Estimation of pairwise relatedness between individuals and characterization of isolation‐by‐distance processes using dominant genetic markers
Identifieur interne : 000262 ( Istex/Corpus ); précédent : 000261; suivant : 000263Estimation of pairwise relatedness between individuals and characterization of isolation‐by‐distance processes using dominant genetic markers
Auteurs : Olivier J. HardySource :
- Molecular Ecology [ 0962-1083 ] ; 2003-06.
English descriptors
Abstract
A new estimator of the pairwise relatedness coefficient between individuals adapted to dominant genetic markers is developed. This estimator does not assume genotypes to be in Hardy–Weinberg proportions but requires a knowledge of the departure from these proportions (i.e. the inbreeding coefficient). Simulations show that the estimator provides accurate estimates, except for some particular types of individual pairs such as full‐sibs, and performs better than a previously developed estimator. When comparing marker‐based relatedness estimates with pedigree expectations, a new approach to account for the change of the reference population is developed and shown to perform satisfactorily. Simulations also illustrate that this new relatedness estimator can be used to characterize isolation by distance within populations, leading to essentially unbiased estimates of the neighbourhood size. In this context, the estimator appears fairly robust to moderate errors made on the assumed inbreeding coefficient. The analysis of real data sets suggests that dominant markers (random amplified polymorphic DNA, amplified fragment length polymorphism) may be as valuable as co‐dominant markers (microsatellites) in studying microgeographic isolation‐by‐distance processes. It is argued that the estimators developed should find major applications, notably for conservation biology.
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DOI: 10.1046/j.1365-294X.2003.01835.x
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ISTEX:A331189A3A6405875400949FE61DF0145B4D4303Le document en format XML
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This estimator does not assume genotypes to be in Hardy–Weinberg proportions but requires a knowledge of the departure from these proportions (i.e. the inbreeding coefficient). Simulations show that the estimator provides accurate estimates, except for some particular types of individual pairs such as full‐sibs, and performs better than a previously developed estimator. When comparing marker‐based relatedness estimates with pedigree expectations, a new approach to account for the change of the reference population is developed and shown to perform satisfactorily. Simulations also illustrate that this new relatedness estimator can be used to characterize isolation by distance within populations, leading to essentially unbiased estimates of the neighbourhood size. In this context, the estimator appears fairly robust to moderate errors made on the assumed inbreeding coefficient. The analysis of real data sets suggests that dominant markers (random amplified polymorphic DNA, amplified fragment length polymorphism) may be as valuable as co‐dominant markers (microsatellites) in studying microgeographic isolation‐by‐distance processes. It is argued that the estimators developed should find major applications, notably for conservation biology.</div></front></TEI><istex><corpusName>wiley</corpusName><author><json:item><name>Olivier J. 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This estimator does not assume genotypes to be in Hardy–Weinberg proportions but requires a knowledge of the departure from these proportions (i.e. the inbreeding coefficient). Simulations show that the estimator provides accurate estimates, except for some particular types of individual pairs such as full‐sibs, and performs better than a previously developed estimator. When comparing marker‐based relatedness estimates with pedigree expectations, a new approach to account for the change of the reference population is developed and shown to perform satisfactorily. Simulations also illustrate that this new relatedness estimator can be used to characterize isolation by distance within populations, leading to essentially unbiased estimates of the neighbourhood size. In this context, the estimator appears fairly robust to moderate errors made on the assumed inbreeding coefficient. The analysis of real data sets suggests that dominant markers (random amplified polymorphic DNA, amplified fragment length polymorphism) may be as valuable as co‐dominant markers (microsatellites) in studying microgeographic isolation‐by‐distance processes. 