Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations

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Mostowy , R , Croucher , N J , Andam , C P , Corander , J , Hanage , W P & Marttinen , P 2017 , ' Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations ' Molecular Biology and Evolution , vol. 34 , no. 5 , pp. 1167-1182 . DOI: 10.1093/molbev/msx066

Title: Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations
Author: Mostowy, Rafal; Croucher, Nicholas J.; Andam, Cheryl P.; Corander, Jukka; Hanage, William P.; Marttinen, Pekka
Other contributor: University of Helsinki, Department of Mathematics and Statistics


Date: 2017-05
Language: eng
Number of pages: 16
Belongs to series: Molecular Biology and Evolution
ISSN: 0737-4038
DOI: https://doi.org/10.1093/molbev/msx066
URI: http://hdl.handle.net/10138/183632
Abstract: Prokaryotic evolution is affected by horizontal transfer of genetic material through recombination. Inference of an evolutionary tree of bacteria thus relies on accurate identification of the population genetic structure and recombination-derived mosaicism. Rapidly growing databases represent a challenge for computational methods to detect recombinations in bacterial genomes. We introduce a novel algorithm called fastGEAR which identifies lineages in diverse microbial alignments, and recombinations between them and from external origins. The algorithm detects both recent recombinations (affecting a few isolates) and ancestral recombinations between detected lineages (affecting entire lineages), thus providing insight into recombinations affecting deep branches of the phylogenetic tree. In simulations, fastGEAR had comparable power to detect recent recombinations and outstanding power to detect the ancestral ones, compared with state-of-the-art methods, often with a fraction of computational cost. We demonstrate the utility of the method by analyzing a collection of 616 whole-genomes of a recombinogenic pathogen Streptococcus pneumoniae, for which the method provided a high-resolution view of recombination across the genome. We examined in detail the penicillin-binding genes across the Streptococcus genus, demonstrating previously undetected genetic exchanges between different species at these three loci. Hence, fastGEAR can be readily applied to investigate mosaicism in bacterial genes across multiple species. Finally, fastGEAR correctly identified many known recombination hotspots and pointed to potential new ones. Matlab code and Linux/Windows executables are available at https://users.ics.aalto.fi/similar to pemartti/fastGEAR/ (last accessed February 6, 2017).
Subject: bacterial population genetics
recombination detection
population structure
hidden Markov models
Streptococcus pneumoniae
antibiotic resistance
STREPTOCOCCUS-PNEUMONIAE
GENE-TRANSFER
EVOLUTION
EVENTS
RESISTANCE
DIFFERENTIATION
DIVERSITY
GENOMICS
SAMPLES
IMPACT
1183 Plant biology, microbiology, virology
1181 Ecology, evolutionary biology
112 Statistics and probability
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