skyline plots from SNP data

[Michael Harvey]

All,

I have some datasets of a few thousand SNPs (from genotyping by sequencing), and I'm interested in modeling changes in effective population size over time within populations using skyline plots. I know I *can* do an EBSP analysis in BEAST, but would this be appropriate? I could input the entire tag sequences as alignments, but they are only ~60 bp in length and each will contain only the single SNP. Or is anyone aware of a similar method specifically for SNP data with no linkage information? Perhaps this will be implemented in SNAPP at some point?

Thanks,

Mike Harvey

[Michael Harvey]

I found out MIGRATE (Beerli) can estimate rough skyline plots for population size (and migration). It assumes equal rates across loci, but may be a good alternative for some folks.

Mike Harvey