured when individual(s) were experiencing neither heat nor cold stress (i.e. are in their thermoneutral zone); are resting and calm; and are post–absorptive (are not digesting or absorbing a meal) and data were only accepted where there was also a measure of body mass for the same individual(s). |
mL.O2/hr |
971 |
559 |
573 |
(8) 5-2_BasalMetRateMass_g: Mass of individual(s) from which the basal metabolic rate was taken. |
grams |
971 |
559 |
573 |
(9) 6-1_DietBreadth: Number of dietary categories eaten by each species measured using any qualitative or quantitative dietary measure, over any period of time, using any assessment method, for non-captive or non-provisioned populations; adult or age unspecified individuals, male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. Categories were defined as vertebrate, invertebrate, fruit, flowers/nectar/pollen, leaves/branches/bark, seeds, grass and roots/tubers. |
No. of diet categories |
4631 |
2153 |
2161 |
(10) 7-1_DispersalAge_d: Age at which young permanently leave the parent, parental group, social group or any associated territories, using non-captive, wild, non-provisioned or unspecified populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. |
days |
175 |
145 |
144 |
(11) 9-1_GestationLen_d: Length of time of non-inactive fetal growth, using captive, wild, provisioned, or unspecified populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. Gestation was measured between specified start and end points as follows: Start points – conception, fertilization, first observed copulation, fertilization, implantation, laying, palpably pregnant, removal of pouch young, capture (except marsupials) or unspecified. End points – birth, hatching or unspecified. |
days |
6537 |
1354 |
1362 |
(12) 12-1_HabitatBreadth: Number of habitat layers used by each species measured using any qualitative or quantitative time measure, for non-captive populations; adult or age unspecified individuals, male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. Categories were defined as above ground dwelling, aquatic, fossorial and ground dwelling. |
No. of habitat layers |
3933 |
2759 |
2724 |
(13) 22-1_HomeRange_km2: Size of the area within which everyday activities of individuals or groups (of any type) are typically restricted, estimated by either direct observation, radio telemetry, trapping or unspecified methods over any duration of time, using non-captive populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. |
km2 |
3269 |
699 |
707 |
(14) 22-2_HomeRange_Indiv_km2: Size of the area within which everyday activities of individuals are typically restricted, estimated by either direct observation, radio telemetry, trapping or unspecified methods over any duration of time, using non-captive populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. |
km2 |
2675 |
624 |
626 |
(15) 14-1_InterBirthInterval_d: The length of time between successive births of the same female(s) after a successful or unspecified litter using non-captive, wild, provisioned, or unspecified populations; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. |
days |
1732 |
687 |
698 |
(16) 15-1_LitterSize: Number of offspring born per litter per female, either counted before birth, at birth or after birth, using captive, wild, provisioned, or unspecified populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. |
no. of offspring |
15020 |
2473 |
2501 |
(17) 16-1_LittersPerYear: Number of litters per female per year using non-captive, wild, provisioned, or unspecified populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. |
no. of litters |
2501 |
896 |
894 |
(18) 17-1_MaxLongevity_m: Maximum adult age measured either through direct observation, capture-recapture estimates, projected from physical wear or unspecified, using captive, wild, provisioned, or unspecified populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; in all localities. |
months |
3294 |
1009 |
1013 |
(19) 5-3_NeonatalBodyMass_g: Mass of live or freshly-killed specimens of infants at either a near term embryonic stage, birth, immediately after birth or up to an age of seven days after birth, using captive, wild, provisioned, or unspecified populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. |
grams |
4308 |
1078 |
1085 |
(20) 13-2_NeonateHeadBodyLen_mm : Total length from tip of nose to anus or base of tail of live, freshly-killed, or museum specimens of infants at either a near term embryonic stage, birth, immediately after birth or up to an age of seven days after birth, using captive, wild, provisioned, or unspecified populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. |
mm |
346 |
226 |
226 |
(21) 21-1_PopulationDensity: Number of individuals per square kilometer, estimated with either direct, indirect or unspecified counts, measured in any area size within a human, ecological or unspecified boundary, over any duration of time, using non-captive, non-provisioned populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. |
number /km2 |
5244 |
929 |
956 |
(22) 10-1_PopulationGrpSize: Number of individuals, adults or definition unspecified in a group that spends the majority of their time in a 24 hour cycle together, measured over any duration of time, using non-captive populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. |
no. of individuals, adults or unspecified |
905 |
386 |
388 |
(23) 23-1_SexualMaturityAge_d: Age when individuals are first physically capable of reproducing, defined as either physically sexually mature, age at first mating or unspecified (males and females), age at first estrus or age at first pregnancy (females only), age at spermatogenesis or age at testes descent (males only), using captive, wild, provisioned, or unspecified populations; male, female, or sex unspecified individuals, primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. |
days |
4680 |
1042 |
1051 |
