ArticlePLoS computational biology2009
Identifying currents in the gene pool for bacterial populations using an integrative approach.
Article in PLoS computational biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
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- Prevalence and Persistence of Ceftiofur-ResistantAnimals : an open access journal from MDPI · 2022Article
- Assessment of genetic relationships among native and introduced Himalayan balsam (Ecology and evolution · 2021Article
- High-Zinc Supplementation of Weaned Piglets Affects Frequencies of Virulence and Bacteriocin Associated Genes Among IntestinalFrontiers in veterinary science · 2020Article
- Postglacial colonization history reflects in the genetic structure of natural populations ofEcology and evolution · 2019Article
- A fast likelihood solution to the genetic clustering problem.Methods in ecology and evolution · 2018Article
- Gene flow during glacial habitat shifts facilitates character displacement in a Neotropical flycatcher radiation.BMC evolutionary biology · 2017Article
- The Bacterial Sequential Markov Coalescent.Genetics · 2017Article
- Article
- Rapid Gene Turnover as a Significant Source of Genetic Variation in a Recently Seeded Population of a Healthcare-Associated Pathogen.Frontiers in microbiology · 2017Article
- Trans-Atlantic exchanges have shaped the population structure of the Lyme disease agent Borrelia burgdorferi sensu stricto.Scientific reports · 2016Article
- Chlamydiaceae Genomics Reveals Interspecies Admixture and the Recent Evolution of Chlamydia abortus Infecting Lower Mammalian Species and Humans.Genome biology and evolution · 2015Article
- The post-vaccine microevolution of invasive Streptococcus pneumoniae.Scientific reports · 2015Article
- Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori.Genetics · 2015Article
- Gene Loss and Lineage-Specific Restriction-Modification Systems Associated with Niche Differentiation in the Campylobacter jejuni Sequence Type 403 Clonal Complex.Applied and environmental microbiology · 2015Article
- Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis.Nature communications · 2015Article
- Patterns of genome evolution that have accompanied host adaptation in Salmonella.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Natural and Anthropogenic Hybridization in Two Species of Eastern Brazilian Marmosets (Callithrix jacchus and C. penicillata).PloS one · 2015Article
- Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae.Scientific data · 2015Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The evolution of bacterial populations has recently become considerably better understood due to large-scale sequencing of population samples. It has become clear that DNA sequences from a multitude of genes, as well as a broad sample coverage of a target population, are needed to obtain a relatively unbiased view of its genetic structure and the patterns of ancestry connected to the strains. However, the traditional statistical methods for evolutionary inference, such as phylogenetic analysis, are associated with several difficulties under such an extensive sampling scenario, in particular when a considerable amount of recombination is anticipated to have taken place. To meet the needs of large-scale analyses of population structure for bacteria, we introduce here several statistical tools for the detection and representation of recombination between populations. Also, we introduce a model-based description of the shape of a population in sequence space, in terms of its molecular variability and affinity towards other populations. Extensive real data from the genus Neisseria are utilized to demonstrate the potential of an approach where these population genetic tools are combined with an phylogenetic analysis. The statistical tools introduced here are freely available in BAPS 5.2 software, which can be downloaded from http://web.abo.fi/fak/mnf/mate/jc/software/baps.html.
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