Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated
In a recent article, Nelson-Sathi et al. (NS) report that the origins of major archaeal lineages (MAL) correspond to massive group-specific gene acquisitions via HGT from bacteria (Nelson-Sathi et al. 2015. Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature 517(75...
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| Veröffentlicht in: | Molecular biology and evolution 2016-02, Vol.33 (2), p.305-310 |
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| creator | Groussin, Mathieu Boussau, Bastien Szöllõsi, Gergely Eme, Laura Gouy, Manolo Brochier-Armanet, Céline Daubin, Vincent |
| description | In a recent article, Nelson-Sathi et al. (NS) report that the origins of major archaeal lineages (MAL) correspond to massive group-specific gene acquisitions via HGT from bacteria (Nelson-Sathi et al. 2015. Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature 517(7532):77-80.). If correct, this would have fundamental implications for the process of diversification in microbes. However, a reexamination of these data and results shows that the methodology used by NS systematically inflates the number of genes acquired at the root of each MAL, and incorrectly assumes bacterial origins for these genes. A reanalysis of their data with appropriate phylogenetic models accounting for the dynamics of gene gain and loss between lineages supports the continuous acquisition of genes over long periods in the evolution of Archaea. |
| doi_str_mv | 10.1093/molbev/msv249 |
| format | Article |
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(NS) report that the origins of major archaeal lineages (MAL) correspond to massive group-specific gene acquisitions via HGT from bacteria (Nelson-Sathi et al. 2015. Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature 517(7532):77-80.). If correct, this would have fundamental implications for the process of diversification in microbes. However, a reexamination of these data and results shows that the methodology used by NS systematically inflates the number of genes acquired at the root of each MAL, and incorrectly assumes bacterial origins for these genes. A reanalysis of their data with appropriate phylogenetic models accounting for the dynamics of gene gain and loss between lineages supports the continuous acquisition of genes over long periods in the evolution of Archaea.</description><identifier>ISSN: 0737-4038</identifier><identifier>EISSN: 1537-1719</identifier><identifier>DOI: 10.1093/molbev/msv249</identifier><identifier>PMID: 26541173</identifier><language>eng</language><publisher>United States: Oxford University Press</publisher><subject>Archaea ; Archaea - classification ; Archaea - genetics ; Bacteria ; Bacteria - genetics ; Biodiversity ; Biodiversity and Ecology ; Ecology, environment ; Environmental Sciences ; Evolution, Molecular ; Evolutionary biology ; Fast Track ; Gene Transfer, Horizontal ; Genes ; Genes, Archaeal ; Genes, Bacterial ; Genetics ; Genomics ; Genotype ; Life Sciences ; Molecular biology ; Phylogenetics ; Phylogeny ; Populations and Evolution ; Statistics ; Systematics, Phylogenetics and taxonomy</subject><ispartof>Molecular biology and evolution, 2016-02, Vol.33 (2), p.305-310</ispartof><rights>The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. 2015</rights><rights>The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.</rights><rights>Copyright Oxford Publishing Limited(England) Feb 2016</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c515t-370428884d30f5733868725106325f2705693de91ae6dbaed407042b2e0d1d293</citedby><cites>FETCH-LOGICAL-c515t-370428884d30f5733868725106325f2705693de91ae6dbaed407042b2e0d1d293</cites><orcidid>0000-0003-0776-4460 ; 0000-0002-0510-8868 ; 0000-0001-8269-9430 ; 