(24) 10-2_SocialGrpSize: Number of individuals, adults or definition unspecified in a group that spends the majority of their time in a 24 hour cycle together where there is some indication that these individuals form a social cohesive unit, measured over any duration of time, using non-captive populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. |
no. of individuals, adults or unspecified |
1598 |
687 |
707 |
(25) 24-1_TeatNumber: Total number of teats present, using captive, wild, provisioned, or unspecified populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. |
No. of teats |
841 |
639 |
641 |
(26) 12-2_Terrestriality: Degree of terrestriality of each species measured using any qualitative or quantitative time measure, for non-captive populations; adult or age unspecified individuals, male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. Species were defined as (1) fossorial and/or ground dwelling only and (2) above ground dwelling. |
NA |
3933 |
2671 |
2636 |
(27) 6-2_TrophicLevel: Trophic level of each species measured using any qualitative or quantitative dietary measure, over any period of time, using any assessment method, for non-captive or non-provisioned populations; adult or age unspecified individuals, male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. Species were defined as (1) herbivore (not vertebrate and/or invertebrate), (2) omnivore (vertebrate and/or invertebrate plus any of the other categories) and (3) carnivore (vertebrate and/or invertebrate only) |
NA |
4644 |
2153 |
2161 |
(28) 25-1_WeaningAge_d: Age when primary nutritional dependency on the mother ends and independent foraging begins to make a major contribution to the offspring’s energy requirements, measured as either weaning/lactation length, nutritionally independent, first solid food, last observed nursing, age at first flight (bats only), age at pouch exit or length of teat Attachment (marsupials only) or unspecified definition, using captive, wild, provisioned, or unspecified populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. |
days |
4858 |
1147 |
1164 |
(29) 5-4_WeaningBodyMass_g: Mass of live or freshly-killed specimens of weanlings, using captive, wild, provisioned, or unspecified populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. |
grams |
1106 |
481 |
487 |
(30) 13-3_WeaningHeadBodyLen_mm: Total length from tip of nose to anus or base of tail of live, freshly-killed, or museum specimens of weanlings, using captive, wild, provisioned, or unspecified populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. |
mm |
60 |
46 |
47 |
References: Index numbers referring to sources of data for each species according to the list of references given in section F below. |
|
|
|
|
Calculating measures of central tendency
We often obtained more than one valid datum for a particular variable within a species, e.g., from different subspecies, populations, years or localities (mean per species per variable for species with data = 3.3, n = 94729 data lines). For each continuous variable, we calculated a single measure of central tendency for each species from the different estimates (as described in Table 2). Categorical variables and values for maximum longevity were treated differently and are as described in Table 1. Two factors may influence the measures of central tendency obtained. Firstly, outliers may bias the value. We ameliorated this problem by calculating the median of the multiple values for each species, which is less sensitive to outliers than the mean. For variables measured as real numbers (e.g. body mass), we calculated medians of unique values, to guard against duplicate entries, but for the variables that are more often measured as integers, i.e. litters per year and teat number, we calculated medians of all values (see Table 2). Secondly, different combinations of the delimiters used for each variable (e.g., age, sex, captivity status, definition of maturity stage) may influence the values of central tendency obtained in two ways: different combinations of the delimiters may actually give unrealistic information (e.g., using captive data to estimate interbirth intervals), or may merely give systematically different values (e.g. male and female body sizes in sexually dimorphic species), so that a species value will be shaped by the relative frequencies of the different delimiters.
To minimize the first problem of including incorrect values, we removed a priori from each variable the delimiter combinations that would generate unrealistic data (see Table 1). To ameliorate the second problem while still maximizing sample sizes, we estimated species values for those variables that contained delimiters that were likely to produce significantly different values (15 variables, see Table 2) using a general linear model (GLM) setting species and the appropriate delimiters as factors (performed separately for each order for (2) 5-1_AdultBodyMass_g and (16) 15-1_LitterSize, and across the whole class for the other 13 variables). For example, the model fitted to sexual maturity age was: ln(sexual maturity age) = species + sex + sexual maturity definition. This is because males and females may reach maturity at different ages, and the recorded maturity age may also depend on the way it is defined. For each factor, we assigned the level with the largest number of values as the base level, against which the model could calculate offsets for all of the other levels (see Table 2). The offsets were then subtracted from each of the original values to give an adjusted value. For cases where there were single values for a species, we calculated adjusted values for these species using as offsets the mean offset value for all other species. In effect, the GLM can be thought of as converting all of the data into the same currency (that of the base factor), by adding an offset that depends upon the delimiters and which is calculated directly from the data themselves. Hence, for age at sexual maturity the offset for values measured as “age at first pregnancy” is 0.04 (on a log scale), relative to the baseline definition, so each original value measured in this way is reduced by this amount.
