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A Bayesian Approach to Inferring the Phylogenetic Structure of Communities from Metagenomic Data

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 th...

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Detalles Bibliográficos
Autores principales: O’Brien, John D., Didelot, Xavier, Iqbal, Zamin, Amenga-Etego, Lucas, Ahiska, Bartu, Falush, Daniel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4096371/
https://www.ncbi.nlm.nih.gov/pubmed/24793089
http://dx.doi.org/10.1534/genetics.114.161299
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author O’Brien, John D.
Didelot, Xavier
Iqbal, Zamin
Amenga-Etego, Lucas
Ahiska, Bartu
Falush, Daniel
author_facet O’Brien, John D.
Didelot, Xavier
Iqbal, Zamin
Amenga-Etego, Lucas
Ahiska, Bartu
Falush, Daniel
author_sort O’Brien, John D.
collection PubMed
description 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.
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spelling pubmed-40963712014-07-16 A Bayesian Approach to Inferring the Phylogenetic Structure of Communities from Metagenomic Data O’Brien, John D. Didelot, Xavier Iqbal, Zamin Amenga-Etego, Lucas Ahiska, Bartu Falush, Daniel Genetics Investigations 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. Genetics Society of America 2014-07 2014-05-01 /pmc/articles/PMC4096371/ /pubmed/24793089 http://dx.doi.org/10.1534/genetics.114.161299 Text en Copyright © 2014 by the Genetics Society of America Available freely online through the author-supported open access option.
spellingShingle Investigations
O’Brien, John D.
Didelot, Xavier
Iqbal, Zamin
Amenga-Etego, Lucas
Ahiska, Bartu
Falush, Daniel
A Bayesian Approach to Inferring the Phylogenetic Structure of Communities from Metagenomic Data
title A Bayesian Approach to Inferring the Phylogenetic Structure of Communities from Metagenomic Data
title_full A Bayesian Approach to Inferring the Phylogenetic Structure of Communities from Metagenomic Data
title_fullStr A Bayesian Approach to Inferring the Phylogenetic Structure of Communities from Metagenomic Data
title_full_unstemmed A Bayesian Approach to Inferring the Phylogenetic Structure of Communities from Metagenomic Data
title_short A Bayesian Approach to Inferring the Phylogenetic Structure of Communities from Metagenomic Data
title_sort bayesian approach to inferring the phylogenetic structure of communities from metagenomic data
topic Investigations
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4096371/
https://www.ncbi.nlm.nih.gov/pubmed/24793089
http://dx.doi.org/10.1534/genetics.114.161299
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