Population Genetics of X and Y Chromosomes in the Dioecious Plant Rumex hastatulus

Sex chromosomes in the dioecious plant Rumex hastatulus are of interest for studying the early stages of sex chromosome evolution, especially the consequences of supressed recombination on the Y-chromosome. Recent work found that genes on the recently derived Y-chromosomes in this species are undergoing genetic degeneration; they are accumulating amino acid substitutions at an elevated rate, contain more unpreferred changes in codon usage, and are reduced in expression relative to X-linked alleles, with the magnitude of these effects being greater for genes that have been nonrecombining for longer. It is predicted that hitchhiking processes associated with this ongoing degeneration should also lower the effective population size of Y-linked genes relative to X or autosomal genes and therefore reduce levels of nucleotide diversity on the Y-chromosome. Here, using transcriptome-wide data, we analyze hundreds of X, Y, and autosomal genes from multiple populations to test whether nucleotide diversity is reduced on the Y-chromosome. In particular, we test whether neutral processes or the effects of linked selection in regions of suppressed recombination can explain differences in nucleotide diversity between sex-linked and autosomal genes. Our study is the first to investigate nucleotide diversity at a genome wide scale in a young plant sex chromosome system, and the results provide novel insights into the effects of suppressed recombination on patterns of genetic diversity.