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The speciation and hybridization history of the genus Salmonella

Bacteria and archaea make up most of natural diversity, but the mechanisms that underlie the origin and maintenance of prokaryotic species are poorly understood. We investigated the speciation history of the genus Salmonella , an ecologically diverse bacterial lineage, within which S. enterica subsp...

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Autores principales: Criscuolo, Alexis, Issenhuth-Jeanjean, Sylvie, Didelot, Xavier, Thorell, Kaisa, Hale, James, Parkhill, Julian, Thomson, Nicholas R., Weill, François-Xavier, Falush, Daniel, Brisse, Sylvain
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Microbiology Society 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6755497/
https://www.ncbi.nlm.nih.gov/pubmed/31347998
http://dx.doi.org/10.1099/mgen.0.000284
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author Criscuolo, Alexis
Issenhuth-Jeanjean, Sylvie
Didelot, Xavier
Thorell, Kaisa
Hale, James
Parkhill, Julian
Thomson, Nicholas R.
Weill, François-Xavier
Falush, Daniel
Brisse, Sylvain
author_facet Criscuolo, Alexis
Issenhuth-Jeanjean, Sylvie
Didelot, Xavier
Thorell, Kaisa
Hale, James
Parkhill, Julian
Thomson, Nicholas R.
Weill, François-Xavier
Falush, Daniel
Brisse, Sylvain
author_sort Criscuolo, Alexis
collection PubMed
description Bacteria and archaea make up most of natural diversity, but the mechanisms that underlie the origin and maintenance of prokaryotic species are poorly understood. We investigated the speciation history of the genus Salmonella , an ecologically diverse bacterial lineage, within which S. enterica subsp. enterica is responsible for important human food-borne infections. We performed a survey of diversity across a large reference collection using multilocus sequence typing, followed by genome sequencing of distinct lineages. We identified 11 distinct phylogroups, 3 of which were previously undescribed. Strains assigned to S. enterica subsp. salamae are polyphyletic, with two distinct lineages that we designate Salamae A and B. Strains of the subspecies houtenae are subdivided into two groups, Houtenae A and B, and are both related to Selander’s group VII. A phylogroup we designate VIII was previously unknown. A simple binary fission model of speciation cannot explain observed patterns of sequence diversity. In the recent past, there have been large-scale hybridization events involving an unsampled ancestral lineage and three distantly related lineages of the genus that have given rise to Houtenae A, Houtenae B and VII. We found no evidence for ongoing hybridization in the other eight lineages, but detected subtler signals of ancient recombination events. We are unable to fully resolve the speciation history of the genus, which might have involved additional speciation-by-hybridization or multi-way speciation events. Our results imply that traditional models of speciation by binary fission and divergence are not sufficient to account for Salmonella evolution.
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spelling pubmed-67554972019-09-24 The speciation and hybridization history of the genus Salmonella Criscuolo, Alexis Issenhuth-Jeanjean, Sylvie Didelot, Xavier Thorell, Kaisa Hale, James Parkhill, Julian Thomson, Nicholas R. Weill, François-Xavier Falush, Daniel Brisse, Sylvain Microb Genom Research Article Bacteria and archaea make up most of natural diversity, but the mechanisms that underlie the origin and maintenance of prokaryotic species are poorly understood. We investigated the speciation history of the genus Salmonella , an ecologically diverse bacterial lineage, within which S. enterica subsp. enterica is responsible for important human food-borne infections. We performed a survey of diversity across a large reference collection using multilocus sequence typing, followed by genome sequencing of distinct lineages. We identified 11 distinct phylogroups, 3 of which were previously undescribed. Strains assigned to S. enterica subsp. salamae are polyphyletic, with two distinct lineages that we designate Salamae A and B. Strains of the subspecies houtenae are subdivided into two groups, Houtenae A and B, and are both related to Selander’s group VII. A phylogroup we designate VIII was previously unknown. A simple binary fission model of speciation cannot explain observed patterns of sequence diversity. In the recent past, there have been large-scale hybridization events involving an unsampled ancestral lineage and three distantly related lineages of the genus that have given rise to Houtenae A, Houtenae B and VII. We found no evidence for ongoing hybridization in the other eight lineages, but detected subtler signals of ancient recombination events. We are unable to fully resolve the speciation history of the genus, which might have involved additional speciation-by-hybridization or multi-way speciation events. Our results imply that traditional models of speciation by binary fission and divergence are not sufficient to account for Salmonella evolution. Microbiology Society 2019-07-26 /pmc/articles/PMC6755497/ /pubmed/31347998 http://dx.doi.org/10.1099/mgen.0.000284 Text en © 2019 The Authors http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Criscuolo, Alexis
Issenhuth-Jeanjean, Sylvie
Didelot, Xavier
Thorell, Kaisa
Hale, James
Parkhill, Julian
Thomson, Nicholas R.
Weill, François-Xavier
Falush, Daniel
Brisse, Sylvain
The speciation and hybridization history of the genus Salmonella
title The speciation and hybridization history of the genus Salmonella
title_full The speciation and hybridization history of the genus Salmonella
title_fullStr The speciation and hybridization history of the genus Salmonella
title_full_unstemmed The speciation and hybridization history of the genus Salmonella
title_short The speciation and hybridization history of the genus Salmonella
title_sort speciation and hybridization history of the genus salmonella
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6755497/
https://www.ncbi.nlm.nih.gov/pubmed/31347998
http://dx.doi.org/10.1099/mgen.0.000284
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