Similarity coefficients for molecular markers in studies of genetic relationships between individuals for haploid, diploid, and polyploid species
Identifieur interne : 001146 ( Main/Exploration ); précédent : 001145; suivant : 001147Similarity coefficients for molecular markers in studies of genetic relationships between individuals for haploid, diploid, and polyploid species
Auteurs : E. Kosman [Israël] ; K. J. Leonard [États-Unis]Source :
- Molecular Ecology [ 0962-1083 ] ; 2005-02.
English descriptors
- Teeft :
- Aflp, Aflps, Allele, Allele frequencies, Average number, Band positions, Binary, Binary patterns, Blackwell publishing, Codominant, Codominant loci, Codominant markers, Coefficient, Common ancestor, Dice coefficient, Different alleles, Different measures, Different populations, Diploid, Diploid organisms, Dissimilarity, Dissimilarity measures, Dominant markers, Ecology, Euclidean, Euclidean distance, Fingerprint profiles, Genetic, Genetic dissimilarity, Genetic diversity, Genetic relationships, Genetic similarity, Genetic states, Genetics, Genotype, Haploid, Haploid individuals, Heterozygote, Heterozygous, Heterozygous states, Homozygote, Identical measures, Jaccard, Jaccard coefficient, Locus, Marker, Mismatch, Molecular ecology, Molecular markers, Multiallelic, Multiallelic locus, Multilocus, Multistate characters, Other hand, Peakall, Phenotype, Polyploid, Population structure, Rapd, Rapds, Same locus, Sequence divergence, Sequence identity, Similarity, Similarity coefficient, Similarity coefficients, Simple mismatch coefficient, Simple mismatch coefficients, Smouse, Smouse peakall, Specific position, Squared euclidean distance, Ssrs, Suitable measure, Suitable method, Total number.
Abstract
Determining true genetic dissimilarity between individuals is an important and decisive point for clustering and analysing diversity within and among populations, because different dissimilarity indices may yield conflicting outcomes. We show that there are no acceptable universal approaches to assessing the dissimilarity between individuals with molecular markers. Different measures are relevant to dominant and codominant DNA markers depending on the ploidy of organisms. The Dice coefficient is the suitable measure for haploids with codominant markers and it can be applied directly to (0,1)‐vectors representing banding profiles of individuals. None of the common measures, Dice, Jaccard, simple mismatch coefficient (or the squared Euclidean distance), is appropriate for diploids with codominant markers. By transforming multiallelic banding patterns at each locus into the corresponding homozygous or heterozygous states, a new measure of dissimilarity within locus was developed and expanded to assess dissimilarity between multilocus states of two individuals by averaging across all codominant loci tested. There is no rigorous well‐founded solution in the case of dominant markers. The simple mismatch coefficient is the most suitable measure of dissimilarity between banding patterns of closely related haploid forms. For distantly related haploid individuals, the Jaccard dissimilarity is recommended. In general, no suitable method for measuring genetic dissimilarity between diploids with dominant markers can be proposed. Banding patterns of diploids with dominant markers and polyploids with codominant markers represent individuals’ phenotypes rather than genotypes. All dissimilarity measures proposed and developed herein are metrics.
