I want to develop a research proposal to investigate a possible hybridization of a bird species. Also need to understand the direction of the gene flow. If anybody knows the correct procedure to do this or any reference that I can use please let me know..
Thanks
Look up D-statistics- attached some papers. If you have whole genomes to work with, you could calculate this in sliding windows to examine enrichment of introgressed regions throughout the genome (see Dashamaptera et al. 2012).
There are several variants (e.g. 5-taxon, "Dfoil"), but in the original 4-taxon test, for a fixed tree of ((A, B), C), D) you can test for introgression between taxon C and A or C and B by examining the relative frequency of discordant topologies inferred from your various loci throughout the genome.
Of interest are two particular discordant patterns: a polymorphism that seems to unite A and C ("BABA", or a case in which B and D have the ancestral state, and A and C share the derived state) and those which unite B and C ("ABBA"). We could expect these patterns to show up simply due to stochasticity in lineage sorting, so in order to discriminate lineage sorting effects from "hybridization" we look for a bias towards one pattern or another. The assumption here is that random lineage sorting would tend to create a relatively equal number of "ABBA" to "BABA" sites... So we calculate the simple D statistic as sum(ABBA-BABA)/sum(ABBA+BABA).
Hope that helps. There are other useful tests for introgression but the "ABBA-BABA" test (Durand et al. 2011) is very commonly used- but also see the extensions of Eaton and Ree (2012) and Pease and Hahn (2015).
Article Testing for Ancient Admixture between Closely Related Populations
Article Inferring Phylogeny and Introgression using RADseq Data: An ...
Article Detection and Polarization of Introgression in a Five-Taxon Phylogeny
Article Historical introgression among the American live oaks and th...
Article Butterfly genome reveals promiscuous exchange of mimicry ada...
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