Sudden expansion and contraction of a population

[jaurbanChicago]

Hi Stephan!

I am running some tests with msmc2 and some high coverage 1000 Genomes individuals (4 haplotypes per population) and I am observing a sudden expansion and contraction in a very short interval for STU. Do you know if this is more likely to be a result of a technical artifact (e.g., maybe due to phasing errors) or could it also be biological? I have observed similar patterns for other populations in the literature but the papers don't spend any time explaining why this might be happening. Thanks a lot in advance for your help!

Best

[stschiff]

Hmm, not sure. Have you checked whether there is evidence for a recent contraction here? For example via runs of homozygosity? Otherwise I don't know. Have you compared these results to results from running on the single diploid genomes separately, just to rule out that the phasing could be causing this.