Speciation genomics and the role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards / Philip Lavretsky, Jeffrey M. Dacosta, Blanca E. Hernandez-Banos, Andrew Engilis Jr., Michael D. Sorenson, and Jeffrey L. Peters.

Includes bibliographical references (pages 5375-5378).

Speciation is a continuous and dynamic process, and studying organisms during the
early stages of this process can aid in identifying speciation mechanisms. The mallard
(Anas platyrhynchos) and Mexican duck (A. [p.] diazi) are two recently diverged taxa with
a history of hybridization and controversial taxonomy. To understand their evolutionary
history, we conducted genomic scans to characterize patterns of genetic diversity and
divergence across the mitochondrial DNA (mtDNA) control region, 3523 autosomal loci
and 172 Z-linked sex chromosome loci. Between the two taxa, Z-linked loci (ΦST = 0.088)
were 5.2 times more differentiated than autosomal DNA (ΦST = 0.017) but comparable to
mtDNA (ΦST = 0.092). This elevated Z differentiation deviated from neutral expectations
inferred from simulated data that incorporated demographic history and differences in
effective population sizes between marker types. Furthermore, 3% of Z-linked loci, compared
to <0.1% of autosomal loci, were detected as outlier loci under divergent selection
with elevated relative (ΦST) and absolute (dXY) estimates of divergence. In contrast, the
ratio of Z-linked and autosomal differentiation among the seven Mexican duck sampling
locations was close to 1:1 (ΦST = 0.018 for both markers). We conclude that between mallards
and Mexican ducks, divergence at autosomal markers is largely neutral, whereas
greater divergence on the Z chromosome (or some portions thereof) is likely the product
of selection that has been important in speciation. Our results contribute to a growing
body of literature indicating elevated divergence on the Z chromosome and its likely
importance in avian speciation.