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This estimator does not assume genotypes to be in Hardy–Weinberg proportions but requires a knowledge of the departure from these proportions (i.e. the inbreeding coefficient). Simulations show that the estimator provides accurate estimates, except for some particular types of individual pairs such as full‐sibs, and performs better than a previously developed estimator. When comparing marker‐based relatedness estimates with pedigree expectations, a new approach to account for the change of the reference population is developed and shown to perform satisfactorily. Simulations also illustrate that this new relatedness estimator can be used to characterize isolation by distance within populations, leading to essentially unbiased estimates of the neighbourhood size. In this context, the estimator appears fairly robust to moderate errors made on the assumed inbreeding coefficient. The analysis of real data sets suggests that dominant markers (random amplified polymorphic DNA, amplified fragment length polymorphism) may be as valuable as co‐dominant markers (microsatellites) in studying microgeographic isolation‐by‐distance processes. It is argued that the estimators developed should find major applications, notably for conservation biology.</p></abstract><textClass xml:lang="en"><keywords scheme="keyword"><list><head>keywords</head><item><term>AFLP</term></item><item><term>dominant markers</term></item><item><term>isolation by distance</term></item><item><term>neighbourhood size</term></item><item><term>RAPD</term></item><item><term>relatedness</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="2003-06">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/document/A331189A3A6405875400949FE61DF0145B4D4303/fulltext/txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Wiley, elements deleted: body"><istex:xmlDeclaration>version="1.0" encoding="UTF-8" standalone="yes"</istex:xmlDeclaration><istex:document><component version="2.0" type="serialArticle" xml:lang="en"><header><publicationMeta level="product"><publisherInfo><publisherName>Blackwell Publishing Ltd.</publisherName><publisherLoc>Oxford, UK</publisherLoc></publisherInfo><doi origin="wiley" registered="yes">10.1111/(ISSN)1365-294X</doi><issn type="print">0962-1083</issn><issn type="electronic">1365-294X</issn><idGroup><id type="product" value="MEC"></id><id type="publisherDivision" value="ST"></id></idGroup><titleGroup><title type="main" sort="MOLECULAR ECOLOGY">Molecular Ecology</title></titleGroup></publicationMeta><publicationMeta level="part" position="06006"><doi origin="wiley">10.1111/mec.2003.12.issue-6</doi><numberingGroup><numbering type="journalVolume" number="12">12</numbering><numbering type="journalIssue" number="6">6</numbering></numberingGroup><coverDate startDate="2003-06">June 2003</coverDate></publicationMeta><publicationMeta level="unit" type="article" position="0157700" status="forIssue"><doi origin="wiley">10.1046/j.1365-294X.2003.01835.x</doi><idGroup><id type="unit" value="MEC1835"></id></idGroup><countGroup><count type="pageTotal" number="12"></count></countGroup><titleGroup><title type="tocHeading1">Kinship, Parentage and Behaviour</title></titleGroup><eventGroup><event type="firstOnline" date="2008-10-10"></event><event type="publishedOnlineFinalForm" date="2008-10-10"></event><event type="xmlConverted" agent="Converter:BPG_TO_WML3G version:2.3.2 mode:FullText source:FullText result:FullText" date="2010-03-10"></event><event type="xmlConverted" agent="Converter:WILEY_ML3G_TO_WILEY_ML3GV2 version:4.0.1" date="2014-03-20"></event><event type="xmlConverted" agent="Converter:WML3G_To_WML3G version:4.1.7 mode:FullText,remove_FC" date="2014-10-31"></event></eventGroup><numberingGroup><numbering type="pageFirst" number="1577">1577</numbering><numbering type="pageLast" number="1588">1588</numbering></numberingGroup><correspondenceTo>Olivier Hardy. Fax: + 32 2650 91 70; E‐mail: <email>ohardy@ulb.ac.be</email></correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:MEC.MEC1835.pdf"></link></linkGroup></publicationMeta><contentMeta><unparsedEditorialHistory>Received 19 November 2002; revision received 30 January 2003; accepted 30 January 2003</unparsedEditorialHistory><countGroup><count type="figureTotal" number="6"></count><count type="tableTotal" number="1"></count><count type="formulaTotal" number="41"></count><count type="referenceTotal" number="30"></count><count type="wordTotal" number="7660"></count></countGroup><titleGroup><title type="main">Estimation of pairwise relatedness between individuals and characterization of isolation‐by‐distance processes using dominant genetic markers</title><title type="shortAuthors">O. J. HARDY</title><title type="short">ESTIMATING RELATEDNESS WITH DOMINANT MARKERS</title></titleGroup><creators><creator creatorRole="author" xml:id="cr1" affiliationRef="#a1" corresponding="yes"><personName><givenNames>Olivier J.</givenNames><familyName>Hardy</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="a1" countryCode="BE"><unparsedAffiliation>Laboratoire de Génétique et Ecologie végétales, Université Libre de Bruxelles, 1850 chaussée de Wavre, B‐1160 Bruxelles, Belgium</unparsedAffiliation></affiliation></affiliationGroup><keywordGroup xml:lang="en"><keyword xml:id="k1">AFLP</keyword><keyword xml:id="k2">dominant markers</keyword><keyword xml:id="k3">isolation by distance</keyword><keyword xml:id="k4">neighbourhood size</keyword><keyword xml:id="k5">RAPD</keyword><keyword xml:id="k6">relatedness </keyword></keywordGroup><abstractGroup><abstract type="main" xml:lang="en"><title type="main">Abstract</title><p>A new estimator of the pairwise relatedness coefficient between individuals adapted to dominant genetic markers is developed. This estimator does not assume genotypes to be in Hardy–Weinberg proportions but requires a knowledge of the departure from these proportions (i.e. the inbreeding coefficient). Simulations show that the estimator provides accurate estimates, except for some particular types of individual pairs such as full‐sibs, and performs better than a previously developed estimator. When comparing marker‐based relatedness estimates with pedigree expectations, a new approach to account for the change of the reference population is developed and shown to perform satisfactorily. Simulations also illustrate that this new relatedness estimator can be used to characterize isolation by distance within populations, leading to essentially unbiased estimates of the neighbourhood size. In this context, the estimator appears fairly robust to moderate errors made on the assumed inbreeding coefficient. The analysis of real data sets suggests that dominant markers (random amplified polymorphic DNA, amplified fragment length polymorphism) may be as valuable as co‐dominant markers (microsatellites) in studying microgeographic isolation‐by‐distance processes. It is argued that the estimators developed should find major applications, notably for conservation biology.</p></abstract></abstractGroup></contentMeta></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Estimation of pairwise relatedness between individuals and characterization of isolation‐by‐distance processes using dominant genetic markers</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>ESTIMATING RELATEDNESS WITH DOMINANT MARKERS</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Estimation of pairwise relatedness between individuals and characterization of isolation‐by‐distance processes using dominant genetic markers</title></titleInfo><name type="personal"><namePart type="given">Olivier J.</namePart><namePart type="family">Hardy</namePart><affiliation>Laboratoire de Génétique et Ecologie végétales, Université Libre de Bruxelles, 1850 chaussée de Wavre, B‐1160 Bruxelles, Belgium</affiliation><affiliation>E-mail: ohardy@ulb.ac.be</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="article"></genre><originInfo><publisher>Blackwell Publishing Ltd.</publisher><place><placeTerm type="text">Oxford, UK</placeTerm></place><dateIssued encoding="w3cdtf">2003-06</dateIssued><edition>Received 19 November 2002; revision received 30 January 2003; accepted 30 January 2003</edition><copyrightDate encoding="w3cdtf">2003</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><internetMediaType>text/html</internetMediaType><extent unit="figures">6</extent><extent unit="tables">1</extent><extent unit="formulas">41</extent><extent unit="references">30</extent><extent unit="words">7660</extent></physicalDescription><abstract lang="en">A new estimator of the pairwise relatedness coefficient between individuals adapted to dominant genetic markers is developed. This estimator does not assume genotypes to be in Hardy–Weinberg proportions but requires a knowledge of the departure from these proportions (i.e. the inbreeding coefficient). Simulations show that the estimator provides accurate estimates, except for some particular types of individual pairs such as full‐sibs, and performs better than a previously developed estimator. When comparing marker‐based relatedness estimates with pedigree expectations, a new approach to account for the change of the reference population is developed and shown to perform satisfactorily. Simulations also illustrate that this new relatedness estimator can be used to characterize isolation by distance within populations, leading to essentially unbiased estimates of the neighbourhood size. In this context, the estimator appears fairly robust to moderate errors made on the assumed inbreeding coefficient. The analysis of real data sets suggests that dominant markers (random amplified polymorphic DNA, amplified fragment length polymorphism) may be as valuable as co‐dominant markers (microsatellites) in studying microgeographic isolation‐by‐distance processes. It is argued that the estimators developed should find major applications, notably for conservation biology.</abstract><subject lang="en"><genre>keywords</genre><topic>AFLP</topic><topic>dominant markers</topic><topic>isolation by distance</topic><topic>neighbourhood size</topic><topic>RAPD</topic><topic>relatedness</topic></subject><relatedItem type="host"><titleInfo><title>Molecular Ecology</title></titleInfo><genre type="journal">journal</genre><identifier type="ISSN">0962-1083</identifier><identifier type="eISSN">1365-294X</identifier><identifier type="DOI">10.1111/(ISSN)1365-294X</identifier><identifier type="PublisherID">MEC</identifier><part><date>2003</date><detail type="volume"><caption>vol.</caption><number>12</number></detail><detail type="issue"><caption>no.</caption><number>6</number></detail><extent unit="pages"><start>1577</start><end>1588</end><total>12</total></extent></part></relatedItem><identifier type="istex">A331189A3A6405875400949FE61DF0145B4D4303</identifier><identifier type="DOI">10.1046/j.1365-294X.2003.01835.x</identifier><identifier type="ArticleID">MEC1835</identifier><recordInfo><recordContentSource>WILEY</recordContentSource><recordOrigin>Blackwell Publishing Ltd.</recordOrigin></recordInfo></mods></metadata><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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