Imperial College London
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ProfessorAlfriedVogler

Faculty of Natural Sciences, Department of Life Sciences (Silwood Park)

Professor of Molecular Systematics
 
 
 
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Contact

 

+44 (0)20 7942 5613a.vogler

 
 
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Location

 

Sir Alexander Fleming BuildingSouth Kensington Campus

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Summary

 

Publications

Citation

BibTex format

@article{Song:2016:gbe/evw086,
author = {Song, F and Li, H and Jiang, P and Zhou, X and Liu, J and Sun, C and Vogler, AP and Cai, W},
doi = {gbe/evw086},
journal = {Genome Biology and Evolution},
pages = {1411--1426},
title = {Capturing the phylogeny of holometabola with mitochondrial genome data and bayesian site-heterogeneous mixture models},
url = {http://dx.doi.org/10.1093/gbe/evw086},
volume = {8},
year = {2016}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - 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.
AU  - Song,F
AU  - Li,H
AU  - Jiang,P
AU  - Zhou,X
AU  - Liu,J
AU  - Sun,C
AU  - Vogler,AP
AU  - Cai,W
DO  - gbe/evw086
EP  - 1426
PY  - 2016///
SN  - 1759-6653
SP  - 1411
TI  - Capturing the phylogeny of holometabola with mitochondrial genome data and bayesian site-heterogeneous mixture models
T2  - Genome Biology and Evolution
UR  - http://dx.doi.org/10.1093/gbe/evw086
UR  - http://hdl.handle.net/10044/1/33070
VL  - 8
ER  -
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