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Data from: Patterns and drivers of knowledge gaps in global databases of mammal traits

Llorente Culebras, Sonia 1 ; Correia, Ricardo2; Menegotto, André3 1; Santos, Ana M. C.1; Ladle, Richard J.4

Published Apr 07, 2026 on Dryad. https://doi.org/10.5061/dryad.05qfttfdq

Abstract

This dataset contains the data and R code used in the manuscript "Patterns and drivers of gaps in mammal functional trait databases". Specifically, this dataset is composed of:

Trait data for 5,706 terrestrial mammal species compiled from seven global trait databases,
Mammals phylogeny (Upham et al., 2019)
Information collected about some factors potentially influencing the variability in available trait information across different mammal species from relevant sources, and
R code used to perform the GLM regression models.

Dataset DOI: 10.5061/dryad.05qfttfdq

Description of the data and file structure

TRAIT DATA

Metadata of the data used

Trait data compilation for all terrestrial mammal species (5,706) present in the IUCN Red List (version 2023.1) is provided here. The trait data used in this study were compiled from eight global traits databases, namely Amniote life-history database (Myhrvold et al., 2015), Elton traits (Wilman et al., 2014), COMBINE (Soria et al., 2021), Phylacine (Faurby et al., 2018), and the trait compilations of different publications: Cox et al. (2021), Gainsbury et al. (2018), and Pacifici et al. (2013). The data extracted is distributed in eight Excel files described below:

1_AMNIOTE_01.xlsx

Data sheet contains the trait information available in Amniote life-history database (Myhrvold et al., 2015) for the 5,706 mammals species considered in this study. In Matrix_01 sheet, the cells that had trait information in the data sheet have been replaced by 1 to have the matrix of absence/presence of information.

A description of the variables and abbreviations used is included in Variables_info sheet.

The mark used for decimal points is a point (.).

2_ELTON_01.xlsx

Data sheet contains the trait information available in Elton traits (Wilman et al., 2014) for the 5,706 mammals species considered in this study. In Matrix_01 sheet, the cells that had trait information in the data sheet have been replaced by 1 to have the matrix of absence/presence of information. Diet categories of Data sheet have been concatenated in the trait “DIET” in Matrix_01 sheet, as well as Activity. A description of the variables is included in Variables_info sheet.

The mark used for decimal points is a point (.).

3_COMBINE_01.xlsx

Data sheet contains the trait information available in COMBINE (Soria et al., 2021) for the 5,706 mammals species considered in this study. In Matrix_01 sheet, the cells that had trait information in the data sheet have been replaced by 1 to have the matrix of absence/presence of information. Diet categories of Data sheet have been concatenated in the trait “Diet” in Matrix_01 sheet, as well as freshwater, marine, terrestrial_non.volant and terrestrial_volant which have been concatenated as "habitat_type". A description of the variables is included in Variables_info sheet.

The mark used for decimal points is a point (.).

4_PHYLACINE_01.xlsx

Data sheet contains the trait information available in Phylacine (Faurby et al., 2018) for the 5,706 mammals species considered in this study. In Matrix_01 sheet, the cells that had trait information in the data sheet have been replaced by 1 to have the matrix of absence/presence of information. Only reported data have been considered. Diet categories have been merged in the trait “diet” in Matrix_01 sheet. Habitat use categories have been merged in the trait “habitat” in Matrix_01 sheet. A description of the variables is included in Variables_info sheet.

The mark used for decimal points is a point (.).

5_COX_01.xlsx

Data sheet contains the trait information available in Cox et al. (2021) for the 5,706 mammals species considered in this study. In Matrix_01 sheet, the cells that had trait information in the data sheet have been replaced by 1 to have the matrix of absence/presence of information. Only reported data have been considered. A description of the variables is included in Variables_info sheet.

The mark used for decimal points is a point (.).

6_GAINSBURY_01.xlsx

Data sheet contains the trait information available in Gainsbury et al. (2018) for the 5,706 mammals species considered in this study. In Matrix_01 sheet, the cells that had trait information in the data sheet have been replaced by 1 to have the matrix of absence/presence of information. Only reported data have been considered. Diet categories have been merged in the trait “diet”. A description of the variables is included in Variables_info sheet.

The mark used for decimal points is a point (.).

