geiger-data: example datasets

geiger-dataR Documentation

example datasets


providing access to comparative datasets




The objects caudata, chelonia, carnivores, geospiza, and primates each have at least two items, a phy object and a dat object. The phy object is a phylogenetic tree of class 'phylo' (see read.tree). The dat object (e.g., caudata$dat) is a named vector of (natural log-transformed) body sizes for each group. The salamander data (object caudata) also includes the systematics for all recognized taxa (object caudata$tax) as well as a time-calibrated family-level phylogeny (caudata$fam) from Zhang and Wake (2009). The object caudata$phy is an unpublished glomogram of mostly family level phylogenies from the literature. The backbone for that tree is from Zhang and Wake (2009).

The amphibia object is a set of three trees, the last of which is a time-scaled estimate of the Pyron and Wiens (2011) tree (see congruify.phylo).

The whales object is a dataset including a tree and a taxon richness matrix (see medusa).


Data are from the following sources:

AMPHIBIANS (amphibia)

  • Roelants K, DJ Gower, M Wilkinson, SP Loader, SD Biju, K Guillaume, L Moriau, and F Bossuyt. 2007. Global patterns of diversification in the history of modern amphibians. PNAS 104:887-892.

  • Pyron RA and JJ Wiens. 2011. A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians. MPE 61:543-583.


  • Adams DC, CM Berns, KH Kozak, and JJ Wiens. 2009. Are rates of species diversification correlated with rates of morphological evolution? PRSB 276:2729-2738.

  • Bonett RM, PT Chippindale, PE Moler, RW van Devender, and DB Wake. 2009. Evolution of gigantism in amphiumid salamanders. PLoSONE 4(5):e5615.

  • Kozak KH, RW Mendyk, and JJ Wiens. 2009. Can Parallel Diversification Occur in Sympatry? Repeated Patterns of Body-Size Evolution in Coexisting Clades of North American Salamanders. Evolution 63:1769-1784.

  • Weisrock DW, TJ Papenfuss, JR Macey, SN Litvinchuk, R Polymeni, IH Ugurtas, E Zhao, H Jowkar, and A Larson. 2006. A molecular assessment of phylogenetic relationships and lineage accumulation rates within the family Salamandridae (Amphibia, Caudata). MPE 41:368-383.

  • Wiens JJ and JT Hoverman. 2008. Digit reduction, body size, and paedomorphosis in salamanders. Evolution and Development 10:449-463.

  • Zhang P, Y-Q Chen, H Zhou, X-L Wang, TJ Papenfuss, DB Wake and L-H Qu. 2006. Phylogeny, evolution, and biogeography of Asiatic salamanders (Hynobiidae). PNAS 103:7360-7365.

  • Zhang P and DB Wake. 2009. Higher-level salamander relationships and divergence dates inferred from complete mitochondrial genomes. MPE 53:492-508.

PRIMATES (primates)

  • Redding DW, C DeWolff, and AO Mooers. 2010. Evolutionary distinctiveness, threat status and ecological oddity in primates. Conservation Biology 24:1052-1058.

  • Vos RA and AO Mooers. 2006. A new dated supertree of the Primates. Chapter 5. In: VOS RA (Ed.) Inferring large phylogenies: the big tree problem. [Ph.D. thesis]. Burnaby BC, Canada: Simon Fraser University.

CARNIVORES (carnivores)

  • Eizirik E, WJ Murphy, K-P Koepfli, WE Johnson, JW Dragoo, RK Wayne, and SJ O'Brien. 2010. Pattern and timing of diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences. Molecular Phylogenetic and Evolution 56:49-63.

  • Wozencraft WC. 2005. Order Carnivora in Wilson DE and DM Reeder (Eds.) Mammal Species of the World. Johns Hopkins University Press.

  • Jones KE, J Bielby, M Cardillo, et al. 2009. Ecological Archives E090-184.

CANIFORMS (caniformia)

  • Slater GJ, LJ Harmon, and ME Alfaro. 2012. Integrating fossils with molecular phylogenies improves inference of trait evolution. Evolution 66:3931-3944.

TURTLES (chelonia)

  • Jaffe AL, GJ Slater, and ME Alfaro. 2011. Ecological habitat and body size evolution in turtles. Biology Letters 7:558-561.


  • Schluter D

WHALES (whales)

geiger documentation built on April 4, 2023, 1:07 a.m.