For these 15 traits, a central tendency measure was then calculated from the logged adjusted values using unique medians (see Table 2). This method, therefore, takes into account the fact that not all data values for some variables are in the same currency, though they may all contain useful information about the same underlying variable. At the same time, it allows a central tendency measure of a variable to be calculated for all species for which any data have been recorded, avoiding the need to discard valid data. We term this process consolidation, and values generated in this way consolidated values.
In one case it was not clear whether to remove the delimiters a priori or to include them in a GLM (home range area measured for either groups or individuals – see Table 1 and 2). For this case, we consolidated the data first including all values of range measure and performing a GLM with group as a factor ((13) 22-1_HomeRange_km2) and second, excluding the data lines for group home ranges ((14) 22-2_HomeRange_Indiv_km2). Details of the GLM model specifications and the consolidated values for each variable are given in Table 2. The consolidated values analysis was implemented in the program R (R Development Core Team 2005).
TABLE 2. Methods to generate measures of central tendency for species-level traits.
| Variable |
GLM model specification
[method] |
Base factor |
Central tendency measure |
(1) 1-1_ActivityCycle |
None |
None |
Categorical |
(2) 5-1_AdultBodyMass_g |
ln(body mass) = species + sex [within orders] |
Sex = both |
Unique median |
(3) 8-1_AdultForearmLen_mm |
ln(forearm length) = species + sex [across class] |
Sex = unspecified |
Unique median |
(4) 13-1_AdultHeadBodyLen_mm |
ln(head-body length) = species + sex [across class] |
Sex = unspecified |
Unique median |
(5) 2-1_AgeatEyeOpening_d |
None |
None |
Unique median |
(6) 3-1_AgeatFirstBirth_d |
None |
None |
Unique median |
(7) 18-1_BasalMetRate_mLO2hr |
None |
None |
Unique median |
(8) 5-2_BasalMetRateMass_g |
None |
None |
Unique median |
(9) 6-1_DietBreadth |
None |
None |
Sum of diet categories |
(10) 7-1_DispersalAge |
ln(dispersal age) = species + sex [across class] |
Sex = unspecified |
Unique median |
(11) 9-1_GestationLen_d |
ln(gestation length) = species + start point + end point [across class] |
Start point = unspecified, End point = unspecified |
Unique median |
(12) 12-1_HabitatBreadth |
None |
None |
Sum of habitat layers |
(13) 22-1_HomeRange_km2 |
ln(home range) = species + sex + estimation method + range measure [across class] |
Sex = unspecified, Estimation method = unspecified, Range measure = individual |
Unique median |
(14) 22-2_HomeRange_Indiv_km2 |
ln(home range) = species + sex + estimation method [[across class] |
Sex = unspecified, Estimation method = unspecified |
Unique median |
(15) 14-1_InterBirthInterval_d |
None |
None |
Unique median |
(16) 15-1_LitterSize |
ln(litter size) = species + litter size definition [within orders] |
Litter size definition = unspecified |
Unique median |
(17) 16-1_LittersPerYear |
None |
None |
Full median |
(18) 17-1_MaxLongevity |
None |
None |
Maximum |
(19) 5-3_NeonateBodyMass |
ln(body mass) = species + sex + age [across class] |
Sex = unspecified, Age = neonate |
Unique median |
(20) 13-2_NeonateHeadBodyLen_mm |
ln(head-body length) = species + sex + age [across class] |
Sex = unspecified, Age = neonate |
Unique median |
(21) 21-1_PopulationDensity_n/km2 |
ln(population density) = species + estimation method + study area type [across class] |
Estimation method = unspecified, Study area type = unspecified |
Unique median |
(22) 10-1_PopulationGrpSize |
None |
None |
Full median |
(23) 23-1_SexualMaturityAge_d |
ln(sexual maturity age) = species + sex + sexual maturity definition [across class] |
