I have a set of 16 species of nematodes, i build a mitochondrial and nuclear phylogeny with them, and i found discordance between the two phylogenetic hypothesis. One of the common reasons for this discordance is incomplete lineage sorting and introgression, i want to test for this phenomena as the cause of the discordance in my set of species. Is there a software or way you could recommend to test for this two causes?
The ABBA BABA test or D statistic is often used to answer this. Essentially if incomplete lineage sorting is the main cause of phylogenetic incongruence, the portion of ABBA and BABA site will be equal in frequency. A skew towards one particular phylogeny indicates introgression. This is generally used as a qualitative measure however as estimating the magnitude and direction is rather difficult. The D foil statistic however makes uses of a 5 species phylogeny to estimate the magnitude of introgression and direction under some assumptions.
D-statistic: Article Gene flow analysis method, the D-statistic, is robust in a w...
D-foil: https://academic.oup.com/sysbio/article/64/4/651/1650669
hope this helps!
Jordan Orosco Do you know if i can use it with deep divergent species, like non-sistes species of nematodes?. Is imperative to use biallelic genes or i can use orthologues for the test?
Guillermo Gerardo Hernández Robles in the paper i attached, the author explored that question and found: " We have shown that the relative population size, which is the ratio of population size and divergence time in generations, is the most important factor on the sensitivity of the D-statistic. " You need to measure the effective population size and the divergence from your species to determine if you'll have the sensitivity required. Consult the paper for what the minimum ratio is for sensitivity. If you don't have a population sample to determine effective population size you may want to limit the analysis to sister species with recent divergence only. I don't quite understand your last question. Do you mean present/ absent variation of an orthologue?
Jordan Orosco Oh excellent. The species i use aren´t that close, i have two phylogenetic hypothesis that were build with mitochondrial and nuclear markers, in one of them a clade of nematodes are sister to another one, but in nuclear one is ancestral to a bigger clade. So thats my divergence estimate and the reason of the doubt, with millions of years of divergence.
the last question is more like, do i need to use biallelic genes or if i could use dna sequences from orthologue estimation to do the d-statistic?. the divergence times are so deep that i don't know if that information could be useful when i use deep divergent species.
Guillermo Gerardo Hernández Robles you would probably want to use your orthologue estimate and measure the substitutions between species from that DNA sequence.
Hi Guillermo,
ABBA-BABA tests are an excellent place to start. I would also recommend a program called PhyloNetworks. This program tests whether the patterns of incongruence in your gene trees are better explained by a 'tree-like' (~ILS) or 'network-like' (hybridization) model. It also offers a pipeline (the TICR pipeline) to help you generate sets of gene trees that allow you to take phylogenetic reconstruction error into account.
Here's the wiki for PhyloNetworks, with a great tutorial: https://github.com/crsl4/PhyloNetworks.jl/wiki/PhyloNetworks:-estimate-&-plot-phylogenetic-networks
In addition, there's a really nice paper in New Phytologist which uses this method to look for ancient introgression in lupins:
Article Pleistocene glacial cycles drive isolation, gene flow and sp...
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