IntroductionPhylogenies, tree diagrams that represent evolutionary relationships among species (or taxa, more generically), are often estimated from molecular sequences. This estimation process typically occurs in two distinct steps. First, molecular sequences are aligned into a matrix (called an alignment), possibly by adding gap characters within sequences to account for historical insertions and deletions (indels) of nucleotide bases. Second, the phylogeny is estimated from the previously estimated alignment. This sequential approach ignores alignment uncertainty, leading to several problems with phylogenetic inference.If the alignment contains ambiguous regions, ignoring uncertainty in the alignment can result in exaggerated support for inferred phylogenies (Lutzoni et al., ). Moreover, if the sequence alignment is determined by an alignment method that assumes a fixed guide tree, then the estimated phylogenies in the second step may be biased toward this fixed guide tree (Nelesen et al., ). As various alignment methods typically align ambiguous regions differently, phylogenies estimated by the traditional sequential approach can change considerably according to the choice of alignment method (Wong et al., ). (See Web Appendix A for our investigation of the problems of the traditional sequential approach using a simulated data set). A simple approach to avoid these problems is to exclude
Biometrics – Wiley
Published: Jan 1, 2018
Keywords: ; ; ; ; ; ;
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