Sex = female, Sexual maturity definition = unspecified |
Unique median |
(24) 10-2_SocialGrpSize |
None |
None |
Full median |
(25) 24-1_Teat Number |
None |
None |
Full median |
(26) 12-2_Terrestriality |
None |
None |
Categorical |
(27) 6-2_TrophicLevel |
None |
None |
Categorical |
(28) 25-1_WeaningAge |
ln(weaning age) = species + weaning age definition [across class] |
Weaning age definition = weaning/lactation length |
Unique median |
(29) 5-4_WeaningBodyMass_g |
ln(body mass) = species + sex [across class] |
Sex = unspecified |
Unique median |
(30) 13-3_WeaningHeadBodyLen_mm |
ln(head-body length) = species + sex [across class] |
Sex = unspecified |
Unique median |
CLASS V. SUPPLEMENTAL DESCRIPTORS
A. Data acquisition.
Data forms: We developed a standardized data input protocol using a Visual Basic interface programmed within Excel (MammalFormv2.xls) and input protocols (MammalFormv2Protocols.pdf), see Class V, Section D. Data lines were outputted as text files and stored in an Access database.
Location of completed data forms: Raw data is held in an Access database at The Zoological Society of London. These data and input protocols are tools we used to develop the database which are no longer current. We are now in the process of updating these protocols and adding additional data through the development of an online database web portal (YouTHERIA) (contact KEJ for further details).
B. Quality assurance/quality control procedures.
The accuracy of these data was verified by a number of methods:
Taxonomic Accuracy: For each datum, its genus, species, subspecies and authority (publication author) was recorded as given in the source. These original taxon names were transformed into valid Latin binomials using the most comprehensive mammalian taxonomy available, that of Wilson and Reeder. We used the two most recent versions (Wilson and Reeder 1993, 2005) producing a separate data table for each (PanTHERIA1.0_WR93_Aug2008.txt and PanTHERIA1.0_WR05_Aug2008.txt). In most cases, there was an exact match between source names and currently valid names. Where there was a difference, spelling discrepancies accounted for the majority of the mismatches. Further differences were caused because the species was described since version compilation. In these cases the names were valid but unrecognized. The remaining differences were caused by changes to the name given in the source (synonymisation). We used the synonym lists given in Wilson and Reeder (1993, 2005) to trace the original name to its current usage. By keeping the taxonomic name given in each datum’s source, we are able to accommodate many changes in taxonomy and classification without losing data. However, in some cases it was not possible to unambiguously determine taxonomic affiliation (2002 data lines for Wilson and Reeder 1993); (2147 data lines for Wilson and Reeder 2005) and these data were not used in any subsequent analysis. This taxonomic conversion file (SppSynonymID1.0.txt) is available from Class V, Section D.
Input Error: At monthly intervals, all newly inputted data were transformed into a common taxonomic and unit currency (e.g., data on population densities converted into individuals per km2 from the different units given in the sources). All new data were checked for obvious aberrant values, and returned to the original data miner for checking and, where appropriate, correction.
Outlier Analysis: We identified data values in the specific variables that were significant outliers from general trends (standardized residual >+3). These outliers were then checked and, where necessary, corrected or excluded from subsequent analysis. Two types of outliers were identified; firstly, an ANOVA was performed with taxonomic level as the grouping variable to identify data lines unusual with respect to their order, family or genus. Secondly, an ANCOVA was performed to identify outliers that were unusual with respect to their allometric relationship with adult body mass. We generated a mass variable for checking the other variables using an earlier version of (2) 5-1_ AdultBodyMass_g that had been checked for taxonomic outliers and summarized into species value medians (but not adjusted). This file was used to check (4) 13-1_AdultHeadBodyLen_mm and (3) 8-1_AdultForearmLen_mm files to create checked, species value medians (but not adjusted) versions of these traits. Then we generated additional mass values from head-body lengths or forearm lengths for species that were missing mass data using the following equations. For MSW93 species: non-bats ln Adult Body Mass = -9.570 + 2.842 * (ln Adult Head-Body Length) and bats ln Adult Body Mass = -8.255 + 2.852 * (ln Adult Forearm Length). For MSW05 species: non-bats ln Adult Body Mass = -9.580 + 2.844 * (ln Adult Head Body Length) and bats ln Adult Body Mass = -8.298 + 2.864 * (ln Adult Forearm Length). Using this combined mass file we performed allometric checks for all the remaining variables except those variables that take qualitative values and could not be checked this way, i.e.; (1) 1-1_ActivityCycle, (9) 6-1_DietBreadth, (12) 12-1_HabitatBreadth, (26) 12-2_Terrestriality and (27) 6-2_TrophicLevel. The outlier analysis was implemented in R (R Development Core Team 2005).
