ArticlePLoS genetics2009
Inference of microbial recombination rates from metagenomic data.
Article in PLoS genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 35 citations in OpenAlex.
- Dynamics of bacterial recombination in the human gut microbiome.PLoS biology · 2024Article
- Rhometa: Population recombination rate estimation from metagenomic read datasets.PLoS genetics · 2023Article
- Properties of Samples With Segregating Polymerase Chain Reaction (PCR) Dropout Mutations Within a Species.Evolutionary bioinformatics online · 2019Article
- Genetic adaptation of microbial populations present in high-intensity catfish production systems with therapeutic oxytetracycline treatment.Scientific reports · 2017Article
- Molecular Population Genetics.Genetics · 2017Review
- Global biogeography of Prochlorococcus genome diversity in the surface ocean.The ISME journal · 2016Article
- Two-Locus Likelihoods Under Variable Population Size and Fine-Scale Recombination Rate Estimation.Genetics · 2016Article
- Recombination in viruses: mechanisms, methods of study, and evolutionary consequences.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2015Review
- A Scale-Corrected Comparison of Linkage Disequilibrium Levels between Genic and Non-Genic Regions.PloS one · 2015Article
- Genome-wide estimation of linkage disequilibrium from population-level high-throughput sequencing data.Genetics · 2014Article
- Natural competence and the evolution of DNA uptake specificity.Journal of bacteriology · 2014Review
- Deep sequencing of evolving pathogen populations: applications, errors, and bioinformatic solutions.Microbial informatics and experimentation · 2014Article
- Pan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in Epsilonproteobacteria.Frontiers in microbiology · 2014Article
- Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade.Genome biology · 2013Article
- jPopGen Suite: population genetic analysis of DNA polymorphism from nucleotide sequences with errors.Methods in ecology and evolution · 2012Article
- Genome-wide fine-scale recombination rate variation in Drosophila melanogaster.PLoS genetics · 2012Article
- An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination.Genetics · 2011Article
- The influence of rickettsiologists on post-modern microbiology.Frontiers in cellular and infection microbiology · 2011Review
- A principled approach to deriving approximate conditional sampling distributions in population genetics models with recombination.Genetics · 2010Article
- MLTreeMap--accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies.BMC genomics · 2010Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Metagenomic sequencing projects from environments dominated by a small number of species produce genome-wide population samples. We present a two-site composite likelihood estimator of the scaled recombination rate, rho = 2N(e)c, that operates on metagenomic assemblies in which each sequenced fragment derives from a different individual. This new estimator properly accounts for sequencing error, as quantified by per-base quality scores, and missing data, as inferred from the placement of reads in a metagenomic assembly. We apply our estimator to data from a sludge metagenome project to demonstrate how this method will elucidate the rates of exchange of genetic material in natural microbial populations. Surprisingly, for a fixed amount of sequencing, this estimator has lower variance than similar methods that operate on more traditional population genetic samples of comparable size. In addition, we can infer variation in recombination rate across the genome because metagenomic projects sample genetic diversity genome-wide, not just at particular loci. The method itself makes no assumption specific to microbial populations, opening the door for application to any mixed population sample where the number of individuals sampled is much greater than the number of fragments sequenced.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.