In absence of local adaptation, plasticity and spatially varying selection rule: a view from genomic reaction norms in a panmictic species (Anguilla rostrata)
American eel (Anguilla rostrata) is one of the few species for which panmixia has been demonstrated at the scale of the entire species. As such, the development of long term local adaptation is impossible. However, both plasticity and spatially varying selection have been invoked in explaining how A...
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description | American eel (Anguilla rostrata) is one of the few species for which panmixia has been demonstrated at the scale of the entire species. As such, the development of long term local adaptation is impossible. However, both plasticity and spatially varying selection have been invoked in explaining how American eel may cope with an unusual broad scope of environmental conditions. Here, we address this question through transcriptomic analyses and genomic reaction norms of eels from two geographic origins reared in controlled environments.
The null hypothesis of no difference in gene expression between eels from the two origins was rejected. Many unique transcripts and two out of seven gene clusters showed significant difference in expression, both at time of capture and after three months of common rearing. Differences in expression were observed at numerous genes representing many functional groups when comparing eels from a same origin reared under different salinity conditions. Plastic response to different rearing conditions varied among gene clusters with three clusters showing significant origin-environment interactions translating into differential genomic norms of reaction. Most genes and functional categories showing differences between origins were previously shown to be differentially expressed in a study comparing transcription profiles between adult European eels acclimated to different salinities.
These results emphasize that while plasticity in expression may be important, there is also a role for local genetic (and/or epigenetic) differences in explaining differences in gene expression between eels from different geographic origins. Such differences match those reported in genetically distinct populations in other fishes, both in terms of the proportion of genes that are differentially expressed and the diversity of biological functions involved. We thus propose that genetic differences between glass eels of different origins caused by spatially varying selection due to local environmental conditions translates into transcriptomic differences (including different genomic norms of reaction) which may in turn explain part of the phenotypic variance observed between different habitats colonized by eels. |
doi_str_mv | 10.1186/1471-2164-15-403 |
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The null hypothesis of no difference in gene expression between eels from the two origins was rejected. Many unique transcripts and two out of seven gene clusters showed significant difference in expression, both at time of capture and after three months of common rearing. Differences in expression were observed at numerous genes representing many functional groups when comparing eels from a same origin reared under different salinity conditions. Plastic response to different rearing conditions varied among gene clusters with three clusters showing significant origin-environment interactions translating into differential genomic norms of reaction. Most genes and functional categories showing differences between origins were previously shown to be differentially expressed in a study comparing transcription profiles between adult European eels acclimated to different salinities.
These results emphasize that while plasticity in expression may be important, there is also a role for local genetic (and/or epigenetic) differences in explaining differences in gene expression between eels from different geographic origins. Such differences match those reported in genetically distinct populations in other fishes, both in terms of the proportion of genes that are differentially expressed and the diversity of biological functions involved. We thus propose that genetic differences between glass eels of different origins caused by spatially varying selection due to local environmental conditions translates into transcriptomic differences (including different genomic norms of reaction) which may in turn explain part of the phenotypic variance observed between different habitats colonized by eels.</description><identifier>ISSN: 1471-2164</identifier><identifier>EISSN: 1471-2164</identifier><identifier>DOI: 10.1186/1471-2164-15-403</identifier><identifier>PMID: 24884429</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Adaptation, Biological - genetics ; Analysis ; Anguilla - genetics ; Anguilla rostrata ; Animals ; Behavior ; Cluster Analysis ; Computational Biology ; Eels ; Endangered & extinct species ; Environment ; Environmental aspects ; Epigenetic inheritance ; Epigenetics ; Female ; Fishes ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation ; Gene-Environment Interaction ; Genes ; Genetic aspects ; Genomes ; Genomics ; Habitats ; Laboratory animals ; Male ; Molecular Sequence Annotation ; Multigene Family ; Salinity ; Selection, Genetic ; Studies</subject><ispartof>BMC genomics, 2014-05, Vol.15 (1), p.403-403, Article 403</ispartof><rights>COPYRIGHT 2014 BioMed Central Ltd.</rights><rights>2014 Côté et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.</rights><rights>Copyright © 2014 Côté et al.; licensee BioMed Central Ltd. 2014 Côté et al.; licensee BioMed Central Ltd.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c694t-9c7595e65e2f1c9b022f188f22fcce2a489ca8c1ec210a0d962cab974f64dc043</citedby><cites>FETCH-LOGICAL-c694t-9c7595e65e2f1c9b022f188f22fcce2a489ca8c1ec210a0d962cab974f64dc043</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4229938/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4229938/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24884429$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Côté, Caroline L</creatorcontrib><creatorcontrib>Castonguay, Martin</creatorcontrib><creatorcontrib>Kalujnaia, McWilliam Svetlana</creatorcontrib><creatorcontrib>Cramb, Gordon</creatorcontrib><creatorcontrib>Bernatchez, Louis</creatorcontrib><title>In absence of local adaptation, plasticity and spatially varying selection rule: a view from genomic reaction norms in a panmictic species (Anguilla rostrata)</title><title>BMC genomics</title><addtitle>BMC Genomics</addtitle><description>American eel (Anguilla rostrata) is one of the few species for which panmixia has been demonstrated at the scale of the entire species. As such, the development of long term local adaptation is impossible. However, both plasticity and spatially varying selection have been invoked in explaining how American eel may cope with an unusual broad scope of environmental conditions. Here, we address this question through transcriptomic analyses and genomic reaction norms of eels from two geographic origins reared in controlled environments.
