Pinpointing a selective sweep to the chimpanzee MHC class I region by comparative genomics
Chimpanzees experienced a reduction of the allelic repertoire at the major histocompatibility complex (MHC) class I A and B loci, which may have been caused by a retrovirus belonging to the simian immunodeficiency virus (SIV) family. Extended MHC haplotypes were defined in a pedigreed chimpanzee col...
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| Veröffentlicht in: | Molecular ecology 2008-04, Vol.17 (8), p.2074-2088 |
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| creator | DE GROOT, NATASJA G HEIJMANS, CORRINE M.C DE GROOT, NANINE OTTING, NEL DE VOS-ROUWELER, ANNEMIEK J.M REMARQUE, EDMOND J BONHOMME, MAXIME DOXIADIS, GABY G.M CROUAU-ROY, BRIGITTE BONTROP, RONALD E |
| description | Chimpanzees experienced a reduction of the allelic repertoire at the major histocompatibility complex (MHC) class I A and B loci, which may have been caused by a retrovirus belonging to the simian immunodeficiency virus (SIV) family. Extended MHC haplotypes were defined in a pedigreed chimpanzee colony. Comparison of genetic variation at microsatellite markers mapping inside and outside the Mhc region was carried out in humans and chimpanzees to investigate the genomic extent of the repertoire reduction. Multilocus demographic analyses underscored that chimpanzees indeed experienced a selective sweep that mainly targeted the chromosomal segment carrying the Mhc class I region. Probably due to genetic linkage, the sweep also affected other polymorphic loci, mapping in the close vicinity of the Mhc class I region genes. Nevertheless, although the allelic repertoire at particular Mhc class I and II loci appears to be limited, naturally occurring recombination events allowed the establishment of haplotype diversity after the sweep. However, recombination did not have sufficient time to erase the signal of the selective sweep. |
| doi_str_mv | 10.1111/j.1365-294X.2008.03716.x |
| format | Article |
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Extended MHC haplotypes were defined in a pedigreed chimpanzee colony. Comparison of genetic variation at microsatellite markers mapping inside and outside the Mhc region was carried out in humans and chimpanzees to investigate the genomic extent of the repertoire reduction. Multilocus demographic analyses underscored that chimpanzees indeed experienced a selective sweep that mainly targeted the chromosomal segment carrying the Mhc class I region. Probably due to genetic linkage, the sweep also affected other polymorphic loci, mapping in the close vicinity of the Mhc class I region genes. Nevertheless, although the allelic repertoire at particular Mhc class I and II loci appears to be limited, naturally occurring recombination events allowed the establishment of haplotype diversity after the sweep. However, recombination did not have sufficient time to erase the signal of the selective sweep.</description><identifier>ISSN: 0962-1083</identifier><identifier>EISSN: 1365-294X</identifier><identifier>DOI: 10.1111/j.1365-294X.2008.03716.x</identifier><identifier>PMID: 18346126</identifier><language>eng</language><publisher>Oxford, UK: Oxford, UK : Blackwell Publishing Ltd</publisher><subject>Africa, Western ; Animal biology ; Animals ; Biodiversity ; Comparative studies ; DNA, Mitochondrial - chemistry ; DNA, Mitochondrial - genetics ; Ecology ; Ecology, environment ; Genetic Variation ; Genetics ; Genomics ; haplotypes ; Haplotypes - genetics ; Histocompatibility Antigens Class I - genetics ; Histocompatibility Antigens Class I - immunology ; HIV ; Humans ; Life Sciences ; microsatellite ; microsatellite