2013/06/26 by John O'Brien, John O’Brien, Xavier Didelot +10
Biochemistry, Genetics and Molecular Biology · Environmental Science · #FOS: Biological sciences #Genetic diversity and population structure #Genomics and Phylogenetic Studies #Microbial Community Ecology and Physiology #Populations and Evolution (q-bio.PE) #Quantitative Methods (q-bio.QM) #q-bio.PE #q-bio.QM
paper · pdf · doi:10.48550/arxiv.1306.6313
25 pages, 7 figures
arxiv created 2013/06/26 · openalex publication_date 2013/06/26 · arxiv updated 2013/06/27 · openalex created_date 2022/10/02 · openalex updated_date 2026/07/28
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.