0000-0003-4669-3589</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866543/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866543/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,1598,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26541173$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-01913926$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Groussin, Mathieu</creatorcontrib><creatorcontrib>Boussau, Bastien</creatorcontrib><creatorcontrib>Szöllõsi, Gergely</creatorcontrib><creatorcontrib>Eme, Laura</creatorcontrib><creatorcontrib>Gouy, Manolo</creatorcontrib><creatorcontrib>Brochier-Armanet, Céline</creatorcontrib><creatorcontrib>Daubin, Vincent</creatorcontrib><title>Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated</title><title>Molecular biology and evolution</title><addtitle>Mol Biol Evol</addtitle><description>In a recent article, Nelson-Sathi et al. 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A reanalysis of their data with appropriate phylogenetic models accounting for the dynamics of gene gain and loss between lineages supports the continuous acquisition of genes over long periods in the evolution of Archaea.</description><subject>Archaea</subject><subject>Archaea - classification</subject><subject>Archaea - genetics</subject><subject>Bacteria</subject><subject>Bacteria - genetics</subject><subject>Biodiversity</subject><subject>Biodiversity and Ecology</subject><subject>Ecology, environment</subject><subject>Environmental Sciences</subject><subject>Evolution, Molecular</subject><subject>Evolutionary biology</subject><subject>Fast Track</subject><subject>Gene Transfer, Horizontal</subject><subject>Genes</subject><subject>Genes, Archaeal</subject><subject>Genes, Bacterial</subject><subject>Genetics</subject><subject>Genomics</subject><subject>Genotype</subject><subject>Life Sciences</subject><subject>Molecular biology</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Populations and Evolution</subject><subject>Statistics</subject><subject>Systematics, Phylogenetics and taxonomy</subject><issn>0737-4038</issn><issn>1537-1719</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNqNks1v1DAQxS0EokvhyBVZ4gKHUE8cO84FaVlBi7RoL8DVeONJ16sk3tpJpP73OEop0Auc_DE_P78ZPUJeAnsHrOIXnW_3OF10ccqL6hFZgeBlBiVUj8mKlWlfMK7OyLMYj4xBUUj5lJzlUhQAJV-RH5fYI13XN6OLbnC-j7QJvqMfTD1gcIaagQ4HpLvgrl0q-oZ-MUcf6DrUB4OmpZvWWIzpjPS7iUN7S3cTBoyD68yA9jl50pg24ou79Zx8-_Tx6-Yq2-4uP2_W26wWIIaMl6zIlVKF5awRJedKqjIXwCTPRZOXTMiKW6zAoLR7g7Zg84t9jsyCzSt-Tt4vuqdx36GtsR-CafUpJBvhVnvj9N-V3h30tZ90oWSaBk8CbxeBw4NnV-utnu8YVMCrXE6Q2Dd3nwV_M6ZededijW1revRj1FAqJpJx4P-BSjb3LecWXj9Aj34MfZraTCWfIJVMVLZQdfAxBmzuzQLTcyT0Egm9RCLxr_4czD39KwO_Hfrx9A-tn1inv8c</recordid><startdate>20160201</startdate><enddate>20160201</enddate><creator>Groussin, Mathieu</creator><creator>Boussau, Bastien</creator><creator>Szöllõsi, Gergely</creator><creator>Eme, Laura</creator><creator>Gouy, Manolo</creator><creator>Brochier-Armanet, Céline</creator><creator>Daubin, Vincent</creator><general>Oxford University Press</general><general>Oxford University Press (OUP)</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QG</scope><scope>7QP</scope><scope>7QR</scope><scope>7SN</scope><scope>7SS</scope><scope>7TK</scope><scope>7TM</scope><scope>7TO</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>1XC</scope><scope>VOOES</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-0776-4460</orcidid><orcidid>https://orcid.org/0000-0002-0510-8868</orcidid><orcidid>https://orcid.org/0000-0001-8269-9430</orcidid><orcidid>https://orcid.org/0000-0003-4669-3589</orcidid></search><sort><creationdate>20160201</creationdate><title>Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated</title><author>Groussin, Mathieu ; 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| subjects | Archaea Archaea - classification Archaea - genetics Bacteria Bacteria - genetics Biodiversity Biodiversity and Ecology Ecology, environment Environmental Sciences Evolution, Molecular Evolutionary biology Fast Track Gene Transfer, Horizontal Genes Genes, Archaeal Genes, Bacterial Genetics Genomics Genotype Life Sciences Molecular biology Phylogenetics Phylogeny Populations and Evolution Statistics Systematics, Phylogenetics and taxonomy |
| title | Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated |
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