Keywords: c. chromosome structural variation; b. population variation
Understanding how genetic mutations underlie population differentiation is an important question for evolutionary biology. Chromosomal rearrangements can produce new genetic sequences that lead to phenotypic differences between closely related species. We have identified chromosomal rearrangements in two recently diverged populations of Drosophila yakuba from mainland Africa and the island of Mayotte. To understand the effect that a more contiguous reference sequence has on identifying chromosomal rearrangements, we also use a recent long-read Drosophila yakuba assembly. With this new reference we are able to identify many more mutations, many of which occur in centromeric regions.