The null hypothesis of no difference in gene expression between eels from the two origins was rejected. Many unique transcripts and two out of seven gene clusters showed significant difference in expression, both at time of capture and after three months of common rearing. Differences in expression were observed at numerous genes representing many functional groups when comparing eels from a same origin reared under different salinity conditions. Plastic response to different rearing conditions varied among gene clusters with three clusters showing significant origin-environment interactions translating into differential genomic norms of reaction. Most genes and functional categories showing differences between origins were previously shown to be differentially expressed in a study comparing transcription profiles between adult European eels acclimated to different salinities.
These results emphasize that while plasticity in expression may be important, there is also a role for local genetic (and/or epigenetic) differences in explaining differences in gene expression between eels from different geographic origins. Such differences match those reported in genetically distinct populations in other fishes, both in terms of the proportion of genes that are differentially expressed and the diversity of biological functions involved. We thus propose that genetic differences between glass eels of different origins caused by spatially varying selection due to local environmental conditions translates into transcriptomic differences (including different genomic norms of reaction) which may in turn explain part of the phenotypic variance observed between different habitats colonized by eels.</description><subject>Adaptation, Biological - genetics</subject><subject>Analysis</subject><subject>Anguilla - genetics</subject><subject>Anguilla rostrata</subject><subject>Animals</subject><subject>Behavior</subject><subject>Cluster Analysis</subject><subject>Computational Biology</subject><subject>Eels</subject><subject>Endangered & extinct species</subject><subject>Environment</subject><subject>Environmental aspects</subject><subject>Epigenetic inheritance</subject><subject>Epigenetics</subject><subject>Female</subject><subject>Fishes</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation</subject><subject>Gene-Environment Interaction</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Habitats</subject><subject>Laboratory animals</subject><subject>Male</subject><subject>Molecular Sequence Annotation</subject><subject>Multigene Family</subject><subject>Salinity</subject><subject>Selection, Genetic</subject><subject>Studies</subject><issn>1471-2164</issn><issn>1471-2164</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqNkk2LFDEQhhtR3HX17kkCXnbBXpN0-iMehGHxY2BB8OMcatLVbZZ00ibdo_Nn_K2mmXXcEQ-SQ4XKU28llTfLnjJ6yVhTvWSiZjlnlchZmQta3MtOD6n7d_Yn2aMYbyhldcPLh9kJF00jBJen2c-1I7CJ6DQS3xHrNVgCLYwTTMa7F2S0ECejzbQj4FoSx5QHa3dkC2FnXE8iWtQLS8Js8RUBsjX4nXTBD6RH5wejSUDYI86HIRKTepIRXDpK0kkTtcFIzleun421QIKPU4AJLh5nDzqwEZ_cxrPsy9s3n6_e59cf3q2vVte5rqSYcqnrUpZYlcg7puWG8hSbpktBa-QgGqmh0Qw1ZxRoKyuuYSNr0VWi1VQUZ9nrve44bwZsNbrU36oxmCE9U3kw6vjEma-q91slOJeyaJLA-a1A8N9mjJMaTNSYHuPQz1GxUtSNqAUv_gflBaVlvag-_wu98XNwaRILxRpJqZB_qB4sKuM6n66oF1G1KgtZVmVdLW0v_0Gl1WL6B--wMyl_VHBxVJCYCX9MPcwxqvWnj8cs3bM6fV0M2B1Gx6harKoWL6rFi-nmKlk1lTy7O_JDwW9vFr8AJBbkXw</recordid><startdate>20140527</startdate><enddate>20140527</enddate><creator>Côté, Caroline L</creator><creator>Castonguay, Martin</creator><creator>Kalujnaia, McWilliam Svetlana</creator><creator>Cramb, Gordon</creator><creator>Bernatchez, Louis</creator><general>BioMed Central Ltd</general><general>BioMed Central</general><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>ISR</scope><scope>3V.</scope><scope>7QP</scope><scope>7QR</scope><scope>7SS</scope><scope>7TK</scope><scope>7U7</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20140527</creationdate><title>In absence of local adaptation, plasticity and spatially varying selection rule: a view from genomic reaction norms in a panmictic species (Anguilla rostrata)</title><author>Côté, Caroline L ; Castonguay, Martin ; Kalujnaia, McWilliam Svetlana ; Cramb, Gordon ; Bernatchez, Louis</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c694t-9c7595e65e2f1c9b022f188f22fcce2a489ca8c1ec210a0d962cab974f64dc043</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Adaptation, Biological - genetics</topic><topic>Analysis</topic><topic>Anguilla - genetics</topic><topic>Anguilla rostrata</topic><topic>Animals</topic><topic>Behavior</topic><topic>Cluster Analysis</topic><topic>Computational Biology</topic><topic>Eels</topic><topic>Endangered & extinct