Hi Ryan, I noticed a large number ~2.5k sites in the bottleneck VCF are duplicated with the ancestral states flipped. For example : 1 69851 538 A G . PASS AA=A GT 1|0 1|1 1|0 1|1 1|1 1|0 1|1 1|1 1|1 1|1 1|0 1|1 0|1 0|1 1|1 1|1 1|1 0|0 1|1 1|0 1|0 1|0 1 69851 539 G A . PASS AA=G GT 1|0 1|1 1|0 1|1 1|1 1|0 1|1 1|1 1|1 1|1 1|0 1|1 0|1 0|1 1|1 1|1 1|1 0|0 1|1 1|0 1|0 1|0 I didn't see the same for the secondary contact VCF. Just thought it was worth mentioning as it might cause some issues. I also was wondering if we knew for the bottleneck scenario if the bottleneck Ne is the same as the current Ne. That is, do we know that there is no growth after the bottleneck? Best, Solomon

Created by Solomon Sloat solomonsloat
Hi @solomonsloat, Thanks for calling this issue to our attention! Old versions of the bottleneck datasets were accidentally uploaded. They should now be the correct datasets. I'll leave it up to Ryan for your other question, since I'm not sure how much detail he wants to give for each scenario vs. letting participants test different methods/models on their own. Travis

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