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

Molecular Phylogenetics and Evolution

Volumn 61, Issue 3, 2011, Pages 958-963

  Lanfear, Robert ^a   Bromham, Lindell ^a  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

Author keywords

Bayesian; Community; Extant; Extinct; GeneFinder; Macroecology; Supermatrix

Indexed keywords

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 SPECIFICITY;

AVES;

EID: 80055110246     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2011.07.018     Document Type: Article

References (31)

1. Alexandrou M.A., et al. Competition and phylogeny determine community structure in Mullerian co-mimics. Nature 2011, 469:84-88.
2. Bininda-Emonds O.R. The evolution of supertrees. Trends Ecol. Evol. 2004, 19:315-322.
3. Brown J.M., et al. When trees grow too long: investigating the causes of highly inaccurate bayesian branch-length estimates. Syst. Biol. 2010, 59:145-161.
4. Bunce M., et al. Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis. Nature 2003, 425:172-175.
5. Diniz-Filho J.A.F., Bini L.M. Macroecology, global change and the shadow of forgotten ancestors. Global Ecol. Biogeogr. 2008, 17:11-17.
6. Drummond, A.J. et al., 2011. Geneious v5.4. http://www.geneious.com/.
7. Emerson B.C., Gillespie R.G. Phylogenetic analysis of community assembly and structure over space and time. Trends Ecol. Evol. 2008, 23:619-630.
8. Ericson P.G.P., et al. Diversification of Neoaves: integration of molecular sequence data and fossils. Biol. Lett. 2006, 2:543-547.
9. Garcia-Moreno J., Mindell D.P. Rooting a phylogeny with homologous genes on opposite sex chromosomes (gametologs): a case study using avian CHD. Mol. Biol. Evol. 2000, 17:1826-1832.
10. Hackett S.J., et al. A phylogenomic study of birds reveals their evolutionary history. Science 2008, 320:1763-1768.
11. Keane T.M., et al. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol. Biol. 2006, 6:29.
12. Kembel S.W., Hubbell S.P. The phylogenetic structure of a neotropical forest tree community. Ecology 2006, 87:86-99.
13. Kembel S.W., et al. Picante: R tools for integrating phylogenies and ecology. Bioinformatics 2010, 26:1463-1464.
14. Kress W.J., et al. Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama. Proc. Natl. Acad. Sci. USA 2009, 106:18621-18626.
15. Lanfear R., Bromham L. Statistical tests between competing hypotheses of hox cluster evolution. Syst. Biol. 2008, 57:708-718.
16. Mayr G., Clarke J. The deep divergences of neornithine birds: a phylogenetic analysis of morphological characters. Cladistics 2005, 21:527-553.
17. Nylander J.A., et al. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 2008, 24:581-583.
18. OSNZ Checklist Committee, 2010. Checklist of the Birds of New Zealand, Norfolk and Macquarie Islands, and the Ross Dependency, Antarctica, fourth ed. Ornithological Society of New Zealand & Te Papa Press, Wellington.
19. Rabosky D.L. Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions. Ecol. Lett. 2009, 12:735-743.
20. Rambaut A., Drummond A.J. Tracer version 1.3 2003, Evolutionary Biology Group, Univ. of Oxford, Oxford.
21. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
22. Sibley C.G., Ahlquist J.E. Phylogeny and Classification of Birds 1990, Yale University Press, New Haven, CT.
23. Slack K.E., et al. Resolving the root of the avian mitogenomic tree by breaking up long branches. Mol. Phylogen. Evol. 2007, 42:1-13.
24. Smith S.A., et al. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evol. Biol. 2009, 9:37.
25. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
26. Thomas G.H. Phylogenetic distributions of British birds of conservation concern. Proc. Biol. Sci. 2008, 275:2077-2083.
27. Thomson R.C., Shaffer H.B. Sparse supermatrices for phylogenetic inference: taxonomy, alignment, rogue taxa, and the phylogeny of living turtles. Syst. Biol. 2010, 59:42-58.
28. Trewick S.A., Gibb G.C. Vicars, tramps and assembly of the New Zealand avifauna: a review of molecular phylogenetic evidence. Ibis 2010, 152:226-253.
29. Vamosi J.C., Vamosi S.M. Body size, rarity, and phylogenetic community structure: insights from diving beetle assemblages of Alberta. Divers. Distrib. 2007, 13:1-10.
30. Van Tuinen M., et al. Convergence and divergence in the evolution of aquatic birds. Proc. Roy. Soc. London Ser. B - Biol. Sci. 2001, 268:1345-1350.
31. Webb C.O., Donoghue M.J. Phylomatic: tree assembly for applied phylogenetics. Mol. Ecol. Notes 2005, 5:181-183.