UC Riverside

The study of speciation has expanded with the increasing availability and affordability of high-resolution genomic data. How the genome evolves throughout the process of divergence and which regions of the genome are responsible for causing and maintaining that divergence have been central questions in recent work. Here, we use three pairs of species from the recently diverged bee hummingbird clade to investigate differences in the genome at different stages of speciation, using divergence times as a proxy for the speciation continuum. We then use the same study system to compare populations in allopatry with populations in a hybrid zone for each sister species pair. We look for patterns of population structure and introgression across the genome and at different chromosome types. Finally, we use a single species to quantify variation in a species-diagnostic sexually-selected trait. Overall, we found different levels of differentiation and introgression across different chromosome types. Using FST as our relative measure of differentiation we found that the sex chromosome shows signs of divergence early in speciation. Next, small autosomes (microchromosomes) accumulate highly diverged genomic regions, while the large autosomes (macrochromosomes) accumulate genomic regions of divergence at a later stage of speciation. Our finding that genomic windows of elevated FST accumulate on small autosomes earlier in speciation than on larger autosomes is counter to the prediction that FST increases with size of chromosome (i.e. with decreased recombination rate), and is not represented when weighted average FST per chromosome is compared with chromosome size. The results of this dissertation suggest that multiple chromosome characteristics such as recombination rate and gene density combine to influence the genomic signatures of divergence and introgression.