The perils of single gene trees — mitochondrial versus single‐copy nuclear DNA variation in white‐eyes (Aves: Zosteropidae)

Abstract

Phylogenetic relationships among animal populations and species commonly have been inferred from patterns of variation observed within a single gene system, most often the mitochondrial genome. Analysis of restriction site variation in the mitochondrial DNA of two species of white‐eye (Zosterops lateralis and Z. lutea) in Australia produced a single gene tree that does not accurately represent the organismal tree. In contrast, patterns of variation at two anonymous, single‐copy nuclear DNA loci revealed a phylogeography consistent with traditional classification of the species. Discordance between mitochondrial DNA and single‐copy nuclear DNA variation is probably the result of past hybridization between Z. lateralis and Z. lutea, evidence of which has been lost from the nuclear genome by recombination. This study provides a clear empirical demonstration that single gene genealogies cannot be assumed to accurately represent the true phylogenies, and emphasizes the need for composite genetic analyses.