Patterns of Gene Flow Define Species of Thermophilic Archaea
Publication Date
February 21, 2012
Journal
PLOS Biology
Authors
Hinsby Cadillo Quiroz, Xavier Didelot, Nicole L. Held, Alfa Herrera, et al
Volume
10
Issue
2
Pages
e1001265
DOI
https://dx.plos.org/10.1371/journal.pbio.1001265
Publisher URL
http://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.1001265
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/22363207
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3283564
Europe PMC
http://europepmc.org/abstract/MED/22363207
Web of Science
000300951500010
Scopus
84857470045
Mendeley
http://www.mendeley.com/research/patterns-gene-flow-define-species-thermophilic-archaea
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CiteULike | Further Information

Mendeley | Further Information

{"title"=>"Patterns of gene flow define species of thermophilic Archaea", "type"=>"journal", "authors"=>[{"first_name"=>"Hinsby", "last_name"=>"Cadillo-Quiroz", "scopus_author_id"=>"14033806800"}, {"first_name"=>"Xavier", "last_name"=>"Didelot", "scopus_author_id"=>"15070077500"}, {"first_name"=>"Nicole L.", "last_name"=>"Held", "scopus_author_id"=>"35725302700"}, {"first_name"=>"Alfa", "last_name"=>"Herrera", "scopus_author_id"=>"37037454400"}, {"first_name"=>"Aaron", "last_name"=>"Darling", "scopus_author_id"=>"8974024600"}, {"first_name"=>"Michael L.", "last_name"=>"Reno", "scopus_author_id"=>"23668722600"}, {"first_name"=>"David J.", "last_name"=>"Krause", "scopus_author_id"=>"57197229781"}, {"first_name"=>"Rachel J.", "last_name"=>"Whitaker", "scopus_author_id"=>"10142852200"}], "year"=>2012, "source"=>"PLoS Biology", "identifiers"=>{"doi"=>"10.1371/journal.pbio.1001265", "sgr"=>"84857470045", "issn"=>"15449173", "pui"=>"364330651", "isbn"=>"10.1371/journal.pbio.1001265", "pmid"=>"22363207", "scopus"=>"2-s2.0-84857470045"}, "id"=>"8fa8d045-d193-380d-962c-63d938dfada0", "abstract"=>"Despite a growing appreciation of their vast diversity in nature, mechanisms of speciation are poorly understood in Bacteria and Archaea. Here we use high-throughput genome sequencing to identify ongoing speciation in the thermoacidophilic Archaeon Sulfolobus islandicus. Patterns of homologous gene flow among genomes of 12 strains from a single hot spring in Kamchatka, Russia, demonstrate higher levels of gene flow within than between two persistent, coexisting groups, demonstrating that these microorganisms fit the biological species concept. Furthermore, rates of gene flow between two species are decreasing over time in a manner consistent with incipient speciation. Unlike other microorganisms investigated, we do not observe a relationship between genetic divergence and frequency of recombination along a chromosome, or other physical mechanisms that would reduce gene flow between lineages. Each species has its own genetic island encoding unique physiological functions and a unique growth phenotype that may be indicative of ecological specialization. Genetic differentiation between these coexisting groups occurs in large genomic \"continents,\" indicating the topology of genomic divergence during speciation is not uniform and is not associated with a single locus under strong diversifying selection. These data support a model where species do not require physical barriers to gene flow but are maintained by ecological differentiation.", "link"=>"http://www.mendeley.com/research/patterns-gene-flow-define-species-thermophilic-archaea", "reader_count"=>222, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>17, "Researcher"=>53, "Student > Doctoral Student"=>9, "Student > Ph. D. Student"=>80, "Student > Postgraduate"=>3, "Student > Master"=>20, "Other"=>7, "Student > Bachelor"=>15, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>11}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>17, "Researcher"=>53, "Student > Doctoral Student"=>9, "Student > Ph. D. Student"=>80, "Student > Postgraduate"=>3, "Student > Master"=>20, "Other"=>7, "Student > Bachelor"=>15, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>11}, "reader_count_by_subject_area"=>{"Unspecified"=>11, "Engineering"=>4, "Environmental Science"=>13, "Biochemistry, Genetics and Molecular Biology"=>17, "Agricultural and Biological Sciences"=>164, "Medicine and Dentistry"=>1, "Philosophy"=>1, "Physics and Astronomy"=>1, "Social Sciences"=>3, "Computer Science"=>2, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>4}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>4}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>3}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>4}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>164}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>17}, "Unspecified"=>{"Unspecified"=>11}, "Environmental Science"=>{"Environmental Science"=>13}, "Philosophy"=>{"Philosophy"=>1}}, "reader_count_by_country"=>{"Hong Kong"=>1, "United States"=>21, "United Kingdom"=>1, "Russia"=>1, "Spain"=>1, "India"=>1, "Austria"=>1, "Netherlands"=>2, "Sweden"=>1, "Brazil"=>2, "Denmark"=>1, "Mexico"=>3, "France"=>2, "Australia"=>1, "Chile"=>1, "Germany"=>1}, "group_count"=>2}

CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/677931"], "description"=>"<p>(A) 10,000 bp windows on the M.16.27 genome where genome sequence is not present in all 10 strains from the Red and Blue groups. These positions highlight variable portions of the M.16.27 genome. *Indicates a recently integrated plasmid. (B) F<sub>ST</sub> values were calculated for sliding windows of 10 kb moving in 5 kb steps. Empty windows where sequence from M.16.27 is not shared by all strains are not plotted. Shading highlights regions of the chromosome that are less differentiated beginning and ending with the first window with F<sub>ST</sub> values lower than 0.5.</p>", "links"=>[], "tags"=>["groups", "chromosome"], "article_id"=>348416, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Hinsby Cadillo-Quiroz", "Xavier Didelot", "Nicole L. Held", "Alfa Herrera", "Aaron Darling", "Michael L. Reno", "David J. Krause", "Rachel J. Whitaker"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1001265.g004", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_F_ST_values_between_the_Red_and_Blue_groups_along_the_chromosome_of_strain_M_16_27_/348416", "title"=>"F<sub>ST</sub> values between the Red and Blue groups along the chromosome of strain M.16.27.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-21 02:20:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/677848"], "description"=>"<p>For the Red (A) and Blue (B) recipient strains, the total proportion of events that could be assigned as originating from either donor Red (colored red) and Blue (colored blue) strains is shown as a function of coalescent time with 10 being the most recent divergence and 1 being the common ancestor of this set of strains. A coalescent unit of time is equal to the average length of a generation multiplied by the effective population size.</p>", "links"=>[], "tags"=>["recombination", "events", "groups"], "article_id"=>348328, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Hinsby Cadillo-Quiroz", "Xavier Didelot", "Nicole L. Held", "Alfa Herrera", "Aaron Darling", "Michael L. Reno", "David J. Krause", "Rachel J. Whitaker"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1001265.g003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Variation_in_recombination_events_between_the_Red_and_Blue_groups_through_time_/348328", "title"=>"Variation in recombination events between the Red and Blue groups through time.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-21 02:18:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/678032"], "description"=>"<p>Lines are color coded for strains assigned to the Red and Blue groups. Negative control with no inoculum added is shown in grey. Error bars show the variation in growth among three independent replicate cultures.</p>", "links"=>[], "tags"=>["strains", "heterotrophic"], "article_id"=>348514, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Hinsby Cadillo-Quiroz", "Xavier Didelot", "Nicole L. Held", "Alfa Herrera", "Aaron Darling", "Michael L. Reno", "David J. Krause", "Rachel J. Whitaker"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1001265.