Sex chromosomes evolved from a pair of autosomes that gained a sex determining function. It is hypothesized that cessation of recombination was sequentially expanded by the accumulation of sexually antagonistic loci linked to the sex determining locus. Lack of recombination leads to the degeneration of the non-recombining chromosome except a small part that is called the pseudo-autosomal region (PAR). In most systems, PAR is quite small which makes it difficult to infer the effect of sexually antagonistic selection on the surrounding neutral genetic variation. In contrast, the large PAR in ostrich provides an opportunity to look into the effect of sexual antagonism. In this case, we would be mainly interested in the patterns of neutral polymorphisms in the PAR boundary which is located in the proximity of the sex determining locus (DMRT1). The theoretical expectation for patterns of neutral genetic variation under sexual antagonism is developed in (KIRKPATRICK AND GUERRERO 2014) which provides a framework to interpret the observed polymorphism.
Maintenance of recombination in ancient sex chromosomes such as that of ratites could be due to a form of balancing selection, namely, over-dominance, in the heterogametic sex (OTTO 2014). Ostrich sex chromosomes are an interesting system because despite their very old age, have maintained recombination over more than 2/3 of the Z chromosome (YAZDI AND ELLEGREN 2014). Therefore, they provide a very useful system to investigate patterns of neutral genetic variation that could be produced by the presence of sites under balancing selection. Balancing selection leads to increased level of polymorphism in the region linked to the site under selection. A combination of neutrality tests can be used to investigate balancing selection. One of the tests is the HKA test which can be modified to reject neutrality only under excess polymorphism (ANDRES et al. 2009). Another test that can be used to detect excess polymorphism is Tajima’s D. Under balancing selection, alleles are kept at intermediate frequencies. Thus, an excess of pairwise heterozygosity compared to the number segregating sites produces a positive Tajima’s D. Theoretical expectation for patterns of neutral genetic variation in recombining sex chromosomes are developed in (KIRKPATRICK et al. 2010).
Here we will explicitly test if sex chromosomes in ostrich show signature of sexually antagonistic selection and balancing selection by using the whole genome resequencing data of three subspecies of ostrich.