Multinucleotide mutations cause false inferences of lineage-specific positive selection.

ABSTRACT: Phylogenetic tests of adaptive evolution, such as the widely used branch-site test (BST), assume that nucleotide substitutions occur singly and independently. Recent research has shown that errors at adjacent sites often occur during DNA replication, and the resulting multinucleotide mutations (MNMs) are overwhelmingly likely to be non-synonymous. To evaluate whether the BST misinterprets sequence patterns produced by MNMs as false support for positive selection, we analysed two genome-scale datasets-one from mammals and one from flies. We found that codons with multiple differences account for virtually all the support for lineage-specific positive selection in the BST. Simulations under conditions derived from these alignments but without positive selection show that realistic rates of M

SUBMITTER: Venkat A 

PROVIDER: S-EPMC6093625 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature