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

Robert Lanfear, Lindell Bromham

Research output: Contribution to journalArticlepeer-review

18 Citations (Scopus)

Abstract

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 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.
Original languageEnglish
Pages (from-to)958-963
Number of pages6
JournalMolecular Phylogenetics and Evolution
Volume61
Issue number3
DOIs
Publication statusPublished - 2011
Externally publishedYes

Keywords

  • Community
  • GeneFinder
  • Supermatrix
  • Bayesian
  • Extinct
  • Extant
  • Macroecology

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