Hej, I hope my question is not too embarrassing but I am pretty lost in the phylogenetic literature. I am wondering what would be the best and fastest way of estimating the time to the most recent common ancestor of an inversion polymorphism in a non-model species. Most studies I found either used inbred lines (Drosophila) or BAC clones (humans) to derive haplotypes. However, both methods are not an option for me.
I could use SNP data on 1000 individuals. However, inside the inversion would be only a few SNPs. Is there a way to use these kind of data anyways?
I could also imagine sequencing pools of individuals that are homozygous for one or the other type but do not know how to proceed from thereon or if there are easier ways of doing this.
Thanks in advance.