Hello ResearchGate community,
Our lab has recently adopted GBS SNP data to gain a better insight into population dynamics of endangered non-model species in Australia (mainly amphibians, geckos and marsupials).
For most projects, after gaining a first insight into current population structure, we would like to understand whether the observed structure is a result of recent or ancient splits. As most of us are relatively new to the world of GBS and SNP data, we would really appreciate if you could point us to the best methodologies for doing so.
Any help is much appreciated.
Kind regards,
Lorenzo
I am by no means an expert in this but will share what I have come across. I believe BEAST, in particular the extension SNAPP, provides a way to generate phylogenies using allele frequencies. Then you can fix divergence dates on some of your nodes and estimate them for the rest of the tree. BEAST* also offers an option that exploit the actual haplotypes (not just SNPs) to estimate divergence. See Saglam et al. (Article Phylogenetics support an ancient common origin of two scient...
) for an example.I also received some advice to use MCMCtree to do something similar, which is part of the PAML package. Good luck.
Dear Justin,
Thank you greatly for your detailed answer. I have been recommended BEAST and/or SNAPP for this purpose by a few different people, so I think I will look into it as soon as I can find the time. I'll check MCMCtree as well, haven't heard of it but looks promising.
All the best with your work, and once again, thank you for your answer
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