Statistically consistent and computationally efficient inference of ancestral DNA sequences in the TKF91 model under dense taxon sampling.

Statistically consistent and computationally efficient inference of ancestral DNA sequences in the TKF91 model under dense taxon sampling. Bull Math Biol. 2020 Jan 22;82(2):21 Authors: Fan WT, Roch S Abstract In evolutionary biology, the speciation history of living organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves correspond to current species and whose branchings indicate past speciation events. Phylogenetic analyses often rely on molecular sequences, such as DNA sequences, collected from the species of interest, and it is common in this context to employ statistical approaches based on stochastic models of sequence evolution on a tree. For tractability, such models necessarily make simplifying assumptions about the evolutionary mechanisms involved. In particular, commonly omitted are insertions and deletions of nucleotides-also known as indels. Properly accounting for indels in statistical phylogenetic analyses remains a major challenge in computational evolutionary biology. Here, we consider the problem of reconstructing ancestral sequences on a known phylogeny in a model of sequence evolution incorporating nucleotide substitutions, insertions and deletions, specifically the classical TKF91 process. We focus on the case of dense phylogenies of bounded height, which we refer to as the taxon-rich setting, where statistical consistency is achievable. We give the first explicit reconstruction al...
Source: Bulletin of Mathematical Biology - Category: Bioinformatics Authors: Tags: Bull Math Biol Source Type: research