7_GL_01.xlsx

Data sheet contains the trait information available in Pacifici et al. (2013) for the 5,706 mammals species considered in this study. In Matrix_01 sheet, the cells that had trait information in the data sheet have been replaced by 1 to have the matrix of absence/presence of information. Only reported data have been considered. A description of the variables is included in Variables_info sheet.

The mark used for decimal points is a point (.).

DRIVERS

matriz_drivers_update.csv

Information collected about factors potentially influencing the variability in available trait information across different mammal species from relevant sources (see Table 1 in main text of the manuscript). This matrix includes information on the following variables:

Variable	Description
spp_ID	Species ID
scientificName	Species scientific name
genus	Species genus
family	Species family
Order	Species Order
year_description	Year of the first description of a species
Use_trade	Indicates whether individuals of a species (whole, parts or products) are harvested for human use (0 = no, 1 = yes)
redlistCategory	IUCN threat status
Range_Area_KM2	Area (km2) of species’ distribution range
maxGDP	Maximum Gross domestic product (GDP) of the species distribution range (USD, Purchasing Power Parity (PPP)-adjusted)
cityDist	Minimum travel time (min) to the nearest city
islEndemic	Indicates whether a species is island endemic or not (0 = no, 1 = yes)
percPAs	Percentage of the distribution range of each species that overlap with protected areas
Research_capacity_countries_ocurrence	Sum of the Scimago publication proportion of all the countries in which the species is distributed
CITES	Species included (1) or not (0) in the species list of Convention on International Trade in Endangered Species (CITES)
scopus_hits	The number of all scientific publications indexed by Scopus that contain in their title, abstract or keywords the scientific name or any known scientific synonyms of the species
AltMin	The minimum altitude at which this species may be found (m)
AltMax	The maximum altitude at which this species may be found (m)
AltRange	The altitudinal range at which this species may be found (m)
Continentes	Continents where the species is present
N_traits	Number of traits with available data for each species
Prop	Proportion of of traits with available data for each species

PHYLOGENY

output.nex

Mammals phylogenetic tree from Upham et al. (2019)

R CODE

PhyloSig_GLMM.R

R code used to perform phylogenetic signal analysis and the GLM regression models (data needed to perform the analysis contained in matriz_drivers._update.csv).

References

Cox, D. T. C., Gardner, A. S., & Gaston, K. J. (2021). Diel niche variation in mammals associated with expanded trait space. Nature Communications, 12(1), 1753. https://doi.org/10.1038/s41467-021-22023-4

Faurby, S., Davis, M., Pedersen, R. Ø., Schowanek, S. D., Antonelli, A., & Svenning, J.-C. (2018). PHYLACINE 1.2: The phylogenetic atlas of mammal macroecology. Ecology, 99(11), 2626. https://doi.org/10.1002/ecy. 2443

Gainsbury, A. M., Tallowin, O. J. S., & Meiri, S. (2018). An updated global data set for diet preferences in terrestrial mammals: testing the validity of extrapolation. Mammal Review, 48(3), 160–167. https://doi.org/10.1111/mam.12119

Jones, K. E., Bielby, J., Cardillo, M., Fritz, S. A., O’Dell, J., Orme, C. D. L., Safi, K., Sechrest, W., Boakes, E. H., Carbone, C., Connolly, C., Cutts, M. J., Foster, J. K., Grenyer, R., Habib, M., Plaster, C. A., Price, S. A., Rigby, E. A., Rist, J., … & Purvis, A. (2009). PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology, 90(9), 2648. https://doi.org/https://doi.org/10.1890/08-1494.1

Myhrvold, N. P., Baldridge, E., Chan, B., Sivam, D., Freeman, D. L., & Ernest, S. K. M. (2015). An amniote life-history database to perform comparative analyses with birds, mammals, and reptiles. Ecology, 96(11), 3109. https://doi.org/10.1890/15-0846R.1

Pacifici, M., Santini, L., Di Marco, M., Baisero, D., Francucci, L., Grottolo Marasini, G., Visconti, P., & Rondinini, C. (2013). Database on generation length of mammals. Nature Conservation, 5, 89-94. http://doi.org/10.5061/dryad.gd0m3

Soria, C. D., Pacifici, M., Di Marco, M., Stephen, S. M., & Rondinini, C. (2021). COMBINE: a coalesced mammal database of intrinsic and extrinsic traits. Ecology, 102(6), e03344. https://doi.org/10.1002/ecy.3344

Upham, N. S., Esselstyn, J. A., & Jetz, W. (2019).Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation. PLOS Biology, 17(12), e3000494. https://doi.org/10.1371/journal.pbio.3000494

Wilman, H., Belmaker, J., Simpson, J., de la Rosa, C., Rivadeneira, M. M. & Jetz, W. (2014). EltonTraits 1.0: Species-level foraging attributes of the world's birds and mammals. Ecology, 95(7), 2027. https://doi.org/10.1890/13-1917.1n

Code/software

R Core Team (2023). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.