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Growth_of_M_16_strains_under_standard_heterotrophic_conditions_/348514", "title"=>"Growth of M.16 strains under standard heterotrophic conditions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-21 02:21:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/346202", "https://ndownloader.figshare.com/files/346251", "https://ndownloader.figshare.com/files/346300", "https://ndownloader.figshare.com/files/346357", "https://ndownloader.figshare.com/files/346380", "https://ndownloader.figshare.com/files/346403", "https://ndownloader.figshare.com/files/346417", "https://ndownloader.figshare.com/files/346437", "https://ndownloader.figshare.com/files/346460"], "description"=>"<div><p>Despite a growing appreciation of their vast diversity in nature, mechanisms of speciation are poorly understood in <em>Bacteria</em> and <em>Archaea</em>. Here we use high-throughput genome sequencing to identify ongoing speciation in the thermoacidophilic Archaeon <em>Sulfolobus islandicus</em>. Patterns of homologous gene flow among genomes of 12 strains from a single hot spring in Kamchatka, Russia, demonstrate higher levels of gene flow within than between two persistent, coexisting groups, demonstrating that these microorganisms fit the biological species concept. Furthermore, rates of gene flow between two species are decreasing over time in a manner consistent with incipient speciation. Unlike other microorganisms investigated, we do not observe a relationship between genetic divergence and frequency of recombination along a chromosome, or other physical mechanisms that would reduce gene flow between lineages. Each species has its own genetic island encoding unique physiological functions and a unique growth phenotype that may be indicative of ecological specialization. Genetic differentiation between these coexisting groups occurs in large genomic “continents,” indicating the topology of genomic divergence during speciation is not uniform and is not associated with a single locus under strong diversifying selection. These data support a model where species do not require physical barriers to gene flow but are maintained by ecological differentiation.</p> </div>", "links"=>[], "tags"=>["patterns", "thermophilic", "archaea"], "article_id"=>128426, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Hinsby Cadillo-Quiroz", "Xavier Didelot", "Nicole L. Held", "Alfa Herrera", "Aaron Darling", "Michael L. Reno", "David J. Krause", "Rachel J. Whitaker"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1001265.s001", "https://dx.doi.org/10.1371/journal.pbio.1001265.s002", "https://dx.doi.org/10.1371/journal.pbio.1001265.s003", "https://dx.doi.org/10.1371/journal.pbio.1001265.s004", "https://dx.doi.org/10.1371/journal.pbio.1001265.s005", "https://dx.doi.org/10.1371/journal.pbio.1001265.s006", "https://dx.doi.org/10.1371/journal.pbio.1001265.s007", "https://dx.doi.org/10.1371/journal.pbio.1001265.s008", "https://dx.doi.org/10.1371/journal.pbio.1001265.s009"], "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Patterns_of_Gene_Flow_Define_Species_of_Thermophilic_Archaea/128426", "title"=>"Patterns of Gene Flow Define Species of Thermophilic Archaea", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-02-21 02:20:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/677664"], "description"=>"<p>(A) ClonalFrame <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001265#pbio.1001265-Didelot2\" target=\"_blank\">[35]</a> reconstruction based on seven loci from 97 <i>S. islandicus</i> strains from the Mutnovsky Volcano region of Kamchatka, Russia (details in <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001265#pbio.1001265.s004\" target=\"_blank\">Table S1</a>). Strains in purple were isolated from spring M.16. The first number in each name indicates the spring from which strains were isolated, the second indicates the isolate number from that spring, and the third indicates year of isolation. * designates strains selected for genome sequencing and comparison. (B) ClonalFrame phylogeny based on the core genome alignment of 12 <i>S. islandicus</i> strains from hot spring M.16.</p>", "links"=>[], "tags"=>["relationships", "mutnovsky"], "article_id"=>348150, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Hinsby Cadillo-Quiroz", "Xavier Didelot", "Nicole L. Held", "Alfa Herrera", "Aaron Darling", "Michael L. Reno", "David J. Krause", "Rachel J. Whitaker"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1001265.g001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_relationships_among_S_islandicus_from_the_Mutnovsky_Volcano_/348150", "title"=>"Phylogenetic relationships among <i>S. islandicus</i> from the Mutnovsky Volcano.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-21 02:15:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/677737"], "description"=>"<p>Recombination frequency is measured relative to its expectation under the prior of the ClonalOrigin model and color coded according to the upper left color/magnitude legend (light blue and blue for the frequency of recombination events below a 1∶1 ratio and yellow to red for the frequency of recombination events above 1∶1). Light gray cells represent non-significant ratios with less than four observed and expected events. White shows number of events that match the prior expectations. Names of strains are color coded as Blue and Red groups.</p>", "links"=>[], "tags"=>["homologous", "recombination", "branches", "genome", "phylogeny", "12"], "article_id"=>348214, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Hinsby Cadillo-Quiroz", "Xavier Didelot", "Nicole L. Held", "Alfa Herrera", "Aaron Darling", "Michael L. Reno", "David J. Krause", "Rachel J. Whitaker"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1001265.g002", "stats"=>{"downloads"=>1, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Heat_map_representation_of_homologous_recombination_frequency_for_every_donor_recipient_pair_of_branches_of_the_core_genome_phylogeny_of_12_S_islandicus_strains_/348214", "title"=>"Heat map representation of homologous recombination frequency for every donor/recipient pair of branches of the core genome phylogeny of 12 <i>S. islandicus</i> strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-21 02:16:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/678080"], "description"=>"a<p>Previously published in <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001265#pbio.1001265-Reno1\" target=\"_blank\">[30]</a>.</p>b<p>Genome not closed.</p><p>ND, not done.</p>", "links"=>[], "tags"=>["12", "strains"], "article_id"=>348562, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Hinsby Cadillo-Quiroz", "Xavier Didelot", "Nicole L. Held", "Alfa Herrera", "Aaron Darling", "Michael L. Reno", "David J. Krause", "Rachel J. Whitaker"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1001265.t001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_of_12_strains_of_S_islandicus_from_spring_M_16_/348562", "title"=>"Characteristics of 12 strains of <i>S. islandicus</i> from spring M.16.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-02-21 02:22:42"}

PMC Usage Stats | Further Information

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  • {"month"=>"6", "scanned-page-browse"=>"0", "cited-by"=>"0", "abstract"=>"0", "full-text"=>"20", "year"=>"2012", "pdf"=>"17", "unique-ip"=>"17", "figure"=>"1", "scanned-summary"=>"0", "supp-data"=>"1"}
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  • {"unique-ip"=>"12", "full-text"=>"11", "pdf"=>"12", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2012", "month"=>"9"}
  • {"unique-ip"=>"16", "full-text"=>"12", "pdf"=>"6", "abstract"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2012", "month"=>"10"}
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  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2013", "month"=>"10"}
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  • {"unique-ip"=>"10", "full-text"=>"13", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"11", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"8"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"9"}
  • {"unique-ip"=>"20", "full-text"=>"14", "pdf"=>"7", "abstract"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"11", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"10"}
  • {"unique-ip"=>"7", "full-text"=>"3", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"11"}
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  • {"unique-ip"=>"8", "full-text"=>"6", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"1"}
  • {"unique-ip"=>"15", "full-text"=>"11", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"8", "cited-by"=>"0", "year"=>"2015", "month"=>"2"}
  • {"unique-ip"=>"7", "full-text"=>"5", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"3"}
  • {"unique-ip"=>"9", "full-text"=>"9", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"4"}
  • {"unique-ip"=>"3", "full-text"=>"7", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2015", "month"=>"5"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"6"}
  • {"unique-ip"=>"9", "full-text"=>"7", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"7"}
  • {"unique-ip"=>"7", "full-text"=>"6", "pdf"=>"9", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"8"}
  • {"unique-ip"=>"11", "full-text"=>"11", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"9"}
  • {"unique-ip"=>"9", "full-text"=>"7", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"10"}
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