Data Duplication: As our data were collected from both primary and secondary literature sources, data from primary sources may be duplicated within secondary sources. This is easy to identify when the secondary source lists all primary data separately as the duplicate values will be identical. However, when the secondary source summarizes the data value for a number of primary sources then the value will be different and duplication harder to identify. To ameliorate these problems we firstly removed from subsequent analysis non-obvious duplications that we knew of (e.g., bat body mass data in (Smith et al. 2003) is all from the primary data in (Jones 1998) which is already incorporated into the database). Secondly, we used techniques to calculate a value of central tendency that minimized the effects of identical duplicate values (see Calculating measures of central tendency in Class IV, Section B).
C. Related material
We used our existing variables and other spatial databases to calculate 23 additional variables.
Derived variables from existing data. Many of our variables are highly intercorrelated (i.e., one explains a high degree of variation in the other). This is particularly true of size variables in general (Calder 1996). For example, head-body length is an excellent predictor of body mass. We used this fact to estimate fitted values for some variables by fitting across-species GLMs using the species medians of the consolidated values (see Class IV, Section B) for the following 4 variables: (31) 5-5_AdultBodyMass_g_EXT (368 MSW93 species, 394 MSW05 species); (32) 16-2_LittersPerYear_EXT (388, 394 species); (33) 5-6_NeonateBodyMass_g_EXT (22, 24 species); (34) 5-7_WeaningBodyMass_g_EXT (24, 25 species) (see Table 3 for details of the models). The analysis was implemented in R (R Development Core Team 2005).
Table 3. Models for Extrapolated Variables. Which of the three bat models was used depended on whether a species had a value for adult head-body length, adult forearm length, or both.
Derived variables from other data. We derived 19 variables using data from other sources. Firstly, we used digital geographic range maps of all extant, non-marine mammals from Sechrest (2003) and converted them to the two taxonomies used: Wilson and Reeder (1993, 4271 species) and Wilson and Reeder (2005, 4668 species). These ranges were used to generate 7 measures of geographic range extent and occupancy. Spatial analyses were performed using ArcGIS (version 9.0) (ESRI 2005) for areas and R (R Development Core Team 2005) for geographic coordinates. The calculated variables were as follows: (35) 26-1_GR_Area_km2 (4271, 4668 species), calculated using the total extent of a species range with a global equal-area projection (Mollweide); (36) 26-2_GR_MaxLat_dd (4271, 4668 species), maximum latitudinal extent of each species range calculated using a global geographic projection (decimal degrees); (37) 26-3_GR_MinLat_dd (4271, 4668 species), minimum latitudinal extent of each species range calculated using a global geographic projection (decimal degrees); (38) 26-4_GR_MidRangeLat_dd (4271, 4668 species), median latitudinal extent of each species range calculated using a global geographic projection (decimal degrees); (39) 26-5_GR_MaxLong_dd (4271, 4668 species), maximum longitudinal extent of each species range calculated using a global geographic projection (decimal degrees); (40) 26-6_GR_MinLong_dd (4271, 4668 species), minimum longitudinal extent of each species range calculated using a global geographic projection (decimal degrees); (41) 26-7_GR_MidRangeLong_dd (4271, 4668 species), median longitudinal extent of each species range calculated using a global geographic projection (decimal degrees). Secondly, we generated a number of variables for each species describing the anthropogenic and environmental conditions within each geographic range based on the extent of the digital species range maps. The species ranges were first gridded at 0.5 degrees using a global geographic projection and species were scored as present in each cell if any of the range intersected that cell. We then calculated summary statistics for each species by summarizing the value for each anthropogenic and environmental variable (gridded to the same extent) for all the cells the species was present. Except for the variables 27-1_HuPopDen_Min_n/km2 and 27-3_HuPopDen_5p_n/km2, we adjusted the summary statistics for each variable for the fact that area varies with latitude by multiplying each cell by the area and then dividing by the total area of cells for that variable for each species. The anthropogenic and environmental variables calculated across the