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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Bibliographic Details
Main Authors: O'Brien, John, Didelot, Xavier, Iqbal, Zamin, LucasAmenga-Etego, Ahiska, Bartu, Falush, Daniel
Format: Report
Language:unknown
Published: arXiv 2013
Subjects:
Quantitative Methods q-bio.QM
Populations and Evolution q-bio.PE
FOS Biological sciences
Antarctic
Antarc*
Online Access:https://dx.doi.org/10.48550/arxiv.1306.6313
https://arxiv.org/abs/1306.6313
id ftdatacite:10.48550/arxiv.1306.6313
record_format openpolar
spelling ftdatacite:10.48550/arxiv.1306.6313 2023-05-15T13:50:55+02:00 A Bayesian approach to inferring the phylogenetic structure of communities from metagenomic data O'Brien, John Didelot, Xavier Iqbal, Zamin LucasAmenga-Etego Ahiska, Bartu Falush, Daniel 2013 https://dx.doi.org/10.48550/arxiv.1306.6313 https://arxiv.org/abs/1306.6313 unknown arXiv arXiv.org perpetual, non-exclusive license http://arxiv.org/licenses/nonexclusive-distrib/1.0/ Quantitative Methods q-bio.QM Populations and Evolution q-bio.PE FOS Biological sciences Preprint Article article CreativeWork 2013 ftdatacite https://doi.org/10.48550/arxiv.1306.6313 2022-04-01T13:26:03Z 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 strong mixing among samples. 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. : 25 pages, 7 figures Report Antarc* Antarctic DataCite Metadata Store (German National Library of Science and Technology) Antarctic
institution Open Polar
collection DataCite Metadata Store (German National Library of Science and Technology)
op_collection_id ftdatacite
language unknown
topic Quantitative Methods q-bio.QM
Populations and Evolution q-bio.PE
FOS Biological sciences
spellingShingle Quantitative Methods q-bio.QM
Populations and Evolution q-bio.PE
FOS Biological sciences
O'Brien, John
Didelot, Xavier
Iqbal, Zamin
LucasAmenga-Etego
Ahiska, Bartu
Falush, Daniel
A Bayesian approach to inferring the phylogenetic structure of communities from metagenomic data
topic_facet Quantitative Methods q-bio.QM
Populations and Evolution q-bio.PE
FOS Biological sciences
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 strong mixing among samples. 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. : 25 pages, 7 figures
format Report
author O'Brien, John
Didelot, Xavier
Iqbal, Zamin
LucasAmenga-Etego
Ahiska, Bartu
Falush, Daniel
author_facet O'Brien, John
Didelot, Xavier
Iqbal, Zamin
LucasAmenga-Etego
Ahiska, Bartu
Falush, Daniel
author_sort O'Brien, John
title 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_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_sort bayesian approach to inferring the phylogenetic structure of communities from metagenomic data
publisher arXiv
publishDate 2013
url https://dx.doi.org/10.48550/arxiv.1306.6313
https://arxiv.org/abs/1306.6313
geographic Antarctic
geographic_facet Antarctic
genre Antarc*
Antarctic
genre_facet Antarc*
Antarctic
op_rights arXiv.org perpetual, non-exclusive license
http://arxiv.org/licenses/nonexclusive-distrib/1.0/
op_doi https://doi.org/10.48550/arxiv.1306.6313
_version_ 1766254301785620480

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