anoletree: Phylogenetic datasets
In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)
anoletree R Documentation
Phylogenetic datasets
Description
Various phylogenetic datasets for comparative analysis.
Usage
data(anole.data)
data(anoletree)
data(ant.geog)
data(ant.tree)
data(bat.tree)
data(bat_virus.data)
data(betaCoV.tree)
data(bonyfish.data)
data(bonyfish.tree)
data(butterfly.data)
data(butterfly.tree)
data(cordylid.data)
data(cordylid.tree)
data(darter.tree)
data(eel.data)
data(eel.tree)
data(elapidae.tree)
data(flatworm.data)
data(flatworm.tree)
data(liolaemid.tree)
data(mammal.data)
data(mammal.geog)
data(mammal.tree)
data(primate.data)
data(primate.tree)
data(salamanders)
data(sunfish.data)
data(sunfish.tree)
data(tortoise.geog)
data(tortoise.tree)
data(tropidurid.data)
data(tropidurid.tree)
data(vertebrate.data)
data(vertebrate.tree)
data(wasp.data)
data(wasp.trees)
data(whale.tree)
Format
anoletree is an object of class "simmap". anole.data is a data frame.
ant.tree is an object of class "phylo". ant.geog is a vector.
bat.tree and betaCoV.tree are objects of class "phylo". bat_virus.data is a data frame.
bonyfish.tree is an object of class "phylo". bonyfish.data is a data frame.
butterfly.tree is an object of class "phylo". butterfly.data is a data frame.
cordylid.tree is an object of class "phylo". cordylid.data is a data frame.
darter.tree is an object of class "phylo".
eel.tree is an object of class "phylo". eel.data is a data frame.
elapidae.tree is an object of class "phylo".
flatworm.tree is an object of class "phylo". flatworm.data is a data frame.
liolaemid.tree is an object of class "phylo". liolaemid.data is a data frame.
mammal.tree is an object of class "phylo". mammal.data is a data frame. mammal.geog is a numerical matrix.
primate.tree is an object of class "phylo". primate.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.
tortoise.tree is an object of class "phylo". tortoise.geog is a data frame.
tropidurid.tree is an object of class "simmap". tropidurid.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.
whale.tree is an object of class "phylo".
Details
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).
ant.tree is a phylogeny containing 84 species of fungus farming attine ants. ant.geog is a vector containing biogegraphic information for the species of the tree. Both the phylogeny and biogeographic information were originally published by Branstetter et al. (2017).
bat.tree is a ML phylogeny of bats from the families Mormoopidae, Molossidae, and Phyllostomidae, based on GenBank accession numbers reported in Caraballo (2022) and estimated using phangorn. betaCoV.tree is a ML phylogenetic tree of betacoronaviruses based on GenBank accession numbers reported in Caraballo (2022) and estimated using phangorn. bat_virus.data is an association table of host and virus from Caraballo (2022).
butterfly.tree and butterfly.data are a phylogeny and dataset of habitat use in Mycalesina butterflies from Halali et al. (2020). The phylogeny of that study was adapted from one originally published by Brattstrom et al. (2020).
bonyfish.tree and bonyfish.data are a phylogeny and dataset of spawning mode and parental care in bony fishes from Benun Sutton and Wilson (2019). Their phylogenetic tree was adapted from a tree originally published by Betancur-R et al. (2017)
cordylid.tree and cordylid.data are a phylogeny and dataset of morphological traits for three different principal components axes from Broeckhoven et al. (2016).
darter.tree is a phylogeny of 201 species of darter fish (Etheostomatinae) from Near et al. (2011).
eel.tree and eel.data are a phylogeny and dataset of feeding mode and maximum total length from 61 species of elopomorph eels from Collar et al. (2014).
elapidae.tree is a reconstructed phylogeny containing 175 species of snakes of the family Elapidae from Lee et al. (2016).
flatworm.tree and flatworm.data are a phylogeny and dataset of habitat preferences for flatworms from Benitez-Alvarez et al. (2020). flatworm.tree has been made ultrametric using penalized likelihood.
liolaemid.tree and liolaemid.data are a phylogenetic tree and phenotypic trait dataset of lizards from the family Liolaemidae from Esquerre et al. (2019).
mammal.tree and mammal.data are the phylogeny and dataset for mammal body size and home range size from Garland et al. (1992). mammal.geog is a matrix containing geographic coordinates for various of the species in mammal.tree pulled from citizen science observations registered on the iNaturalist web platform.
primate.tree and primate.data are a phylogeny and phenotypic trait dataset from Kirk and Kay (2004).
