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A Bayesian approach to inferring the phylogenetic structure of communities from metagenomic data
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O'Brien, J. D., Didelot, Xavier, Iqbal, Z., Amenga-Etego, L., Ahiska, B. and Falush, D. (2014) A Bayesian approach to inferring the phylogenetic structure of communities from metagenomic data. Genetics, 197 (3). pp. 925-937. doi:10.1534/genetics.114.161299 ISSN 0016-6731.
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Official URL: http://dx.doi.org/10.1534/genetics.114.161299
Abstract
Metagenomics provides a powerful new tool set for investigating evolutionary interactions with the environment. However, an absence of model-based statistical methods means that researchers are often not able to make full use of this complex information. We present a Bayesian method for inferring the phylogenetic relationship among related organisms found within metagenomic samples. Our approach exploits variation in the frequency of taxa among samples to simultaneously infer each lineage haplotype, the phylogenetic tree connecting them, and their frequency within each sample. Applications of the algorithm to simulated data show that our method can recover a substantial fraction of the phylogenetic structure even in the presence of high rates of migration among sample sites. We provide examples of the method applied to data from green sulfur bacteria recovered from an Antarctic lake, plastids from mixed Plasmodium falciparum infections, and virulent Neisseria meningitidis samples
Item Type: | Journal Article | ||||||
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Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||||
Journal or Publication Title: | Genetics | ||||||
Publisher: | Genetics Society of America | ||||||
ISSN: | 0016-6731 | ||||||
Official Date: | 14 July 2014 | ||||||
Dates: |
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Volume: | 197 | ||||||
Number: | 3 | ||||||
Page Range: | pp. 925-937 | ||||||
DOI: | 10.1534/genetics.114.161299 | ||||||
Status: | Peer Reviewed | ||||||
Publication Status: | Published | ||||||
Access rights to Published version: | Open Access (Creative Commons) |
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