Publications

BibTex format

@article{Mostowy:2017:molbev/msx066,
author = {Mostowy, R and Croucher, NJ and Andam, CP and Corander, J and Hanage, WP and Marttinen, P},
doi = {molbev/msx066},
journal = {MOLECULAR BIOLOGY AND EVOLUTION},
pages = {1167--1182},
title = {Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations},
url = {http://dx.doi.org/10.1093/molbev/msx066},
volume = {34},
year = {2017}
}

Download

RIS format (EndNote, RefMan)

TY  - JOUR
AB  - 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/~pemartti/fastGEAR/ (last accessed February 6, 2017).
AU  - Mostowy,R
AU  - Croucher,NJ
AU  - Andam,CP
AU  - Corander,J
AU  - Hanage,WP
AU  - Marttinen,P
DO  - molbev/msx066
EP  - 1182
PY  - 2017///
SN  - 0737-4038
SP  - 1167
TI  - Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations
T2  - MOLECULAR BIOLOGY AND EVOLUTION
UR  - http://dx.doi.org/10.1093/molbev/msx066
UR  - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000399373300011&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
UR  - http://hdl.handle.net/10044/1/48714
VL  - 34
ER  -

Download

DrNicholasCroucher

Contact

Location

Summary

Citation

BibTex format

RIS format (EndNote, RefMan)