Time To Most Common Ancestor Of Inversion Polymorphism

Question

[Ulrich]

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.

[Vitis]

Can you use the SNPs as characters to reconstruct a phylogeny for these individuals? Then you may be able to map the inversion on the phylogeny to trace its origin to certain nodes. It will be very hard to get the time estimate as you need points of known time to calibrate the entire tree.

Answer 1

[Joseph Hughes]

Using your SNPs (but not those from the inversion polymorphism) you could reconstruct a calibrated phylogeny either by using a known rate of substitution over time for your SNPs or by using calibration points on your tree (dated tips or nodes). Once you have your calibrated tree, map onto it the inversion polymorphism and look at the date of the node where this inversion polymorphism has occurred.