geiger-data: example datasets
In geiger: Analysis of Evolutionary Diversification

geiger-data

R Documentation

example datasets

Description

providing access to comparative datasets

Usage

data(amphibia)
data(caniformia)
data(carnivores)
data(caudata)
data(chelonia)
data(geospiza)
data(primates)
data(whales)

Details

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 The object caudata$phy is an unpublished glomogram of mostly family level phylogenies from the literature.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).

References

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.

SALAMANDERS (caudata)

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)