This entry is inspired by conversations and discussions that occurred during the recent British Ecological Society Macroecology Special Interest Group meeting in Oxford (7-8 July 2016). Macroecologists often rely on data collected by other people, which can be compiled into large databases covering wide areas and many species. These data are becoming increasingly available, but it is not always straightforward to find them. There is much potentially valuable information out there, but if we do not know about it then its value is “wasted”. So I decided to put together a list of resources I have used or know about. This a non-(yet)comprehensive list which includes databases describing trait data for terrestrial vertebrate species. Because I work mostly with mammals, there is probably a better representation of mammalian sources. The databases listed here are “freely” available (although some are appendices in subscription journals which may require to request copies from the authors). All include data from multiple species, generally describe several traits, and some provide data from multiple locations or reflect multiple records per species.
Please feel free to add comments to this entry or email me if you know about additional resources that could be added. This list is work-in-progress and it would be great to make it better. For now, I am hoping it may be useful for others; if nothing else, it has helped me organize my own folders.
Species-level data for diverse taxa (not just mammals)
- Animal Diversity Web. Myers, P., R. Espinosa, C. S. Parr, T. Jones, G. S. Hammond, and T. A. Dewey. 2016. The Animal Diversity Web (online). Thanks to Dieter Lukas for pointing out a way to search multiple species here.
- AnAge database. Tacutu, R., Craig, T., Budovsky, A., Wuttke, D., Lehmann, G., Taranukha, D., Costa, J., Fraifeld, V. E., de Magalhaes, J. P. (2013) Human Ageing Genomic Resources: Integrated databases and tools for the biology and genetics of ageing. Nucleic Acids Research 41:D1027-D1033. In addition to online searches, a zipped tab-delimited text file with the complete dataset can be downloaded here.
- Intraspecific thermal response curves for diverse taxa including mammals, birds, reptiles and amphibian. Dell, A. I., Pawar, S. and Savage, V. M. (2013) The thermal dependence of biological traits. Ecology, 94: 1205–1206. DATA HERE
- Trait data for birds, mammals and reptiles. Myhrvold, N. P., Baldridge, E., Chan, B., Sivam, D., Freeman, D. L. and Ernest, S. K. M. (2015) An amniote life-history database to perform comparative analyses with birds, mammals, and reptiles. Ecology, 96: 3109. DATA HERE
- Dietary preferences and body size for birds and mammals – EltonTraits. Wilman, H., Belmaker, J., Simpson, J., de la Rosa, C., Rivadeneira, M. M. and Jetz, W. (2014), EltonTraits 1.0: Species-level foraging attributes of the world’s birds and mammals. Ecology, 95: 2027. DATA HERE Note that some values are derived from genus or family conspecifics.
- Trait data for amphibians. Bielby, J., Cardillo, M., Cooper, N. Purvis, A. (2009) Modelling extinction risk in multispecies data sets: phylogenetically independent contrasts versus decision trees. Biodiversity and Conservation 19: 113-127.
Species-level and population-level data for mammals
- Species-level and individual study (some population-level) trait data for mammals – PanTHERIA 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., Teacher, A., Bininda-Emonds, O. R. P., Gittleman, J. L., Mace, G. M. and Purvis, A. (2009) PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology, 90: 2648. Both the species level and raw (individual study records) can be downloaded at the Utheria website. I have made several corrections to the raw files in the supplementary materials of these two papers published in Ecology Letters and American Naturalist. If you do not have access to these files email me for a copy.
- Species-level dietary preferences for mammals – MammalDiet. Kissling WD, Dalby L, Fløjgaard C, Lenoir J, Sandel B, Sandom C, Trøjelsgaard K, Svenning J-C (2014) Establishing macroecological trait datasets: digitalization, extrapolation, and validation of diet preferences in terrestrial mammals worldwide. Ecology and Evolution 4(14): 2913-2930. DATA HERE (Dryad database) Note some values are imputed from conspecifics.
- Species-level trait data for mammals with multiple records per species. Fisher DO; Owens I P F; Johnson C N (2001) The ecological basis of life history variation in marsupials. Ecology 82: 3531-3540. DATA HERE The format is rather unfriendly, you can download a csv copy I made here.
- Species-level trait data including brain size for mammals. Gonzalez-Voyer, A; González-Suárez, M; Vilà, C; Revilla, E (2016) Large brain size indirectly increases vulnerability to extinction in mammals. Evolution, 70: 1364–1375. DATA HERE (Dryad database)
- Species-level estimates of generation time for mammals. Pacifici M, Santini L, Di Marco M, Baisero D, Francucci L, Grottolo Marasini G, Visconti P, Rondinini C (2013) Generation length for mammals. Nature Conservation 5: 89-94. DATA HERE (Dryad database)
- Species-level basal metabolic rates and ecological traits for mammals. McNab, B. K. An analysis of the factors that influence the level and scaling of mammalian BMR. Comparative Biochemistry and Physiology A: Molecular & Integrative Physiology 151, 5-28 (2008).
