I generated a VCF file including 20 samples belonging to two species (A and B), variant calling was done using GATK best practice pipeline (only autosomes chromosomes). Now I want to detect the introgressed regions from A sp. to B sp. I searched for a way to do that and find more articles used the ABBA BABA test and fd statistics. When I read some articles and some manuals for this test, I found they use 4 populations (P1, P2, P3, and O as outgroup).
Now my question is, how I can handle this analysis using two populations?
Do you have a suggestion for another valid method of identifying introgressed regions?
You may have already thought of it but, is there any supplementary data you can download from previous studies? There is also the possibility to split a sample up? This is a good tutorial for ABBA BABA. But if you only have the two sample and no outgroup, its going to be difficult. There is a three way test discussed here.
Thanks, Vic
What features should the outgroup have? For example, to identify the gene flow between cattle and yak, which species can be a candidate for the outgroup?
If I use the D3 for our work by adding another breed to my work, it tells me if there is an introgression or not, what should I do to identify the location of introgressed regions on the genome?
I don't know about what outgroup you should use, I don't work on cattle or yak, have a look at some phylogenetic trees, you need a good knowledge of your study species to decide what to do.
The D statistic will let you know if there is introgression, the the f (fd) statistics will allow you to investigate the overall proportion of admixture and you can also perform that on a sliding window along the genome to locate loci. Have a look at Dsuite .
Good luck!
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ABBA BABA needs 4 populations by definition, so you won't be able to do it using only 2. I couldn't say if you could use another method, but hopefully someone else will.