Does local adaptation cause high population differentiation of Silene latifolia Y chromosomes?

Natural selection can reduce the effective population size of the nonrecombining Y chromosome, whereas local adaptation of Y‐linked genes can increase the population divergence and overall intra‐species polymorphism of Y‐linked sequences. The plant Silene latifolia evolved a Y chromosome relatively recently, and most known X‐linked genes have functional Y homologues, making the species interesting for comparisons of X‐ and Y‐linked diversity and subdivision. Y‐linked genes show higher population differentiation, compared to X‐linked genes, and this might be maintained by local adaptation in Y‐linked genes (or low sequence diversity). Here we attempt to test between these causes by investigating DNA polymorphism and population differentiation using a larger set of Y‐linked and X‐linked S. latifolia genes (than used previously), and show that net sequence divergence for Y‐linked sequences (measured by Da, also known as δ) is low, and not consistently higher than X‐linked genes. This does not support local adaptation, instead, the higher values of differentiation measures for the Y‐linked genes probably result largely from reduced total variation on the Y chromosome, which in turn reflect deterministic processes lowering effective population sizes of evolving Y‐chromosomes.