geographic ranges of each species ranges were as follows: (46) 27-1_HuPopDen_Min_n/km2 (4271, 4668 species), minimum human population density (persons per km2) using the Gridded Population of the World (GPW) (CIESIN and CIAT 2005) for 1995; (47) 27-2_HuPopDen_Mean_n/km2 (4271, 4668 species), mean human population density (persons per km2) using the Gridded Population of the World (GPW) (CIESIN and CIAT 2005) for 1995; (48) 27-3_HuPopDen_5p_n/km2 (4271, 4668 species), 5th percentile human population density (persons per km2) using the Gridded Population of the World (GPW) (CIESIN and CIAT 2005) for 1995; (49) 27-4_HuPopDen_Change (4234, 4625 species), mean rate of increase in human population density using the Gridded Population of the World (GPW) (CIESIN and CIAT 2005) for 1990 and 1995 as: (1995–1990)/1990; (50) 28-1_Precip_Mean_mm (4160, 4533 species) mean monthly precipitation (mm) calculated using data from
ftp://ftp.ngdc.noaa.gov/Solid_Earth/Ecosystems/GEDII_a/datasets/a03/lc.htm; (51) 28-2_Temp_Mean_01degC (4160, 4533 species), mean monthly temperature (0.1°C) calculated using data from
ftp://ftp.ngdc.noaa.gov/Solid_Earth/Ecosystems/GEDII_a/datasets/a03/lc.htm; (52) 30-1_AET_Mean_mm (3973, 4305 species), mean monthly AET (Actual Evapotranspiration Rate) from 1920 to 1980 (mm) calculated using the Global Resource Information Database of UNEP and is available from
http://www.grid.unep.ch/data/grid/gnv183.php), and (53) 30-2_PET_Mean_mm (3973, 4305 species), mean monthly PET (Potential Evapotranspiration Rate) from 1920 to 1980 (mm) calculated using the Global Resource Information Database of UNEP and is available from
http://www.grid.unep.ch/data/grid/gnv183.php).
D. Computer programs and data processing algorithms.
The following files were developed to collate or generate our species-level data sheets:
(1) MammalFormv2.1.xls. A Visual Basic program within Excel that uses a standardized data input protocol to generate text files which are imported into PanTHERIA.
(2) MammalFormv2.1.pdf. Protocols to inputting data into MammalForm v2.
(3) SppSynonymID1.0.txt. Taxonomic conversion file used to convert names in original sources into the taxonomy of Wilson and Reeder (1993) and Wilson and Reeder (2005).
(4) MammalFormVB.zip. Provides VBA code for the data input forms, along with a binary file which contains the layout of each form and fields within it. MammalForm.bas contains the bulk of the code for the main form.
E. Archiving: n/a
F. Publications and results
Publications citing the data set
These data and earlier versions of these data sets have been cited in the following publications: Jones et al. (2005); Cardillo et al. (2005); Cardillo et al. (2006); Ezenwa et al. (2006); Grenyer et al. (2006); Jeschke and Strayer (2006); Bielby et al. (2007); Lindenfors et al. (2007a) Lindenfors et al. (2007b); Pedersen et al. (2007); Price and Gittleman (2007); Cardillo et al. (2008); Davies et al. (2008); Shai et al. (2008); Welch et al. (2008); Jones et al. (in press); Cardillo and Purvis (in preparation). This version of PanTHERIA differs from earlier versions because of minor corrections in the values for the related material. Earlier versions can be obtained from the first author on request.
Reference list for the data set: References are given as indexed values in accordance with the following reference list.
1. Abbas, A. 1991. Feeding Strategy of Coypu (Myocastor coypus) in Central Western France. Journal of Zoology 224:385-401.
2. Abe, Y. 1931. A Synopsis of the Leporine Mammals of Japan. Journal of Science of the Hiroshima University, Series B, Zoology 1:45-63.
3. Abenspergtraun, M., C. R. Dickman, and E. S. Deboer. 1991. Patch Use and Prey Defense in a Mammalian Myrmecophage, the Echidna (Tachyglossus aculeatus) (Monotremata, Tachyglossidae) - a Test of Foraging Efficiency in Captive and Free-Ranging Animals. Journal of Zoology 225:481-493.
4. Abenspergtraun, M., and E. S. Deboer. 1992. The Foraging Ecology of a Termite-Eating and Ant-Eating Specialist, the Echidna Tachyglossus aculeatus (Monotremata, Tachyglossidae). Journal of Zoology 226:243-257.
5. Acevedo, A., and S. Burkhart. 1998. Seasonal distribution of bottlenose (Tursiops truncatus) and pan-tropical spotted (Stenella attenuata) dolphins (Cetacea: Delphinidae) in Golfo Dulce, Costa Rica. Revista de Biologia Tropical 46.
6. Acevedo, G. A. 1999. Aerial behavior is not a social facilitator in bottlenose dolphins hunting in small groups. Journal of Mammalogy 80:768-776.
7. Acharjyo, L. N., and S. Mohapatra. 1978. A note on the breeding and longevity of the Indian Pangolin (Manis crassicaudata) in captivity. Journal of the Bombay Natural History Society 75:921-923.