Access information

Trait Data was derived from the following sources:

Cox, D. T. C., Gardner, A. S., & Gaston, K. J. (2021). Diel niche variation in mammals associated with expanded trait space. Nature Communications, 12(1), 1753. https://doi.org/10.1038/s41467-021-22023-4
Faurby, S., Davis, M., Pedersen, R. Ø., Schowanek, S. D., Antonelli, A., & Svenning, J.-C. (2018). PHYLACINE 1.2: The phylogenetic atlas of mammal macroecology. Ecology, 99(11), 2626. https://doi.org/10.1002/ecy. 2443
Gainsbury, A. M., Tallowin, O. J. S., & Meiri, S. (2018). An updated global data set for diet preferences in terrestrial mammals: testing the validity of extrapolation. Mammal Review, 48(3), 160–167. https://doi.org/10.1111/mam.12119
Myhrvold, N. P., Baldridge, E., Chan, B., Sivam, D., Freeman, D. L., & Ernest, S. K. M. (2015). An amniote life-history database to perform comparative analyses with birds, mammals, and reptiles. Ecology, 96(11), 3109. https://doi.org/10.1890/15-0846R.1
Pacifici, M., Santini, L., Di Marco, M., Baisero, D., Francucci, L., Grottolo Marasini, G., Visconti, P., & Rondinini, C. (2013). Database on generation length of mammals. Nature Conservation, 5, 89-94. http://doi.org/10.5061/dryad.gd0m3
Soria, C. D., Pacifici, M., Di Marco, M., Stephen, S. M., & Rondinini, C. (2021). COMBINE: a coalesced mammal database of intrinsic and extrinsic traits. Ecology, 102(6), e03344. https://doi.org/10.1002/ecy.3344
Wilman, H., Belmaker, J., Simpson, J., de la Rosa, C., Rivadeneira, M. M. & Jetz, W. (2014). EltonTraits 1.0: Species-level foraging attributes of the world's birds and mammals. Ecology, 95(7), 2027. https://doi.org/10.1890/13-1917.1n

Drivers Data was derived from the following sources:

SCImago (2024). SJR — SCImago Journal & Country Rank. Retrieved 29-02-2024, from http://www.scimagojr.com
Scopus (2024). Scopus: Comprehensive, multidisciplinary, trusted abstract and citation database. https://www.scopus.com
UNEP-WCMC & IUCN (2024). Protected Planet: The World Database on Protected Areas (WDPA) and World Database on Other Effective Area-based Conservation Measures (WD-OECM) [Online], February 2024, Cambridge, UK: UNEP-WCMC and IUCN. Available at: www.protectedplanet.net
Nelson, A., Weiss, D. J., Etten, J. Van, Cattaneo, A., Mcmenomy, T. S., & Koo, J. (2019). A suite of global accessibility indicators. Scientific Data, 6, 1–9. https://doi.org/10.1038/s41597-019-0265-5
Martin, M., Sayre, R., VanGraafeiland, K., McDermott Long, O.,Weatherdon, L., Will, D., Spatz, D. R., & Holmes, N. D. (2020). Global islands. In Encyclopedia of the World's Biomes, M. I. Goldstein and W. B. DellaSala (Eds.). Pp 47-50. Elsevier. https://doi.org/10.1016/B978-0-12-409548-9.12475-3
IUCN (2024). The IUCN Red List of Threatened Species. Version 2024-1. https://www.iucnredlist.org
Becker, J. J., Sandwell, D. T., Smith, W. H. F., Braud, J., Binder, B., Depner, J., Fabre, D., Factor, J., Ingalls, S., Kim, S.-H., Ladner, R., Marks, K., Nelson, S., Pharaoh, A., Trimmer, R., Von Rosenberg, J., Wallace, G., & Weatherall, P. (2009). Global Bathymetry and Elevation Data at 30 Arc Seconds Resolution: SRTM30_PLUS. Marine Geodesy, 32(4), 355–371. https://doi.org/10.1080/01490410903297766