species</topic><topic>Environment</topic><topic>Environmental aspects</topic><topic>Epigenetic inheritance</topic><topic>Epigenetics</topic><topic>Female</topic><topic>Fishes</topic><topic>Gene expression</topic><topic>Gene Expression Profiling</topic><topic>Gene Expression Regulation</topic><topic>Gene-Environment Interaction</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Habitats</topic><topic>Laboratory animals</topic><topic>Male</topic><topic>Molecular Sequence Annotation</topic><topic>Multigene Family</topic><topic>Salinity</topic><topic>Selection, Genetic</topic><topic>Studies</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Côté, Caroline L</creatorcontrib><creatorcontrib>Castonguay, Martin</creatorcontrib><creatorcontrib>Kalujnaia, McWilliam Svetlana</creatorcontrib><creatorcontrib>Cramb, Gordon</creatorcontrib><creatorcontrib>Bernatchez, Louis</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>BMC genomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Côté, Caroline L</au><au>Castonguay, Martin</au><au>Kalujnaia, McWilliam Svetlana</au><au>Cramb, Gordon</au><au>Bernatchez, Louis</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>In absence of local adaptation, plasticity and spatially varying selection rule: a view from genomic reaction norms in a panmictic species (Anguilla rostrata)</atitle><jtitle>BMC genomics</jtitle><addtitle>BMC Genomics</addtitle><date>2014-05-27</date><risdate>2014</risdate><volume>15</volume><issue>1</issue><spage>403</spage><epage>403</epage><pages>403-403</pages><artnum>403</artnum><issn>1471-2164</issn><eissn>1471-2164</eissn><abstract>American eel (Anguilla rostrata) is one of the few species for which panmixia has been demonstrated at the scale of the entire species. As such, the development of long term local adaptation is impossible. However, both plasticity and spatially varying selection have been invoked in explaining how American eel may cope with an unusual broad scope of environmental conditions. Here, we address this question through transcriptomic analyses and genomic reaction norms of eels from two geographic origins reared in controlled environments.
The null hypothesis of no difference in gene expression between eels from the two origins was rejected. Many unique transcripts and two out of seven gene clusters showed significant difference in expression, both at time of capture and after three months of common rearing. Differences in expression were observed at numerous genes representing many functional groups when comparing eels from a same origin reared under different salinity conditions. Plastic response to different rearing conditions varied among gene clusters with three clusters showing significant origin-environment interactions translating into differential genomic norms of reaction. Most genes and functional categories showing differences between origins were previously shown to be differentially expressed in a study comparing transcription profiles between adult European eels acclimated to different salinities.
These results emphasize that while plasticity in expression may be important, there is also a role for local genetic (and/or epigenetic) differences in explaining differences in gene expression between eels from different geographic origins. Such differences match those reported in genetically distinct populations in other fishes, both in terms of the proportion of genes that are differentially expressed and the diversity of biological functions involved. We thus propose that genetic differences between glass eels of different origins caused by spatially varying selection due to local environmental conditions translates into transcriptomic differences (including different genomic norms of reaction) which may in turn explain part of the phenotypic variance observed between different habitats colonized by eels.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>24884429</pmid><doi>10.1186/1471-2164-15-403</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Adaptation, Biological - genetics Analysis Anguilla - genetics Anguilla rostrata Animals Behavior Cluster Analysis Computational Biology Eels Endangered & extinct species Environment Environmental aspects Epigenetic inheritance Epigenetics Female Fishes Gene expression Gene Expression Profiling Gene Expression Regulation Gene-Environment Interaction Genes Genetic aspects Genomes Genomics Habitats Laboratory animals Male Molecular Sequence Annotation Multigene Family Salinity Selection, Genetic Studies |
title | In absence of local adaptation, plasticity and spatially varying selection rule: a view from genomic reaction norms in a panmictic species (Anguilla rostrata) |
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