repeats ; Microsatellite Repeats - genetics ; Molecular biology ; Pan troglodytes ; Pan troglodytes - genetics ; Pan troglodytes - immunology ; Phylogeny ; Polymerase Chain Reaction ; primate evolution ; Primates ; selection ; Sequence Analysis, DNA ; Simian immunodeficiency virus</subject><ispartof>Molecular ecology, 2008-04, Vol.17 (8), p.2074-2088</ispartof><rights>2008 The Authors</rights><rights>Journal compilation © 2008 Blackwell Publishing Ltd</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5216-a467b02c6f5fcae9849de58e8dc57fcc9115e21bdbf8c92356331021ece94bab3</citedby><cites>FETCH-LOGICAL-c5216-a467b02c6f5fcae9849de58e8dc57fcc9115e21bdbf8c92356331021ece94bab3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fj.1365-294X.2008.03716.x$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1365-294X.2008.03716.x$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>230,314,776,780,881,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18346126$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-00281908$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>DE GROOT, NATASJA G</creatorcontrib><creatorcontrib>HEIJMANS, CORRINE M.C</creatorcontrib><creatorcontrib>DE GROOT, NANINE</creatorcontrib><creatorcontrib>OTTING, NEL</creatorcontrib><creatorcontrib>DE VOS-ROUWELER, ANNEMIEK J.M</creatorcontrib><creatorcontrib>REMARQUE, EDMOND J</creatorcontrib><creatorcontrib>BONHOMME, MAXIME</creatorcontrib><creatorcontrib>DOXIADIS, GABY G.M</creatorcontrib><creatorcontrib>CROUAU-ROY, BRIGITTE</creatorcontrib><creatorcontrib>BONTROP, RONALD E</creatorcontrib><title>Pinpointing a selective sweep to the chimpanzee MHC class I region by comparative genomics</title><title>Molecular ecology</title><addtitle>Mol Ecol</addtitle><description>Chimpanzees experienced a reduction of the allelic repertoire at the major histocompatibility complex (MHC) class I A and B loci, which may have been caused by a retrovirus belonging to the simian immunodeficiency virus (SIV) family. Extended MHC haplotypes were defined in a pedigreed chimpanzee colony. Comparison of genetic variation at microsatellite markers mapping inside and outside the Mhc region was carried out in humans and chimpanzees to investigate the genomic extent of the repertoire reduction. Multilocus demographic analyses underscored that chimpanzees indeed experienced a selective sweep that mainly targeted the chromosomal segment carrying the Mhc class I region. Probably due to genetic linkage, the sweep also affected other polymorphic loci, mapping in the close vicinity of the Mhc class I region genes. Nevertheless, although the allelic repertoire at particular Mhc class I and II loci appears to be limited, naturally occurring recombination events allowed the establishment of haplotype diversity after the sweep. However, recombination did not have sufficient time to erase the signal of the selective sweep.</description><subject>Africa, Western</subject><subject>Animal biology</subject><subject>Animals</subject><subject>Biodiversity</subject><subject>Comparative studies</subject><subject>DNA, Mitochondrial - chemistry</subject><subject>DNA, Mitochondrial - genetics</subject><subject>Ecology</subject><subject>Ecology, environment</subject><subject>Genetic Variation</subject><subject>Genetics</subject><subject>Genomics</subject><subject>haplotypes</subject><subject>Haplotypes - genetics</subject><subject>Histocompatibility Antigens Class I - genetics</subject><subject>Histocompatibility Antigens Class I - immunology</subject><subject>HIV</subject><subject>Humans</subject><subject>Life Sciences</subject><subject>microsatellite</subject><subject>microsatellite