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...
| Main Authors: | , , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
Genetics
2014
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| _version_ | 1797070522889011200 |
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| author | O'Brien, J Didelot, X Iqbal, Z Amenga-Etego, L Ahiska, B Falush, D |
| author_facet | O'Brien, J Didelot, X Iqbal, Z Amenga-Etego, L Ahiska, B Falush, D |
| author_sort | O'Brien, J |
| collection | OXFORD |
| 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. |
| first_indexed | 2024-03-06T22:40:06Z |
| format | Journal article |
| id | oxford-uuid:5b3fb6b6-d51b-4538-ac9a-784f2ce1027d |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T22:40:06Z |
| publishDate | 2014 |
| publisher | Genetics |
| record_format | dspace |
| spelling | oxford-uuid:5b3fb6b6-d51b-4538-ac9a-784f2ce1027d2022-03-26T17:21:03ZA Bayesian approach to inferring the phylogenetic structure of communities from metagenomic data.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:5b3fb6b6-d51b-4538-ac9a-784f2ce1027dEnglishSymplectic Elements at OxfordGenetics2014O'Brien, JDidelot, XIqbal, ZAmenga-Etego, LAhiska, BFalush, DMetagenomics 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. |
| spellingShingle | O'Brien, J Didelot, X Iqbal, Z Amenga-Etego, L Ahiska, B Falush, D 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 |
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