Genetic distance metrics for subtle pop structure

[Sarah Tomke]

Hi, does anyone have recommendations for which genetic distance metrics we should report when there are no discernable populations on the landscape? For example, I'm working with RADseq data from white-tailed deer that have been sampled quite evenly across my entire study area. There's evidence to suggest subtle population structure due to landscape barriers (admixture is still very high), but metrics like Fst seem inappropriate here since there's no clear cut populations? Thanks!

[Melanie Murphy]

I would recommend something you can use at the indivudal level, which is true for some of the D statistics (Dps, Dcord, Nei's D adapted for individuals).  Fst tends to be not as sensitive to recent patterns as D statistics in general.  

[Nathan Alexander]

I would also recommend this paper by Shirk et al. that looks at individual genetic metric performance:

 https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12684

For individual landscape genetic studies, I often have used Dps (microsatellite data), but I think that PCA is a promising approach that relaxes a lot of the assumptions that other genetic metrics have.

[Jane Dostart]

I have been using Nei's Da for individual, pairwise, genetic distances. Equation 7 in paper attached. 

The R package hierfstat has a Da function you could use. 

[Melanie Murphy]

One that that is nice about Dps and Dcord is that they make no pop gen assumptions (and very little other assumptions as well).