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).
tortoise.tree and tortoise.geog are a phylogeny and dataset of geographic coordinates for Galapagos tortoises. The geographic locality information was approximated from Figure 1 of Poulakakis et al. (2020), and the tree was estimated from nucleotide sequence data published with the same study.
tropidurid.tree and tropidurid.data are the phylogeny and bivariate quantitative trait dataset of tropidurid lizards from Revell et al. (2022).
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).
whale.tree is a phylogeny of cetaceans originally published in Steeman et al. (2009).
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.
Benun Sutton, F., and A. B. Wilson (2019) Where are all the moms? External fertilization predicts the rise of male parental care in bony fishes. Evolution, 73, 2451-2460.
Betancur-R, R., E. O. Wiley, G. Arratia, A. Acero, N. Bailly, M. Miya, G. Lecointre, and G. Orti (2017) Phylogenetic classification of bony fishes. BMC Ecology and Evolution, 17, 162.
Branstetter, M. G., A. Jesovnik, J. Sosa-Calvo, M. W. Lloyd, B. C. Faircloth, S. G. Brady, and T. R. Schultz (2017) Dry habitats were crucibles of domestication in the evolution of agriculture in ants. Proceedings of the Royal Society B, 284, 20170095.
Brattstrom, O., K. Aduse-Poku, E. van Bergen, V. French, and P. M. Brakefield (2020) A release from developmental bias accelerates morphological diversification in butterfly eyespots. Proceedings of the National Academy of Sciences, 177, 27474-27480.
Broeckhoven, C., G. Diedericks, C. Hui, B. G. Makhubo, P. le Fras N. Mouton (2016) Enemy at the gates: Rapid defensive trait diversification in an adaptive radiation of lizards. Evolution, 70, 2647-2656.
Caraballo, D. A. (2022) Cross-species transmission of bat coronaviruses in the Americas: Contrasting patterns between alphacoronavirus and betacoronavirus. Microbiology Spectrum, 10, e01411-22.
Collar, D. C., P. C. Wainwright, M. E. Alfaro, L. J. Revell, and R. S. Mehta (2014) Biting disrupts integration to spur skull evolution in eels. Nature Communications, 5, 5505.
Esquerre, D., D. Ramirez-Alvarez, C. J. Pavon-Vazquez, J. Troncoso-Palacios, C. F. Garin, J. S. Keogh, and A. D. Leache (2019) Speciation across mountains: Phylogenomics, species delimitation and taxonomy of the Liolaemus leopardinus clade (Squamata, Liolaemidae). Molecular Phylogenetics and Evolution, 139, 106524.
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.
Kirk, E. C., and R. F. Kay (2004) The evolution of high visual acuity in the Anthropoidea. In: Ross, C. F., Kay R. F. (Eds), Anthropoid Origins. Developments in Primatology: Progress and Prospects, 539-602. Springer, Boston, MA.
Halali, S., E. van Bergen, C. J. Breuker, P. M. Brakefield, and O. Brattstrom (2020) Seasonal environments drive convergent evolution of a faster pace-of-life in tropical butterflies. Ecology Letters, 24, 102-112.
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.
Lee, M. S. Y., K. L. Saunders, B. King, and A. Palci (2016) Diversification rates and phenotypic evolution in venomous snakes (Elapidae). Royal Society Open Science, 3, 150277.
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.
Near, T. J., C. M. Bossu, G. S. Bradburd, R. L. Carlson, R. C. Harrington, P. R. Hollingsworth Jr., B. P. Keck, and D. A. Etnier. (2011) Phylogeny and temporal diversification of darters (Percidae: Etheostomatinae). Systematic Biology, 60, 565-595.
Poulakakis, N., J. M. Miller, E. L. Jensen, L. B. Beheregaray, M. A. Russello, S. Glaberman, J. Boore, and A. Caccone. (2020) Colonization history of Galapagos giant tortoises: Insights from mitogenomes support the progression rule. Journal of Zoological Systematics and Evolutionary Research, 58, 1262-1275.
Revell, L. J., and D. C. Collar (2009) Phylogenetic analysis of the evolutionary correlation using likelihood. Evolution, 63, 1090-1100.
Revell, L. J., K. S. Toyama, and D. L. Mahler (2022) A simple hierarchical model for heterogeneity in the evolutionary correlation a phylogenetic tree. PeerJ, 10, e13910.
Steeman, M. E., M. B. Hebsgaard, R. E. Fordyce, S. Y. W. Ho, D. L. Rabosky, R. Nielsen, C. Rahbek, H. Glenner, M. V. Sorensen, and E. Willerslev (2009) Radiation of extant cetaceans driven by restructuring of the oceans. Systematic Biology, 58, 573-585.
phytools documentation built on June 22, 2024, 10:39 a.m.
