Speciation is an important evolutionary process that occurs when barriers to gene flow evolve between previously panmictic populations. Although individual barriers to gene flow have been studied extensively, we know relatively little regarding the number of barriers that isolate species or whether these barriers are polymorphic within species. Herein, we use a series of field and lab experiments to quantify phenotypic divergence and identify possible barriers to gene flow between the butterfly species Lycaeides idas and Lycaeides melissa. We found evidence that L. idas and L. melissa have diverged along multiple phenotypic axes. Specifically, we identified major phenotypic differences in female oviposition preference and diapause initiation, and more moderate divergence in mate preference. Multiple phenotypic differences might operate as barriers to gene flow, as shown by correlations between genetic distance and phenotypic divergence and patterns of phenotypic variation in admixed Lycaeides populations. Although some of these traits differed primarily between species (e.g., diapause initiation), several traits also varied among conspecific populations (e.g., male mate preference and oviposition preference).

The study of genome-wide variation in population genetic processes (termed population genomics) will advance our understanding of adaption, speciation, and the nature of species boundaries. Progress in population genomics is limited by inadequate statistical models. I proposed and implemented hierarchical Bayesian models to study variation in introgression and genetic differentiation across the genome. Variable introgression and genetic differentiation are informative regarding the genetics of adaptation and reproduction isolation. I tested these models using simulated and empirical data sets. Both models performed well under a variety of conditions, although specific demographic histories resulted in a weak correspondence between the genetic architecture of isolation and introgression. My analyses of published empirical data sets identified putatively adaptive genetic variation at previously noted and novel loci in mice and humans. I used these Bayesian models coupled with additional analyses of genetic, morphological, and behavioral data to study hybridization and speciation in Lycaeides butterflies, and particularly to examine the genetics and evolution of reproductive isolation between two butterfly species: Lycaeides idas and L. melissa. Using DNA sequences and morphological data, I identified several geographic regions of hybridization and introgression between these butterfly species. I documented extensive admixture and introgression in the Jackson Hole region of the central Rocky mountains, which indicates reproductive isolation between L. idas and L. melissa populations in this area is incomplete. Model-based analyses of DNA sequence data revealed considerable genome-wide variation in genetic differentiation and introgression in Jackson Hole Lycaeides . Moreover, genetic regions with a history of divergent selection in L. idas and L. melissa populations also affected hybrid fitness. These results are consistent with the hypothesis that reproductive isolation is a property of specific loci and evolves primarily by divergent selection. Morphological analyses and field experiments identified multiple axes of phenotype divergence between L. idas and L. melissa, and several of these trait differences might contribute to reproductive isolation. My future research will attempt to link these phenotypic differences with genomic data to more fully understand the genetics and evolution of isolation.

Speciation is the process by which reproductively isolated lineages arise, and is one of the fundamental means by which the diversity of life increases. Whereas numerous studies have documented an association between ecological divergence and reproductive isolation, relatively little is known about the role of natural selection in genome divergence during the process of speciation. Here, we use genome-wide DNA sequences and Bayesian models to test the hypothesis that loci under divergent selection between two butterfly species (Lycaeides idas and L. melissa) also affect fitness in an admixed population. Locus-specific measures of genetic differentiation between L. idas and L. melissa and genomic introgression in hybrids varied across the genome. The most differentiated genetic regions were characterized by elevated L. idas ancestry in the admixed population, which occurs in L. idas-like habitat, consistent with the hypothesis that local adaptation contributes to speciation. Moreover, locus-specific measures of genetic differentiation (a metric of divergent selection) were positively associated with extreme genomic introgression (a metric of hybrid fitness). Interestingly, concordance of differentiation and introgression was only partial. We discuss multiple, complementary explanations for this partial concordance.

The distribution of genetic variation within and among populations is commonly used to infer their demographic and evolutionary histories. This endeavour has the potential to benefit substantially from high-throughput next-generation sequencing technologies through a rapid increase in the amount of data available and a corresponding increase in the precision of parameter estimation. Here we report the results of a phylogeographic study of the North American butterfly genus Lycaeides using 454 sequence data. This study serves the dual purpose of demonstrating novel molecular and analytical methods for population genetic analyses with 454 sequence data and expanding our knowledge of the phylogeographic history of Lycaeides. We obtained 341 045 sequence reads from 12 populations that we were able to assemble into 15 262 contigs (most of which were variable), representing one of the largest population genetic data sets for a non-model organism to date. We examined patterns of genetic variation using a hierarchical Bayesian analysis of molecular variance model, which provides precise estimates of genome-level øST while appropriately modelling uncertainty in locus-specific øST. We found that approximately 36% of sequence variation was partitioned among populations, suggesting historical or current isolation among the sampled populations. Estimates of pairwise genome-level øST were largely consistent with a previous phylogeographic model for Lycaeides, suggesting fragmentation into two to three refugia during Pleistocene glacial cycles followed by post-Pleistocene range expansion and secondary contact leading to introgressive hybridization. This study demonstrates the potential of using genome-level data to better understand the phylogeographic history of populations.a.