Congruence between nuclear and mitochondrial DNA: Combination of multiple nuclear introns resolves a well-supported phylogeny of New World orioles (Icterus)
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Abstract
Darwin's vision of a "Tree of Life" showing evolutionary relationships among all extant
species seems an increasingly feasible goal, at least for vertebrate animals. However,
virtually all published molecular phylogenies for closely related animals are based
on a single locus - maternally inherited mitochondrial DNA. New approaches using multiple
nuclear loci are needed to test published trees and better resolve the twigs of the
entire tree of life. Here we use New World orioles (Icterus) to test an approach based
on combined analysis of six independent Z chromosome introns. Combined analysis of
multiple introns using traditional phylogenetic methods resolved a well-supported
species phylogeny of New World orioles. In fact, all major lineages of orioles and
several sub-clades that are well-supported by previously published mtDNA data are
also strongly supported by the combined nuclear Z-intron tree. The male-biased Z-intron
tree presented here is overwhelmingly congruent with the female-exclusive mtDNA tree.
A slow rate of mutation relative to mtDNA resulted in generally poorly resolved gene
trees when intron loci were analyzed separately. However, strong phylogenetic signal
for all but the most recent divergences emerged once multiple loci were concatenated
and analyzed in combination. Although there clearly are conditions under which concatenation
analysis of nuclear DNA can be misleading, the congruence between mitochondrial and
nuclear estimates of the Icterus phylogeny suggests that concatenation remains a powerful
tool for inferring phylogenetic relationships for all but very recent divergences.
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