Background: The study of speciation has expanded with the increasing availability and affordability of highresolution 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. Results: Population measures of relative differentiation between hybridizing species reveal that different chromosome types diverge at different stages of speciation. Using F ST 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. Conclusions: Our finding that genomic windows of elevated F ST accumulate on small autosomes earlier in speciation than on larger autosomes is counter to the prediction that F ST increases with size of chromosome (i.e. with decreased recombination rate), and is not represented when weighted average F ST per chromosome is compared with chromosome size. The results of this study suggest that multiple chromosome characteristics such as recombination rate and gene density combine to influence the genomic locations of signatures of divergence.

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