Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods.

Abstract excerpt

Discord in the estimated gene trees among loci can be attributed to both the process of mutation and incomplete lineage sorting. Effectively modeling these two sources of variation--mutational and coalescent variance--provides two distinct challenges for phylogenetic studies. Despite extensive investigation on mutational models for gene-tree estimation over the past two decades and recent attention to modeling of...

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