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Tutorials on phylogenetic and phylogenomic inference
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How to indentify the introgression region #1

Closed liufy11 closed 5 years ago

liufy11 commented 5 years ago

Both SNP data and Chromosome-Length Alignments can test whether exist introgression between two species ,More over, D-statistic can indentify the introgression region . But can you tell me how to judge the introgression region in detail ? To my knowledge ,the low D value or fD value refers to an introgression ,is that true ? if any, how to decide the threshold value, and Can Chromosome-Length Alignments indentify introgression region ? Thanks for your Detailed sharing . It's appreciated if you can illuminate my question.

mmatschiner commented 5 years ago

The introgressed region should have elevated D or fd. In principle, the identification of such regions is possible with chromosome-length alignments; however, in practice, the patterns are usually not very clear. But just check the fd in sliding-windows (and test different window sizes) and you will see how clear or ambiguous the introgression patterns are in your dataset.