A Bayesian Approach to Inferring the Phylogenetic Structure of Communities from Metagenomic Data
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 inf...
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Oxford University Press (OUP)
2014
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Online Access: | http://dx.doi.org/10.1534/genetics.114.161299 https://academic.oup.com/genetics/article-pdf/197/3/925/50036917/genetics0925.pdf |
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croxfordunivpr:10.1534/genetics.114.161299 2024-09-15T17:48:22+00:00 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 2014 http://dx.doi.org/10.1534/genetics.114.161299 https://academic.oup.com/genetics/article-pdf/197/3/925/50036917/genetics0925.pdf en eng Oxford University Press (OUP) https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model Genetics volume 197, issue 3, page 925-937 ISSN 1943-2631 journal-article 2014 croxfordunivpr https://doi.org/10.1534/genetics.114.161299 2024-08-05T04:28:57Z 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. Article in Journal/Newspaper Antarc* Antarctic Oxford University Press Genetics 197 3 925 937 |
institution |
Open Polar |
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Oxford University Press |
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croxfordunivpr |
language |
English |
description |
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. |
format |
Article in Journal/Newspaper |
author |
O’Brien, John D Didelot, Xavier Iqbal, Zamin Amenga-Etego, Lucas Ahiska, Bartu Falush, Daniel |
spellingShingle |
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 |
author_facet |
O’Brien, John D Didelot, Xavier Iqbal, Zamin Amenga-Etego, Lucas Ahiska, Bartu Falush, Daniel |
author_sort |
O’Brien, John D |
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 |
Oxford University Press (OUP) |
publishDate |
2014 |
url |
http://dx.doi.org/10.1534/genetics.114.161299 https://academic.oup.com/genetics/article-pdf/197/3/925/50036917/genetics0925.pdf |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_source |
Genetics volume 197, issue 3, page 925-937 ISSN 1943-2631 |
op_rights |
https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model |
op_doi |
https://doi.org/10.1534/genetics.114.161299 |
container_title |
Genetics |
container_volume |
197 |
container_issue |
3 |
container_start_page |
925 |
op_container_end_page |
937 |
_version_ |
1810289511003848704 |