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Estimating phylogenies for species assemblages: A complete phylogeny for the past and present native birds of New Zealand

Lanfear, Robert; Bromham, Lindell

Description

Phylogenies of species assemblages are vital to many studies of community ecology and macroecology. However, few assemblage phylogenies are currently available, and the approaches that have been used to construct them have had a number of important limitations. Here, we estimate a Bayesian posterior sample of phylogenies for all 275 known extinct and extant native birds of New Zealand. To do this, we use an approach that uses freely-available data and software, can incorporate both extinct and...[Show more]

dc.contributor.authorLanfear, Robert
dc.contributor.authorBromham, Lindell
dc.date.accessioned2015-12-10T23:13:08Z
dc.identifier.issn1055-7903
dc.identifier.urihttp://hdl.handle.net/1885/64286
dc.description.abstractPhylogenies of species assemblages are vital to many studies of community ecology and macroecology. However, few assemblage phylogenies are currently available, and the approaches that have been used to construct them have had a number of important limitations. Here, we estimate a Bayesian posterior sample of phylogenies for all 275 known extinct and extant native birds of New Zealand. To do this, we use an approach that uses freely-available data and software, can incorporate both extinct and extant taxa, does not rely on having DNA sequence data available for all species in the assemblage, and explicitly accounts for phylogenetic uncertainty. This approach produces a set of phylogenies that describes our knowledge and uncertainty about the relationships among the NZ birds. We also present a python script, GeneFinder, which can be used to efficiently gather publicly available sequence data in order to construct a supermatrix of DNA sequences for constructing assemblage phylogenies. The approach we describe paves the way for estimating assemblage phylogenies for any species assemblage.
dc.publisherAcademic Press
dc.sourceMolecular Phylogenetics and Evolution
dc.subjectKeywords: animal; article; bird; genetics; molecular genetics; New Zealand; nucleotide sequence; phylogeny; species difference; species extinction; Animals; Base Sequence; Birds; Extinction, Biological; Molecular Sequence Data; New Zealand; Phylogeny; Species Speci Bayesian; Community; Extant; Extinct; GeneFinder; Macroecology; Supermatrix
dc.titleEstimating phylogenies for species assemblages: A complete phylogeny for the past and present native birds of New Zealand
dc.typeJournal article
local.description.notesImported from ARIES
local.identifier.citationvolume61
dc.date.issued2011
local.identifier.absfor060301 - Animal Systematics and Taxonomy
local.identifier.absfor060309 - Phylogeny and Comparative Analysis
local.identifier.ariespublicationu9511635xPUB911
local.type.statusPublished Version
local.contributor.affiliationLanfear, Robert, College of Medicine, Biology and Environment, ANU
local.contributor.affiliationBromham, Lindell, College of Medicine, Biology and Environment, ANU
local.description.embargo2037-12-31
local.bibliographicCitation.issue3
local.bibliographicCitation.startpage958
local.bibliographicCitation.lastpage963
local.identifier.doi10.1016/j.ympev.2011.07.018
local.identifier.absseo970106 - Expanding Knowledge in the Biological Sciences
dc.date.updated2016-02-24T12:09:24Z
local.identifier.scopusID2-s2.0-80055110246
local.identifier.thomsonID000297387600035
CollectionsANU Research Publications

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