8. Acharya, L. 1992. Epomophorus wahlbergi. Mammalian Species 394:1-4.
9. Acosta, C. E., and R. D. Owen. 1993. Koopmania concolor. Mammalian Species 429:1-3.
10. Acosta, H., J. Cavelier, and S. Londono. 1996. Contribution to the biological knowledge of the mountain tapir Tapirus pinchaque in the Central Andes of Colombia. Biotropica 28:258-266.
11. Adam, M. D., and J. P. Hayes. 1998. Arborimus pomo. Mammalian Species 593:1-5.
12. Adam, P. J. 1999. Choloepus didactylus. Mammalian Species 621:1-8.
13. Adams, W. H. 1956. The Nutria in coastal Louisiana. Proceedings of La. Academy of Science. 19:28-41.
14. Adams, C. E. 1976. Measurements and characteristics of fox squirrel, Sciurus niger rufiventer, home ranges. American Midland Naturalist 95:211-215.
15. Adams, J. 1989. Pteronotus davyi. Mammalian Species 346:1-5.
16. Addink, M., H. M. Garcia, and B. Couperus. 1997. A note on life-history parameters of the Atlantic white-sided dolphin (Lagenorhynchus acutus) from animals bycaught in the northeastern Atlantic. Report of the International Whaling Commission.
17. Aderounmu, E. A. 1973. Parasites of the straw-coloured fruit-bat at the University of Ife. The Nigerian Field:138-141.
18. Adler, G. H., M. Endries, and S. Piotter. 1997. Spacing patterns within populations of a tropical forest rodent, Proechimys semispinosus, on five Panamanian islands. Journal of Zoology 241:43-53.
19. Adler, G. H., M. T. Becerra, F. Prado, and B. L. Travi. 2000. Ecology of spiny rats, Proechimys canicollis, in northern Colombia. Mammalia 64:145-153.
20. Adler, G. H. 2000. Tropical tree diversity, forest structure and the demography of a frugivorous rodent, the spiny rat (Proechimys semispinosus). Journal of Zoology 250:57-74.
21. Advani, R. 1983. Reproductive biology of Pipistrellus minus minus (Wroughton) in the Indian desert. Zeitschrift fur Saugetierkunde 48:211-217.
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300. Best, T. L. 1986. Dipodomys elephantinus. Mammalian Species 255:1-4.
301. Best, T. L. 1988. Dipodomys nelsoni. Mammalian Species 326:1-4.
302. Best, T. L. 1988. Dipodomys spectabilis. Mammalian Species 311:1-10.
303. Best, T. L., N. J. Hildreth, and C. Jones. 1989. Dipodomys deserti. Mammalian Species 339:1-8.
304. Best, T. L., C. L. Lewis, K. Caesar, and A. S. Titus. 1990. Ammospermophilus interpres. Mammalian Species 365:1-6.
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308. Best, T. L. 1991. Dipodomys nitratoides. Mammalian Species 381:1-7.
309. Best, T. L., and H. H. Thomas. 1991. Dipodomys insularis. Mammalian Species 374:1-3.
310. Best, T. L., and H. H. Thomas. 1991. Spermophilus madrensis. Mammalian Species 378:1-2.
311. Best, T. L. 1992. Dipodomys venustus. Mammalian Species 403:1-4.
312. Best, P. B., and H. Ruther. 1992. Aerial photogrammetry of southern right whales, Eubalaena australis. Journal of Zoology 228:595-614.
313. Best, T. L. 1992. Dipodomys margaritae. Mammalian Species 400:1-3.
314. Best, T. L., J. L. Bartig, and S. L. Burt. 1992. Tamias canipes. Mammalian Species 411:1-5.
315. Best, T. L., and J. A. Lackey. 1992. Chaetodipus artus. Mammalian Species 418:1-3.
316. Best, T. L., and J. A. Lackey. 1992. Chaetodipus pernix. Mammalian Species 420:1-3.
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318. Best, T. L. 1993. Tamias palmeri. Mammalian Species 443:1-6.
