Abstract
AbstractWhen phylogenetic trees inferred from different genes are incongruent, several methods are available to reconcile gene trees and extract the shared phylogenetic information from the sequence data. Bayesian Concordance Analysis, implemented in BUCKy, aims to extract the vertical signal and to infer clusters of genes that share the same tree topology. The new version of BUCKy includes a quartet-based estimate of the species tree with branch lengths in coalescent units.
Highlights
Inference is made on the genomic support of clades, measured as the proportion of genes that truly have the clade in their tree, or the concordance factor of the clade
This genomic support is fundamentally different from the statistical support for a clade to be in the concordance tree, which is determined by the precision in estimated concordance factors
This is illustrated by the analysis of over 30,000 gene fragments in apes: BUCKy inferred a 1.0 posterior probability for the concordance tree even though one clade had a 76% concordance factor, showing substantial true variability among gene trees
Summary
Gene tree reconciliation: new developments in Bayesian concordance analysis with BUCKy When different genes provide incongruent gene trees, some method for gene tree reconciliation is needed to extract the phylogenetic information from the sequence data. Bayesian Concordance Analysis aims to extract the vertical signal and to infer clusters of genes that share the same tree topology. Inference is made on the genomic support of clades, measured as the proportion of genes that truly have the clade in their tree, or the concordance factor of the clade.
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