Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution.

ABSTRACT: Inference of gene sequences in ancestral species has been widely used to test hypotheses concerning the process of molecular sequence evolution. However, the approach may produce spurious results, mainly because using the single best reconstruction while ignoring the suboptimal ones creates systematic biases. Here we implement methods to correct for such biases and use computer simulation to evaluate their performance when the substitution process is nonstationary. The methods we evaluated include parsimony and likelihood using the single best reconstruction (SBR), averaging over reconstructions weighted by the posterior probabilities (AWP), and a new method called expected Markov counting (EMC) that produces maximum-likelihood estimates of substitution counts for any branch under a nonsta

SUBMITTER: Matsumoto T 

PROVIDER: S-EPMC4512549 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature