Post date: Nov 14, 2013 11:26:27 PM
We want to identify the sex chromosomes among the timema linkage groups. Thus, I grabbed the sex information for about half the individuals from the extraction logs Patrik sent, but this information was missing for the other half of the individuals (the sex ids are in projects/timema_wgwild/variants/sexIds./txt). Based on these data I calculated the mean heterozygosity for males and females for each SNP. I then calculated means in each case by linkage group. Although mean heterozygosity (across all lg SNPs) was slightly higher in females (0.202) than males (0.196) this was not caused by exceptionally low male heterozygosity for any individual linkage group. So, I also looked at this by scaffold (in case our linkage groups were not as good as we think), but again there was no signal (i.e., we don't find individual scaffolds with particularly low male heterozygosity). I even repeated this for the non-lg SNPs (at the scaffold level only) and again we find no evidence that individual scaffolds have particularly low heterozygosity (i.e., heterozygosity approaching 0). Perhaps this is an assembly or variant calling issue such that (i) the sex chromosomes are not represented in the genome assembly, or (ii) we didn't call SNPs on these chromosomes. Alternatively this could be driven by too low of coverage to exclude heterozygosity for males (I kind of doubt this). This result also suggest that two of our linkage groups might eventually need to be merged to make room for the sex chromosomes (but again, they do not appear to be among the non-lg scaffolds either).