repeats</subject><subject>Microsatellite Repeats - genetics</subject><subject>Molecular biology</subject><subject>Pan troglodytes</subject><subject>Pan troglodytes - genetics</subject><subject>Pan troglodytes - immunology</subject><subject>Phylogeny</subject><subject>Polymerase Chain Reaction</subject><subject>primate evolution</subject><subject>Primates</subject><subject>selection</subject><subject>Sequence Analysis, DNA</subject><subject>Simian immunodeficiency virus</subject><issn>0962-1083</issn><issn>1365-294X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkk9v0zAchiMEYmXwFcDiMIlDgv_Ern3gMJWxTrRl0piYuFiO-0vrksYlTreWT4-zVEXiAr7Ysp_3la3HSYIIzkgc71cZYYKnVOV3GcVYZpgNich2T5LB8eBpMsBK0JRgyU6SFyGsMCaMcv48OSGS5YJQMUi-X7t6413dunqBDApQgW3dPaDwALBBrUftEpBduvXG1L8A0HQ8QrYyIaAr1MDC-RoVe2R9PG_MY3IBtV87G14mz0pTBXh1mE-T208XX0fjdPLl8mp0Pkktp0SkJhfDAlMrSl5aA0rmag5cgpxbPiytVYRwoKSYF6W0ijIuGCOYErCg8sIU7DR51_cuTaU3jVubZq-9cXp8PtHdHsZUEoXlPYnsWc9uGv9zC6HVaxcsVJWpwW-DFopgLkn-T5BiqVROO_DtX-DKb5s6PlhTgoXKZc4jJHvINj6EBsrjPQnWnVG90p043YnTnVH9aFTvYvT1oX9brGH-J3hQGIEPPfDgKtj_d7GeXoy6Vcynfd6FFnbHvGl-aDFkQ66_zS717OO1nN7NPuubyL_p-dJ4bRaNC_r2hsavFcslIzJnvwHzK8ah</recordid><startdate>200804</startdate><enddate>200804</enddate><creator>DE GROOT, NATASJA G</creator><creator>HEIJMANS, CORRINE M.C</creator><creator>DE GROOT, NANINE</creator><creator>OTTING, NEL</creator><creator>DE VOS-ROUWELER, ANNEMIEK J.M</creator><creator>REMARQUE, EDMOND J</creator><creator>BONHOMME, MAXIME</creator><creator>DOXIADIS, GABY G.M</creator><creator>CROUAU-ROY, BRIGITTE</creator><creator>BONTROP, RONALD E</creator><general>Oxford, UK : Blackwell Publishing Ltd</general><general>Blackwell Publishing Ltd</general><general>Wiley</general><scope>FBQ</scope><scope>BSCLL</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>7SN</scope><scope>7SS</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7T5</scope><scope>7U9</scope><scope>H94</scope><scope>7X8</scope><scope>1XC</scope></search><sort><creationdate>200804</creationdate><title>Pinpointing a selective sweep to the chimpanzee MHC class I region by comparative genomics</title><author>DE GROOT, NATASJA G ; HEIJMANS, CORRINE M.C ; DE GROOT, NANINE ; OTTING, NEL ; DE VOS-ROUWELER, ANNEMIEK J.M ; REMARQUE, EDMOND J ; BONHOMME, MAXIME ; DOXIADIS, GABY G.M ; CROUAU-ROY, BRIGITTE ; BONTROP, RONALD E</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5216-a467b02c6f5fcae9849de58e8dc57fcc9115e21bdbf8c92356331021ece94bab3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2008</creationdate><topic>Africa, Western</topic><topic>Animal biology</topic><topic>Animals</topic><topic>Biodiversity</topic><topic>Comparative studies</topic><topic>DNA, Mitochondrial - chemistry</topic><topic>DNA, Mitochondrial - genetics</topic><topic>Ecology</topic><topic>Ecology, environment</topic><topic>Genetic Variation</topic><topic>Genetics</topic><topic>Genomics</topic><topic>haplotypes</topic><topic>Haplotypes - genetics</topic><topic>Histocompatibility Antigens Class I - genetics</topic><topic>Histocompatibility Antigens Class I - immunology</topic><topic>HIV</topic><topic>Humans</topic><topic>Life Sciences</topic><topic>microsatellite</topic><topic>microsatellite repeats</topic><topic>Microsatellite Repeats - genetics</topic><topic>Molecular biology</topic><topic>Pan troglodytes</topic><topic>Pan troglodytes - genetics</topic><topic>Pan troglodytes - immunology</topic><topic>Phylogeny</topic><topic>Polymerase Chain Reaction</topic><topic>primate evolution</topic><topic>Primates</topic><topic>selection</topic><topic>Sequence Analysis, DNA</topic><topic>Simian immunodeficiency virus</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>DE GROOT, NATASJA