Abstract
The correct interpretation of any phylogenetic tree is dependent on that tree being correctly rooted. We present STRIDE, a fast, effective, and outgroup-free method for identification of gene duplication events and species tree root inference in large-scale molecular phylogenetic analyses. STRIDE identifies sets of well-supported in-group gene duplication events from a set of unrooted gene trees, and analyses these events to infer a probability distribution over an unrooted species tree for the location of its root. We show that STRIDE correctly identifies the root of the species tree in multiple large-scale molecular phylogenetic data sets spanning a wide range of timescales and taxonomic groups. We demonstrate that the novel probability model implemented in STRIDE can accurately represent the ambiguity in species tree root assignment for data sets where information is limited. Furthermore, application of STRIDE to outgroup-free inference of the origin of the eukaryotic tree resulted in a root probability distribution that provides additional support for leading hypotheses for the origin of the eukaryotes.
Highlights
The rooting of a phylogenetic tree is critical for the correct interpretation of the tree
STRIDE Identifies the Correct Root of Species Trees Given Simulated Gene Tree Data Sets The ability of STRIDE to correctly infer the root of a known species tree was tested using three published, simulated gene tree data sets
STRIDE is an automated method for identifying and analyzing gene duplication events to infer the root of species trees
Summary
The rooting of a phylogenetic tree is critical for the correct interpretation of the tree. For the presented tree, identifying a wrong branch as the root A species tree only gives the correct evolutionary relationships when rooted correctly It is of critical importance to our interpretation of relationships, and the evolutionary history of life on earth, that we have accurate methods of inferring the root of species phylogenies. Correct species tree rooting is of critical importance for the inference of orthology relationships between genes. 1B) is required to correctly root the gene tree An incorrect rooting of the species tree 1C–F) leads to an incorrect inference of the root of the gene tree Our ability to compare the biology of species, through comparisons between orthologous genes, is reliant on accurate methods of inferring the root of species phylogenies
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