© 2008 Society of Systematic Biologists
Comparison of Species Tree Methods for Reconstructing the Phylogeny of Bearded Manakins (Aves: Pipridae, Manacus) from Multilocus Sequence Data
1 Museum of Natural Science Baton Rouge, Louisiana 70803, USA; E-mail: brumfld{at}lsu.edu
2 Department of Biological Sciences, Louisiana State University Baton Rouge, Lousiana, 70803, USA
3 Department of Organismic and Evolutionary Biology, Harvard University Cambridge, Massachusetts 02138, USA; E-mail: lliu{at}oeb.harvard.edu (L.L.); sedwards{at}fas.harvard.edu (S.V.E.)
4 Department of Biological Sciences, University of Washington Seattle, Washington 98195, USA
5 Current address: 95-390 Kuahelani Ave., Suite 3E, Mililani, Hawaii 96789, USA
Edited by Allan Baker
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Abstract |
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Although the power of multi-locus data in estimating species trees is apparent, it is also clear that the analytical methodologies for doing so are still maturing. For example, of the methods currently available for estimating species trees from multiocus data, the Bayesian method introduced by Liu and Pearl (2007 BEST) is the only one that provides nodal support values. Using gene sequences from five nuclear loci, we explored two analytical methods (deep coalescence and BEST) to reconstruct the species tree of the five primary Manacus OTUs: M. aurantiacus, M. candei, M. vitellinus, populations of M. manacus from west of the Andes (M. manacus (w)), and populations of M. manacus from east of the Andes (M. manacus (e)). Both BEST and deep coalescence supported a sister relationship between M. vitellinus and M. manacus (w). A lower probability tree from the BEST analysis and one of the most parsimonious deep coalescence trees also supported a sister relationship between M. candei and M. aurantiacus. Because hybrid zones connect the distributions of most Manacus species, we examined the potential influence of post-divergence gene flow on the sister relationship of parapatrically distributed M. vitellinus and M. manacus (w). An isolation-with-migration (IM) analysis found relatively high levels of gene flow between M. vitellinus and M. manacus (w). Whether the gene flow is obscuring a true sister relationship between M. manacus (w) and M. manacus (e) remained unclear, pointing to the need for more detailed models accommodating multispecies, multilocus DNA sequence data.
Keywords: Gene trees; incomplete lineage sorting; manakin; phylogeny; species tree
Received November 9, 2007; Revised December 26, 2007; Accepted June 6, 2008
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