Using the birdtree.org website to obtain robust phylogenies for avian comparative studies

A primer

Diego Rubolini, A. Likér, László Z. Garamszegi, Anders P. Møller, Nicola Saino

Research output: Contribution to journalArticle

61 Citations (Scopus)

Abstract

Comparative studies of trait evolution require accounting for the shared evolutionary history. This is done by including phylogenetic hypotheses into statistical analyses of species’ traits, for which birds often serve as excellent models. The online publication of the most complete molecular phylogeny of extant bird species (www.birdtree.org, BirdTree hereafter) now allows evolutionary biologists to rapidly obtain sets of equally plausible phylogenetic trees for any set of species to be incorporated as a phylogenetic hypothesis in comparative analyses. We discuss methods to use BirdTree tree sets for comparative studies, either by building a consensus tree that can be incorporated into standard comparative analyses, or by using tree sets to account for the ef- fect of phylogenetic uncertainty. Methods accounting for phylogenetic uncertainty should be preferred whenever possible because they should provide more reliable parameter estimates and realistic confidence intervals around them. Based on a real compara- tive dataset, we ran simulations to investigate the effect of variation in the size of the random tree sets downloaded from BirdTree on the variability of parameter estimates from a bivariate relationship between mass-specific productivity and body mass. Irre- spective of the method of analysis, using at least 1,000 trees allows obtaining parameter estimates with very small (<0.15%) co- efficients of variation. We argue that BirdTree, due to the ease of use and the major advantages over previous ‘traditional’ meth- ods to obtain phylogenetic hypotheses of bird species (e.g. supertrees or manual coding of published phylogenies), will become the standard reference in avian comparative studies for years to come.

Original languageEnglish
Pages (from-to)959-965
Number of pages7
JournalCurrent Zoology
Volume61
Issue number6
Publication statusPublished - Dec 1 2015

Fingerprint

phylogeny
birds
uncertainty
reference standards
methodology
biologists
confidence interval
history

Keywords

  • Birds
  • BirdTree
  • Comparative method
  • PGLM
  • PGLS
  • Phylogenetic uncertainty

ASJC Scopus subject areas

  • Animal Science and Zoology

Cite this

Rubolini, D., Likér, A., Garamszegi, L. Z., Møller, A. P., & Saino, N. (2015). Using the birdtree.org website to obtain robust phylogenies for avian comparative studies: A primer. Current Zoology, 61(6), 959-965.

Using the birdtree.org website to obtain robust phylogenies for avian comparative studies : A primer. / Rubolini, Diego; Likér, A.; Garamszegi, László Z.; Møller, Anders P.; Saino, Nicola.

In: Current Zoology, Vol. 61, No. 6, 01.12.2015, p. 959-965.

Research output: Contribution to journalArticle

Rubolini, D, Likér, A, Garamszegi, LZ, Møller, AP & Saino, N 2015, 'Using the birdtree.org website to obtain robust phylogenies for avian comparative studies: A primer', Current Zoology, vol. 61, no. 6, pp. 959-965.
Rubolini, Diego ; Likér, A. ; Garamszegi, László Z. ; Møller, Anders P. ; Saino, Nicola. / Using the birdtree.org website to obtain robust phylogenies for avian comparative studies : A primer. In: Current Zoology. 2015 ; Vol. 61, No. 6. pp. 959-965.
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