The probability of correctly resolving a split as an experimental design criterion in phylogenetics

Systematic Biology
Edward Susko, Andrew J Roger

Abstract

We illustrate how recently developed large sequence-length approximations to probabilities of correct phylogenetic reconstruction for maximum likelihood estimation can be used to evaluate experimental design strategies. The specific criterion of interest is the probability of correctly resolving an a priori defined split of interest in a phylogenetic tree. Design strategies considered include increased taxon sampling and increasing sequence length. Our analyses of specific examples strongly suggest that it is better to sample taxa that connect as close as possible to the split of interest. Assuming this can be done, these examples suggest it is better to sample additional taxa than to add a comparable number of sites for the existing taxa. If the rates of evolution in the added taxa are slow, it is better to choose taxa connecting to a long edge, but if rates are comparable to a sister lineage, it is not necessarily the best strategy to sample taxa connected to a long edge. We also examined deleting taxa while increasing the number of sites. Although deleting a small number of taxa distant from the split of interest can be beneficial, deleting too many or making poor choices as to what should be deleted can lead to smaller prob...Continue Reading

References

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Jul 27, 2007·Systematic Biology·Koen GeutenNick Goldman

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Citations

Jan 16, 2014·BMC Evolutionary Biology·Per G P EricsonJohan A A Nylander
Aug 15, 2015·Systematic Biology·Seraina KlopfsteinFredrik Ronquist
Jun 9, 2017·Systematic Biology·Seraina KlopfsteinNick Goldman
May 14, 2021·Molecular Biology and Evolution·Nicolás Mongiardino Koch
Sep 12, 2021·Systematic Biology·David A DuchêneSimon Y W Ho

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