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| anoletree | R Documentation |
Phylogenetic datasets
Description
Various phylogenetic datasets for comparative analysis.
Usage
data(anole.data)
data(anoletree)
data(ant.geog)
data(ant.tree)
data(bat.tree)
data(bat_virus.data)
data(betaCoV.tree)
data(bonyfish.data)
data(bonyfish.tree)
data(butterfly.data)
data(butterfly.tree)
data(cordylid.data)
data(cordylid.tree)
data(darter.tree)
data(eel.data)
data(eel.tree)
data(elapidae.tree)
data(flatworm.data)
data(flatworm.tree)
data(liolaemid.tree)
data(mammal.data)
data(mammal.geog)
data(mammal.tree)
data(primate.data)
data(primate.tree)
data(salamanders)
data(sunfish.data)
data(sunfish.tree)
data(tortoise.geog)
data(tortoise.tree)
data(tropidurid.data)
data(tropidurid.tree)
data(vertebrate.data)
data(vertebrate.tree)
data(wasp.data)
data(wasp.trees)
data(whale.tree)
Format
anoletree is an object of class "simmap". anole.data is a data frame.
ant.tree is an object of class "phylo". ant.geog is a vector.
bat.tree and betaCoV.tree are objects of class "phylo". bat_virus.data is a data frame.
bonyfish.tree is an object of class "phylo". bonyfish.data is a data frame.
butterfly.tree is an object of class "phylo". butterfly.data is a data frame.
cordylid.tree is an object of class "phylo". cordylid.data is a data frame.
darter.tree is an object of class "phylo".
eel.tree is an object of class "phylo". eel.data is a data frame.
elapidae.tree is an object of class "phylo".
flatworm.tree is an object of class "phylo". flatworm.data is a data frame.
liolaemid.tree is an object of class "phylo". liolaemid.data is a data frame.
mammal.tree is an object of class "phylo". mammal.data is a data frame. mammal.geog is a numerical matrix.
primate.tree is an object of class "phylo". primate.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.
tortoise.tree is an object of class "phylo". tortoise.geog is a data frame.
tropidurid.tree is an object of class "simmap". tropidurid.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.
whale.tree is an object of class "phylo".
Details
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).
ant.tree is a phylogeny containing 84 species of fungus farming attine ants. ant.geog is a vector containing biogegraphic information for the species of the tree. Both the phylogeny and biogeographic information were originally published by Branstetter et al. (2017).
bat.tree is a ML phylogeny of bats from the families Mormoopidae, Molossidae, and Phyllostomidae, based on GenBank accession numbers reported in Caraballo (2022) and estimated using phangorn. betaCoV.tree is a ML phylogenetic tree of betacoronaviruses based on GenBank accession numbers reported in Caraballo (2022) and estimated using phangorn. bat_virus.data is an association table of host and virus from Caraballo (2022).
butterfly.tree and butterfly.data are a phylogeny and dataset of habitat use in Mycalesina butterflies from Halali et al. (2020). The phylogeny of that study was adapted from one originally published by Brattstrom et al. (2020).
bonyfish.tree and bonyfish.data are a phylogeny and dataset of spawning mode and parental care in bony fishes from Benun Sutton and Wilson (2019). Their phylogenetic tree was adapted from a tree originally published by Betancur-R et al. (2017)
cordylid.tree and cordylid.data are a phylogeny and dataset of morphological traits for three different principal components axes from Broeckhoven et al. (2016).
darter.tree is a phylogeny of 201 species of darter fish (Etheostomatinae) from Near et al. (2011).
eel.tree and eel.data are a phylogeny and dataset of feeding mode and maximum total length from 61 species of elopomorph eels from Collar et al. (2014).
elapidae.tree is a reconstructed phylogeny containing 175 species of snakes of the family Elapidae from Lee et al. (2016).
flatworm.tree and flatworm.data are a phylogeny and dataset of habitat preferences for flatworms from Benitez-Alvarez et al. (2020). flatworm.tree has been made ultrametric using penalized likelihood.
liolaemid.tree and liolaemid.data are a phylogenetic tree and phenotypic trait dataset of lizards from the family Liolaemidae from Esquerre et al. (2019).
mammal.tree and mammal.data are the phylogeny and dataset for mammal body size and home range size from Garland et al. (1992). mammal.geog is a matrix containing geographic coordinates for various of the species in mammal.tree pulled from citizen science observations registered on the iNaturalist web platform.
primate.tree and primate.data are a phylogeny and phenotypic trait dataset from Kirk and Kay (2004).
