Genomic architecture of speciation in a warbler species complex

My PhD research investigated the mechanism of speciation in natural populations. Despite a great progress made since the ‘modern synthesis’ on the genetic basis of speciation, no consensus has been reached in terms of the genomic architecture of speciation: whether speciation is initiated by many regions (scattered across the genome), each of small effects on traits under weak selection (divergent selection or reinforcement), or a few regions that have strong effects on traits under strong selection. Understanding the genomic architecture of speciation is important because it determines whether reproductive isolation could effectively evolve when the diverging lineages still hybridize. I investigated this question in a Setophaga warbler species pair at the early stage of divergence: Townsend’s (Setophaga townsendi) and Hermit warblers (S. occidentalis). These two species hybridize extensively in the hybrid zone in Washington Cascades, demonstrating stable genomic clines over decades. This species complex demonstrates clear pattern of ‘selection with gene flow’, in which a few regions of large effects under strong divergent selection are highly differentiated between lineages, although the rest of the genomes are homogenized by gene flow. These nuclear genomic regions under selection are related to plumage coloration and mitochondrial fatty acid metabolism and are tightly associated with climatic variation among sites. Altogether, mitonuclear adaptation and selection on pigment patterning are prevailing evolutionary forces that counteract gene flow and allow speciation in this warbler system to proceed, despite ancient admixture and ongoing hybridization.Science, Faculty ofZoology, Department ofGraduat