The effect of alignment uncertainty, substitution models and priors in building and dating the mammal tree of life.

ABSTRACT:

Background

The flood of genomic data to help build and date the tree of life requires automation at several critical junctures, most importantly during sequence assembly and alignment. It is widely appreciated that automated alignment protocols can yield inaccuracies, but the relative impact of various sources error on phylogenomic analysis is not yet known. This study employs an updated mammal data set of 5162 coding loci sampled from 90 species to evaluate the effects of alignment uncertainty, substitution models, and fossil priors on gene tree, species tree, and divergence time estimation. Additionally, a novel coalescent likelihood ratio test is introduced for comparing competing species trees against a given set of gene trees.

Results

The aligned DNA sequences of 5162 l

SUBMITTER: Du Y 

PROVIDER: S-EPMC6833305 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature