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From the abstract: "However, because these approaches infer a single best tree, they mask signatures of phylogenetic conflict that result from incomplete lineag
by inciampati 3y ago
From the abstract: "However, because these approaches infer a single best tree, they mask signatures of phylogenetic conflict that result from incomplete lineage sorting and historical hybridization."
So it can't be avoided, and the solution of making more trees from different stuff is somewhat unsatisfying. They have to work with the methods they have today.
- f6v 3y agoThey used maximum likelihood tree building. In Bayesian approach it’s possible to sample from a distribution of trees which can help with the uncertainty. Anyway, I only have very limited knowledge on this from my evolutionary biology course.
- runeblaze 3y agoReading the paper I think they used both SVDquartets (coalescence-based explicitly for ILS) and concatenation + maximum likelihood, which is a very sane combination for the analysis. Not contradicting you here, but at their scale it is unlikely any Bayesian approach will converge, so they had to settle with whatever they had to quantify uncertainty (branch supports and others). Edit: and also the Bayesian approaches might have model mismatch, for example I am not sure what's an accurate Bayesian method that models hybridization and ILS