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).
tortoise.tree and tortoise.geog are a phylogeny and dataset of geographic coordinates for Galapagos tortoises. The geographic locality information was approximated from Figure 1 of Poulakakis et al. (2020), and the tree was estimated from nucleotide sequence data published with the same study.
tropidurid.tree and tropidurid.data are the phylogeny and bivariate quantitative trait dataset of tropidurid lizards from Revell et al. (2022).
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).
whale.tree is a phylogeny of cetaceans originally published in Steeman et al. (2009).
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.
Benun Sutton, F., and A. B. Wilson (2019) Where are all the moms? External fertilization predicts the rise of male parental care in bony fishes. Evolution, 73, 2451-2460.
Betancur-R, R., E. O. Wiley, G. Arratia, A. Acero, N. Bailly, M. Miya, G. Lecointre, and G. Orti (2017) Phylogenetic classification of bony fishes. BMC Ecology and Evolution, 17, 162.
Branstetter, M. G., A. Jesovnik, J. Sosa-Calvo, M. W. Lloyd, B. C. Faircloth, S. G. Brady, and T. R. Schultz (2017) Dry habitats were crucibles of domestication in the evolution of agriculture in ants. Proceedings of the Royal Society B, 284, 20170095.
Brattstrom, O., K. Aduse-Poku, E. van Bergen, V. French, and P. M. Brakefield (2020) A release from developmental bias accelerates morphological diversification in butterfly eyespots. Proceedings of the National Academy of Sciences, 177, 27474-27480.
Broeckhoven, C., G. Diedericks, C. Hui, B. G. Makhubo, P. le Fras N. Mouton (2016) Enemy at the gates: Rapid defensive trait diversification in an adaptive radiation of lizards. Evolution, 70, 2647-2656.
Caraballo, D. A. (2022) Cross-species transmission of bat coronaviruses in the Americas: Contrasting patterns between alphacoronavirus and betacoronavirus. Microbiology Spectrum, 10, e01411-22.
Collar, D. C., P. C. Wainwright, M. E. Alfaro, L. J. Revell, and R. S. Mehta (2014) Biting disrupts integration to spur skull evolution in eels. Nature Communications, 5, 5505.
Esquerre, D., D. Ramirez-Alvarez, C. J. Pavon-Vazquez, J. Troncoso-Palacios, C. F. Garin, J. S. Keogh, and A. D. Leache (2019) Speciation across mountains: Phylogenomics, species delimitation and taxonomy of the Liolaemus leopardinus clade (Squamata, Liolaemidae). Molecular Phylogenetics and Evolution, 139, 106524.
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.
Kirk, E. C., and R. F. Kay (2004) The evolution of high visual acuity in the Anthropoidea. In: Ross, C. F., Kay R. F. (Eds), Anthropoid Origins. Developments in Primatology: Progress and Prospects, 539-602. Springer, Boston, MA.
Halali, S., E. van Bergen, C. J. Breuker, P. M. Brakefield, and O. Brattstrom (2020) Seasonal environments drive convergent evolution of a faster pace-of-life in tropical butterflies. Ecology Letters, 24, 102-112.
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.
Lee, M. S. Y., K. L. Saunders, B. King, and A. Palci (2016) Diversification rates and phenotypic evolution in venomous snakes (Elapidae). Royal Society Open Science, 3, 150277.
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.
Near, T. J., C. M. Bossu, G. S. Bradburd, R. L. Carlson, R. C. Harrington, P. R. Hollingsworth Jr., B. P. Keck, and D. A. Etnier. (2011) Phylogeny and temporal diversification of darters (Percidae: Etheostomatinae). Systematic Biology, 60, 565-595.
Poulakakis, N., J. M. Miller, E. L. Jensen, L. B. Beheregaray, M. A. Russello, S. Glaberman, J. Boore, and A. Caccone. (2020) Colonization history of Galapagos giant tortoises: Insights from mitogenomes support the progression rule. Journal of Zoological Systematics and Evolutionary Research, 58, 1262-1275.
Revell, L. J., and D. C. Collar (2009) Phylogenetic analysis of the evolutionary correlation using likelihood. Evolution, 63, 1090-1100.
Revell, L. J., K. S. Toyama, and D. L. Mahler (2022) A simple hierarchical model for heterogeneity in the evolutionary correlation a phylogenetic tree. PeerJ, 10, e13910.
Steeman, M. E., M. B. Hebsgaard, R. E. Fordyce, S. Y. W. Ho, D. L. Rabosky, R. Nielsen, C. Rahbek, H. Glenner, M. V. Sorensen, and E. Willerslev (2009) Radiation of extant cetaceans driven by restructuring of the oceans. Systematic Biology, 58, 573-585.
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