Dear Amanda,

Your questions is interesting but I was wondering why you need to start off with a fossil sample sequence rather than following the approach used by forensic science.

You would first survey the natural populations of the target species and determine the variation in a number of specific loci (i.e., the haplotype; the more sites where variation in sequence occurs the better) to produce a database (this may also uncover regional variation), and then compare the haplotype from a suspicious sample (or individual) to see if it matches any of your protected populations. If you do this population-level analysis, you can design specific PCR primers to target the most informative loci - which is what forensics does for humans.

The underlying idea in surveying populations is of course that natural selection might produce adapted organisms in particular regions and that these may differ in terms of sequence variations from other populations. Having fossil sequences is not really adding anything much, though intellectually it would be exciting to see how far back in time regional differences extend, and how this matches to on-going speciation.

Andrew

Dear Dr. Spiers

Thank you for taking the time to answer my question. I was interested in using fossil samples because this was a resource accessible to me. Given this, the population analysis you've mentioned is an approach I didn't think to consider. Thank you so much for the recommendation!