Capturing the phylogeny of holometabola with mitochondrial genome data and bayesian site-heterogeneous mixture models
File(s)
Published version
Author(s)
Type
Journal Article
Abstract
After decades of debate, a mostly satisfactory resolution of relationships among the 11 recognized holometabolan orders of insects has been reached based on nuclear genes, resolving one of the most substantial branches of the tree-of-life, but the relationships are still not well established with mitochondrial genome data. The main reasons have been the absence of sufficient data in several orders and lack of appropriate phylogenetic methods that avoid the systematic errors from compositional and mutational biases in insect mitochondrial genomes. In this study, we assembled the richest taxon sampling of Holometabola to date (199 species in 11 orders), and analyzed both nucleotide and amino acid data sets using several methods. We find the standard Bayesian inference and maximum-likelihood analyses were strongly affected by systematic biases, but the site-heterogeneous mixture model implemented in PhyloBayes avoided the false grouping of unrelated taxa exhibiting similar base composition and accelerated evolutionary rate. The inclusion of rRNA genes and removal of fast-evolving sites with the observed variability sorting method for identifying sites deviating from the mean rates improved the phylogenetic inferences under a site-heterogeneous model, correctly recovering most deep branches of the Holometabola phylogeny. We suggest that the use of mitochondrial genome data for resolving deep phylogenetic relationships requires an assessment of the potential impact of substitutional saturation and compositional biases through data deletion strategies and by using site-heterogeneous mixture models. Our study suggests a practical approach for how to use densely sampled mitochondrial genome data in phylogenetic analyses.
Date Issued
2016-04-22
Date Acceptance
2016-04-11
Citation
Genome Biology and Evolution, 2016, 8 (5), pp.1411-1426
ISSN
1759-6653
Publisher
Oxford University Press
Start Page
1411
End Page
1426
Journal / Book Title
Genome Biology and Evolution
Volume
8
Issue
5
Copyright Statement
© The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
License URL
Identifier
PII: evw086
Subjects
Mitochondrial phylogenomics
PhyloBayes, Holometabola phylogeny
compositional bias
rate variation
tree-of-life
Developmental Biology
0604 Genetics
0603 Evolutionary Biology
Publication Status
Published