The Trees in the Peaks

We suggest a gene-tree/species-tree approach to speciation and whole genome duplication (WGD) to resolve the occurrence of these events in phylogenetic analysis. We propose a more principled way of estimating the parameters of gene divergence and fractionation than the standard mixture of normals analysis. We formulate an algorithm for resolving data on local peaks in the distributions of duplicate gene similarities for a number of related genomes. Illustrating with a comprehensive analysis of WGD-origin duplicate gene data from six members of the family Brassicaceae, we discuss the effects of variable evolutionary rates and data degradation due to fractionation. We introduce the notion of peak tree, as a template for all gene trees evolving by speciation, WGD and fractionation.

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