- Individual study records for litter size among Carnivora (mammals). Devenish-Nelson, E. S., Stephens, P. A., Harris, S., Soulsbury, C., & Richards, S. A. (2013). Does litter size variation affect models of terrestrial carnivore extinction risk and management?. PloS one, 8(2), e58060.
- Species-level traits for mammals. Ernest, S. K. M. (2003), Life history characteristics of placental non-volant mammals. Ecology, 84: 3402. DATA HERE
- Species-level trait and environmental data for mammals. Botero CA, Dor R, McCain CM, Safran RJ (2013) Environmental harshness is positively correlated with intraspecific divergence in mammals and birds. Molecular Ecology 23: 259–268. DATA HERE (Dryad database)
- Individual records of parasites on mammals (some taxa). Stephens, P.R., Pappalardo, P., Huang, S., Byers, J.E., Farrell, M.J., Gehman, A., Ghai, R.R., Haas, S.E., Han, B., Park, A.W., Schmidt, J.P., Altizer, S., Ezenwa, V.O., & Nunn C.L. (2017). Global Mammal Parasite Database version 2.0. Ecology. DOI: 10.1002/ecy.1799. DATA HERE
- OLDER VERSION Global Mammal Parasite Database Nunn, C. L., and S. Altizer. 2005. The Global Mammal Parasite Database: an online resource for infectious disease records in wild primates. Evolutionary Anthropology 14:1. Note: these data are NOT freely available but require contacting the authors
- Species-level data on sleep-related traits for mammals – Phylogeny of Sleep. McNamara, P., Capellini, I., Harris, E., Nunn, C. L., Barton, R. A., & Preston, B. (2008). The phylogeny of sleep database: a new resource for sleep scientists. The open sleep journal, 1, 11.
- Species-level mammalian home range data. Not one but two datasets!
- Tucker, M. A., Ord, T. J. and Rogers, T. L. (2014) Evolutionary predictors of mammalian home range size: body mass, diet and the environment. Global Ecology and Biogeography, 23: 1105–1114. DATA HERE
- Tamburello N, Côté IM, Dulvy NK (2015) Energy and the scaling of animal space use. The American Naturalist 186(2): 196-211 DATA HERE (Dryad database)
- Species-level (sex-specific) for dispersal distance data for mammals. Two sources, both in far from ideal formats (pdf and word)…
- Santini L, Di Marco M, Visconti P, Daniele B, Luigi B, Rondinini C (2013) Ecological correlates of dispersal distance in terrestrial mammals. Hystrix, the Italian Journal of Mammalogy, 24, 181–186. DATA HERE (Supporting information)
- Whitmee, S. and Orme, C. D. L. (2013) Predicting dispersal distance in mammals: a trait-based approach. Journal of Animal Ecology, 82: 211–221. DATA HERE (Supporting information)
- Population-level ecological data for primates, including population density and home range. Pearce, F., Carbone, C., Cowlishaw, G., & Isaac, N. J. (2013). Space-use scaling and home range overlap in primates. Proceedings of the Royal Society of London B: Biological Sciences, 280(1751), 20122122. DATA HERE
- Species-level body mass of late Quaternary mammals.Smith FA, Lyons SK, Ernest SK, Jones KE, Kaufman DM, Dayan T, Marquet PA, Brown JH, Haskell JP (2003) Body mass of late Quaternary mammals. Ecology, 84(12), pp.3403-3403. DATA HERE
- Species-level natural (without human impacts) geographic distribution range areas for mammals. Faurby S, Svenning J-C (2015) Historic and prehistoric human-driven extinctions have reshaped global mammal diversity patterns. Diversity and Distributions 21: 1155–1166. DATA HERE
- Species-level longevity and mortality from captive (zoo) and wild mammalian populations. Tidière M, Gaillard JM, Berger V, Müller DW, Lackey LB, Gimenez O, Clauss M, Lemaître JF (2016) Comparative analyses of longevity and senescence reveal variable survival benefits of living in zoos across mammals. Scientific reports 6: Article number 36361. DATA HERE (Supporting information)
- Population-level estimates of Rmax (maximum or intrinsic population growth rate) for diverse mammalian species. Duncan, R. P., Forsyth, D. M. and Hone, J. (2007) Testing the metabolic theory of ecology: allometric scaling exponents in mammals. Ecology, 88: 324–333. DATA HERE (Figshare database)
Other useful links
- Diverse R tools to access online databases. This is not a database per se, but a useful resource.
- EcoData Retriever is a website listing available datasets with a broader scope than those above (includes data on plants, climate, and much more) and includes an R package to make their use even easier!
- Dr. Dieter Lukas website includes links to R tools, phylogenetic trees and trait datasets.
- Dr. Charles Nuun website includes links to several databases and resources including the Global Mammal Parasite Database and the Phylogeny of Sleep listed above.
Many thanks to Dieter Lukas for pointing this out several new sources (within hours of posting this list!).