G</creatorcontrib><creatorcontrib>HEIJMANS, CORRINE M.C</creatorcontrib><creatorcontrib>DE GROOT, NANINE</creatorcontrib><creatorcontrib>OTTING, NEL</creatorcontrib><creatorcontrib>DE VOS-ROUWELER, ANNEMIEK J.M</creatorcontrib><creatorcontrib>REMARQUE, EDMOND J</creatorcontrib><creatorcontrib>BONHOMME, MAXIME</creatorcontrib><creatorcontrib>DOXIADIS, GABY G.M</creatorcontrib><creatorcontrib>CROUAU-ROY, BRIGITTE</creatorcontrib><creatorcontrib>BONTROP, RONALD E</creatorcontrib><collection>AGRIS</collection><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>Immunology Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><jtitle>Molecular ecology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>DE GROOT, NATASJA G</au><au>HEIJMANS, CORRINE M.C</au><au>DE GROOT, NANINE</au><au>OTTING, NEL</au><au>DE VOS-ROUWELER, ANNEMIEK J.M</au><au>REMARQUE, EDMOND J</au><au>BONHOMME, MAXIME</au><au>DOXIADIS, GABY G.M</au><au>CROUAU-ROY, BRIGITTE</au><au>BONTROP, RONALD E</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Pinpointing a selective sweep to the chimpanzee MHC class I region by comparative genomics</atitle><jtitle>Molecular ecology</jtitle><addtitle>Mol Ecol</addtitle><date>2008-04</date><risdate>2008</risdate><volume>17</volume><issue>8</issue><spage>2074</spage><epage>2088</epage><pages>2074-2088</pages><issn>0962-1083</issn><eissn>1365-294X</eissn><abstract>Chimpanzees experienced a reduction of the allelic repertoire at the major histocompatibility complex (MHC) class I A and B loci, which may have been caused by a retrovirus belonging to the simian immunodeficiency virus (SIV) family. Extended MHC haplotypes were defined in a pedigreed chimpanzee colony. Comparison of genetic variation at microsatellite markers mapping inside and outside the Mhc region was carried out in humans and chimpanzees to investigate the genomic extent of the repertoire reduction. Multilocus demographic analyses underscored that chimpanzees indeed experienced a selective sweep that mainly targeted the chromosomal segment carrying the Mhc class I region. Probably due to genetic linkage, the sweep also affected other polymorphic loci, mapping in the close vicinity of the Mhc class I region genes. Nevertheless, although the allelic repertoire at particular Mhc class I and II loci appears to be limited, naturally occurring recombination events allowed the establishment of haplotype diversity after the sweep. However, recombination did not have sufficient time to erase the signal of the selective sweep.</abstract><cop>Oxford, UK</cop><pub>Oxford, UK : Blackwell Publishing Ltd</pub><pmid>18346126</pmid><doi>10.1111/j.1365-294X.2008.03716.x</doi><tpages>15</tpages></addata></record> |
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| ispartof | Molecular ecology, 2008-04, Vol.17 (8), p.2074-2088 |
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| subjects | Africa, Western Animal biology Animals Biodiversity Comparative studies DNA, Mitochondrial - chemistry DNA, Mitochondrial - genetics Ecology Ecology, environment Genetic Variation Genetics Genomics haplotypes Haplotypes - genetics Histocompatibility Antigens Class I - genetics Histocompatibility Antigens Class I - immunology HIV Humans Life Sciences microsatellite microsatellite repeats Microsatellite Repeats - genetics Molecular biology Pan troglodytes Pan troglodytes - genetics Pan troglodytes - immunology Phylogeny Polymerase Chain Reaction primate evolution Primates selection Sequence Analysis, DNA Simian immunodeficiency virus |
| title | Pinpointing a selective sweep to the chimpanzee MHC class I region by comparative genomics |
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