Nucleotide diversity in Silene latifolia autosomal and sex-linked genes

Abstract

The plant Silene latifolia has separate sexes and sex chromosomes, and is of interest for studying the early stages of sex chromosome evolution, especially the evolution of non-recombining regions on the Y chromosome. Hitch-hiking processes associated with ongoing genetic degeneration of the non-recombining Y chromosome are predicted to reduce Y-linked genes' effective population sizes, and S. latifolia Y-linked genes indeed have lower diversity than X-linked ones. We tested whether this represents a true diversity reduction on the Y, versus the alternative possibility, elevated diversity at X-linked genes, by collecting new data on nucleotide diversity for autosomal genes, which had previously been little studied. We find clear evidence that Y-linked genes have reduced diversity. However, another alternative explanation for a low Y effective size is a high variance in male reproductive success. Autosomal genes should then also have lower diversity than expected, relative to the X, but this is not found in our loci. Taking into account the higher mutation rate of Y-linked genes, their low sequence diversity indicates a strong effect of within-population hitch-hiking on the Y chromosome.

Figure 1.

Summary of nucleotide diversity estimates using silent sites for X, A and PAR genes of S. latifolia (grey bars) and for the Y-linked homologues of the X-linked loci (black bars). The numbers of sites analysed, and references for the data sources are in the electronic supplementary material, table S3.

Figure 2.

Plot X/Y ratios predicted using equation (4) of Pool and Nielsen (Pool & Nielsen 2007). The calculations assumed the same mutation rate for all chromosomes, and a fivefold decrease (black symbols and line) or increase (grey symbols and line) in population size from an initial value of 10 000.