Challenges to Inferring Evolutionary Relationships of Closely-related Species: Multilocus Approaches Resolve the Evolutionary History of New World Orioles (Icterus)

Mitochondrial DNA (mtDNA) has demonstrated great utility for phylogeography and phylogenetics, but has several limitations and must be corroborated by independent nuclear evidence. Stochastic lineage sorting and introgressive hybridization frequently cause gene genealogies to be incongruent with the species tree and can render even the most strongly supported gene tree misleading. I utilized multiple nuclear introns and several multilocus approaches to investigate the evolutionary relationships between New World orioles within genus Icterus. First, I tested the utility of nuclear introns for inferring species-level phylogenies (Ch. 1). Concatenation analysis of six sex-linked introns yielded a well-resolved phylogeny that corroborated many nodes supported by mtDNA, especially deeper in the oriole tree. Second, I assessed the performance of four species tree algorithms by inferring a phylogeny of a recent radiation of eleven oriole species (Ch. 2). I sequenced seven independent introns from multiple individuals of each species, and found overall agreement between methods and previous data sets. Concatenation and Bayesian concordance analysis were mostly congruent and agreed on eight nodes. One of two coalescent-based methods used (*BEAST) supported six of these eight nodes. I found strong conflict between mtDNA and nDNA regarding the relationships within the well-studied "northern oriole" group. MtDNA supported a sister relationship between I. galbula and I. abeillei, whereas nDNA supported a sister relationship between I. bullockii and I. abeillei. Finally, I tested the utility of an extended IM model to examine the divergence population genetics of the three northern orioles (Ch. 3). Multi-population IMa2.0 analysis revealed extensive introgression between I. galbula and I. bullockii. In contrast, there was no gene flow between I. bullockii and I. abeillei , suggesting that their close nDNA relationship is not due to extensive introgression. However, previously undocumented substantial introgression between I. galbula and I. abeillei suggests that their close mtDNA relationship is likely due to mtDNA introgression and replacement in I. abeillei, causing the mtDNA tree to be misleading. Increased documentation of introgression in nature highlights the need for methods that can infer both trees and population parameters so that we can account for gene flow when inferring the evolutionary history of closely-related species.