319. Best, T. L. 1993. Tamias ruficaudus. Mammalian Species 452:1-7.
320. Best, T. L. 1993. Tamias sonomae. Mammalian Species 444:1-5.
321. Best, T. L., S. L. Burt, and J. L. Bartig. 1993. Tamias durangae. Mammalian Species 437:1-4.
322. Best, T. L. 1993. Chaetodipus lineatus. Mammalian Species 451:1-3.
323. Best, T. L. 1993. Perognathus inornatus. Mammalian Species 450:1-5.
324. Best, T. L., and T. H. Henry. 1993. Lepus callotis. Mammalian Species:1-6.
325. Best, T. L., and T. H. Henry. 1994. Lepus arcticus. Mammalian Species:1-9.
326. Best, T. L., and T. H. Henry. 1994. Lepus othus. Mammalian Species:1-5.
327. Best, T. L. 1994. Chaetodipus nelsoni. Mammalian Species 484:1-6.
328. Best, T. L., R. G. Clawson, and J. A. Clawson. 1994. Tamias panamintinus. Mammalian Species 468:1-7.
329. Best, T. L., R. G. Clawson, and J. A. Clawson. 1994. Tamias speciosus. Mammalian Species 478:1-9.
330. Best, T. L., and N. J. Granai. 1994. Tamias merriami. Mammalian Species 476:1-9.
331. Best, T. L., and N. J. Granai. 1994. Tamias obscurus. Mammalian Species 472:1-6.
332. Best, T. L., and M. P. Skupski. 1994. Perognathus flavus. Mammalian Species 471:1-10.
333. Best, T. L., and M. P. Skupski. 1994. Perognathus merriami. Mammalian Species 473:1-7.
334. Best, T. L. 1994. Perognathus alticolus. Mammalian Species 463:1-4.
335. Best, T. L., S. L. Burt, and J. L. Bartig. 1994. Tamias quadrivittatus. Mammalian Species 466:1-7.
336. Best, T. L. 1995. Sciurus alleni. Mammalian Species 501:1-4.
337. Best, T. L. 1995. Sciurus deppei. Mammalian Species 505:1-5.
338. Best, T. L. 1995. Sciurus variegatoides. Mammalian Species 500:1-6.
339. Best, T. L. 1995. Spermophilus adocetus. Mammalian Species 504:1-4.
340. Best, T. L. 1995. Spermophilus mohavensis. Mammalian Species 509:1-7.
341. Best, T. L., and G. Ceballos. 1995. Spermophilus perotensis. Mammalian Species 507:1-3.
342. Best, T. L., and S. Riedel. 1995. Sciurus arizonensis. Mammalian Species 496:1-5.
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G. History of data set usage
December 2003. Patrik Lindenfors and Charlie Nunn requested the use of the carnivore trait data for the project ‘Host correlates of parasite characteristics in carnivores’ (analysis outputs: Lindenfors et al. 2007b).
July 2004. Sonia Altzier requested use of hoofed mammal trait data for a project ‘Host correlates of the diversity, characteristics and prevalence of parasites in hoofed mammals’ (analysis outputs: Ezenwa et al. 2006, Pedersen et al. 2007).
August 2004. Chris Carbone requested the use of the carnivore population density and diet trait data for the project ‘Patterns in population density and body mass in meat-eating carnivores’.
Jan 2005. Jonathan Jeschke and Dave Strayer requested the use of European and North American mammal trait data for the project ‘Species introductions’ (analysis outputs: Jeschke and Strayer 2006).
February 2006. Shai Meiri requested the use of the mammal trait data for the project ‘Body sizes of insular and mainland mammals’ (analysis outputs: Meiri et al. 2008).
May 2005. Patrik Lindenfors requested the use of the mammal trait data for the project ‘Sexual Size Dimorphism in Mammals’ (analysis outputs: Lindenfors et al. 2007a).
May 2005 - John Welch and Lindell Bromham requested the use of mammal trait data for the project ‘Gene and lineage effects in rates of molecular evolution’ {analysis outputs: \Welch, 2008 #163}.
March 2006 – Simon Goodman requested the use mammal trait data for the project ‘Comparative analysis of immunophysiological parameters with ecological and life history correlates of disease exposure in ungulates’.
January 2007 - Tim Blackburn and Craig White requested use of the mammalian trait data for the project ‘Population energy use’.
January 2007 - Vincent Savolainen and Thomas Galewski requested the use of the mammalian trait data for the project ‘Sexual selection and horn lengths in bovids’.
H. Data set update history
Review history: n/a
Questions and comments from secondary users: n/a
ACKNOWLEDGMENTS
This work was financially supported through NSF (Grant No. DEB/0129009); NERC (Grant No. NER/A/S/2001/00581); Earth Institute Fellowship, Columbia University and University of Virginia (KEJ); and the European Commission (FP6 Early-Stage Training Network HOTSPOTS) (SAF). We also thank Louise Endler, Sophie Gauss and Paul Racey for assistance and two anonymous referees for comments on the manuscript.
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