anoletree: Phylogenetic datasets

anoletreeR Documentation

Phylogenetic datasets

Description

anoletree is a phylogeny of Greater Antillean anole species with a mapped discrete character - ecomorph class. anole.data is a data frame of morphological characters. Data and tree are from Mahler et al. (2010).

flatworm.tree and flatworm.data are a phylogeny and dataset of habitat preferences for flatworms from Benitez-Alvarez et al. (2000). flatworm.tree has been made ultrametric using penalized likelihood.

mammal.tree and mammal.data are the phylogeny and dataset for mammal body size and home range size from Garland et al. (1992).

salamanders is a phylogeny of Plethodon salamanders from Highton and Larson (1979). According to Wikipedia, the genus Plethodon contains 55 species in total.

sunfish.tree and sunfish.data are the phylogeny and dataset for Centrarchidae and buccal morphology (respectively) from Revell and Collar (2009).

vertebrate.tree is a time-calibrated phylogeny of vertebrates and vertebrate.data is a dataset of phenotypic traits. The phylogeny is from http://www.timetree.org/ (Hedges et al. 2006).

wasp.trees and wasp.data are the phylogeny and host-parasite associations from Lopez-Vaamonde et al. (2001).

Usage

data(anole.data)
data(anoletree)
data(flatworm.tree)
data(flatworm.data)
data(mammal.data)
data(mammal.tree)
data(salamanders)
data(sunfish.data)
data(sunfish.tree)
data(vertebrate.tree)
data(vertebrate.data)
data(wasp.data)
data(wasp.trees)

Format

anoletree is an object of class "simmap". anole.data is a data frame.

flatworm.tree is an object of class "phylo". flatworm.data is a data frame.

mammal.tree is an object of class "phylo". mammal.data is a data frame.

salamanders is an object of class "phylo".

sunfish.tree is an object of class "simmap". sunfish.data is a data frame.

vertebrate.tree is an object of class "phylo". vertebrate.data is a data frame.

wasp.trees is an object of class "multiPhylo". wasp.data is a data frame.

Source

Benitez-Alvarez, L., A. Maria Leal-Zanchet, A. Oceguera-Figueroa, R. Lopes Ferreira, D. de Medeiros Bento, J. Braccini, R. Sluys, and M. Riutort. (2020) Phylogeny and biogeography of the Cavernicola (Platyhelminthes: Tricladida): Relicts of an epigean group sheltering in caves? Molecular Phylogenetics and Evolution, 145, 106709.

Garland, T., Jr., P. H. Harvey, and A. R. Ives. (1992) Procedures for the analysis of comparative data using phylogenetically independent contrasts. Systematic Biology, 41, 18-32.

Hedges, S. B., J. Dudley, and S. Kumar. (2006) TimeTree: A public knowledgebase of divergence times among organisms. Bioinformatics, 22, 2971-2972.

Highton, R., and A. Larson. (1979) The genetic relationships of the salamanders of the genus Plethodon. Systematic Zoology, 28, 579-599.

Lopez-Vaamonde, C., J. Y. Rasplus, G. D. Weiblen, and J. M. Cook. (2001) Molecular phylogenies of fig wasps: Partial cocladogenesis of pollinators and parasites. Molecular Phylogenetics and Evolution, 21, 55-71.

Mahler, D. L, L. J. Revell, R. E. Glor, and J. B. Losos. (2010) Ecological opportunity and the rate of morphological evolution in the diversification of Greater Antillean anoles. Evolution, 64, 2731-2745.

Revell, L. J., and D. C. Collar. (2009) Phylogenetic analysis of the evolutionary correlation using likelihood. Evolution, 63, 1090-1100.


phytools documentation built on Sept. 2, 2022, 1:06 a.m.