Congruence between nuclear and mitochondrial DNA: Combination of multiple nuclear introns resolves a well-supported phylogeny of New World orioles (Icterus)

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.