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integrating phylogenetic and population genetic analyses of multiple loci to test species divergence hypotheses in passerina buntings


作者單位:Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 708031 Corresponding author: Museum of Natural Science, 119 Foster Hall, Baton Rouge, LA 70803.

【摘要】 phylogenetic and population genetic analyses of dna sequence data from 10 nuclear loci were used to test species divergence hypotheses within passerina buntings, with special focus on a strongly supported, but controversial, sister relationship between passerina amoena and p. caerulea inferred from a previous mitochondrial study. here, a maximum-likelihood analysis of a concatenated 10-locus data set, as well as minimize-deep-coalescences and maximum-likelihood analyses of the locus-specific gene trees, recovered the traditional sister relationship between p. amoena and p. cyanea. in addition, a more recent divergence time estimate between p. amoena and p. cyanea than between p. amoena and p. caerulea provided evidence for the traditional sister relationship. these results provide a compelling example of how lineage sorting stochasticity can lead to incongruence between gene trees and species trees, and illustrate how phylogenetic and population genetic analyses can be integrated to investigate evolutionary relationships between recently diverged taxa.

【關鍵詞】 integrating phylogenetic population analyses multiple divergence hypotheses passerina buntings


inferring the species tree of recently diverged taxa can be a challenging exercise ( m addison 1997; f elsenstein 2004; m addison and k nowles 2006 ). the difficulty arises in part because the stochastic sorting of ancestral polymorphisms after speciation can result in gene trees that are discordant with species trees ( p amilo and n ei 1988; t akahata 1989; m addison 1997; r osenberg 2002, 2003; m addison and k nowles 2006 ). for recently diverged taxa that have not yet attained complete reproductive isolation, gene flow introduces another source of discordance between the gene trees and the species tree ( t akahata and s latkin 1990; t akahata 1995; w akeley 1996; w akeley and h ey 1998 ). the impact of these processes on species tree reconstruction has long been recognized ( g illespie and l angley 1979; n ei and l i 1979 ), but it is only recently that a model-based phylogenetic framework has integrated one of them (ancestral sorting) into the species tree inference. because postspeciation, interspecific gene flow has yet to be incorporated into a phylogenetic framework, nonphylogenetic methods must be used to infer species relationships indirectly. here, phylogenetic and divergence population genetic analyses of a multilocus nuclear data set are used to examine a controversial sister species relationship in passerina buntings.

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