Url:
DOI: 10.1111/j.1365-294X.2005.02416.x
Affiliations:
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Leonard</name><affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108</wicri:regionArea><placeName><region type="state">Minnesota</region></placeName></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Molecular Ecology</title><title level="j" type="alt">MOLECULAR ECOLOGY</title><idno type="ISSN">0962-1083</idno><idno type="eISSN">1365-294X</idno><imprint><biblScope unit="vol">14</biblScope><biblScope unit="issue">2</biblScope><biblScope unit="page" from="415">415</biblScope><biblScope unit="page" to="424">424</biblScope><biblScope unit="page-count">10</biblScope><publisher>Blackwell Science Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2005-02">2005-02</date></imprint><idno type="ISSN">0962-1083</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0962-1083</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="Teeft" xml:lang="en"><term>Aflp</term><term>Aflps</term><term>Allele</term><term>Allele frequencies</term><term>Average number</term><term>Band positions</term><term>Binary</term><term>Binary patterns</term><term>Blackwell publishing</term><term>Codominant</term><term>Codominant loci</term><term>Codominant markers</term><term>Coefficient</term><term>Common ancestor</term><term>Dice coefficient</term><term>Different alleles</term><term>Different measures</term><term>Different populations</term><term>Diploid</term><term>Diploid organisms</term><term>Dissimilarity</term><term>Dissimilarity measures</term><term>Dominant markers</term><term>Ecology</term><term>Euclidean</term><term>Euclidean distance</term><term>Fingerprint profiles</term><term>Genetic</term><term>Genetic dissimilarity</term><term>Genetic diversity</term><term>Genetic relationships</term><term>Genetic similarity</term><term>Genetic states</term><term>Genetics</term><term>Genotype</term><term>Haploid</term><term>Haploid individuals</term><term>Heterozygote</term><term>Heterozygous</term><term>Heterozygous states</term><term>Homozygote</term><term>Identical measures</term><term>Jaccard</term><term>Jaccard coefficient</term><term>Locus</term><term>Marker</term><term>Mismatch</term><term>Molecular ecology</term><term>Molecular markers</term><term>Multiallelic</term><term>Multiallelic locus</term><term>Multilocus</term><term>Multistate characters</term><term>Other hand</term><term>Peakall</term><term>Phenotype</term><term>Polyploid</term><term>Population structure</term><term>Rapd</term><term>Rapds</term><term>Same locus</term><term>Sequence divergence</term><term>Sequence identity</term><term>Similarity</term><term>Similarity coefficient</term><term>Similarity coefficients</term><term>Simple mismatch coefficient</term><term>Simple mismatch coefficients</term><term>Smouse</term><term>Smouse peakall</term><term>Specific position</term><term>Squared euclidean distance</term><term>Ssrs</term><term>Suitable measure</term><term>Suitable method</term><term>Total number</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Determining true genetic dissimilarity between individuals is an important and decisive point for clustering and analysing diversity within and among populations, because different dissimilarity indices may yield conflicting outcomes. We show that there are no acceptable universal approaches to assessing the dissimilarity between individuals with molecular markers. Different measures are relevant to dominant and codominant DNA markers depending on the ploidy of organisms. The Dice coefficient is the suitable measure for haploids with codominant markers and it can be applied directly to (0,1)‐vectors representing banding profiles of individuals. None of the common measures, Dice, Jaccard, simple mismatch coefficient (or the squared Euclidean distance), is appropriate for diploids with codominant markers. By transforming multiallelic banding patterns at each locus into the corresponding homozygous or heterozygous states, a new measure of dissimilarity within locus was developed and expanded to assess dissimilarity between multilocus states of two individuals by averaging across all codominant loci tested. There is no rigorous well‐founded solution in the case of dominant markers. The simple mismatch coefficient is the most suitable measure of dissimilarity between banding patterns of closely related haploid forms. For distantly related haploid individuals, the Jaccard dissimilarity is recommended. In general, no suitable method for measuring genetic dissimilarity between diploids with dominant markers can be proposed. Banding patterns of diploids with dominant markers and polyploids with codominant markers represent individuals’ phenotypes rather than genotypes. All dissimilarity measures proposed and developed herein are metrics.</div></front></TEI><affiliations><list><country><li>Israël</li><li>États-Unis</li></country><region><li>Minnesota</li></region></list><tree><country name="Israël"><noRegion><name sortKey="Kosman, E" sort="Kosman, E" uniqKey="Kosman E" first="E." last="Kosman">E. Kosman</name></noRegion></country><country name="États-Unis"><region name="Minnesota"><name sortKey="Leonard, K J" sort="Leonard, K J" uniqKey="Leonard K" first="K. J." last="Leonard">K. J. Leonard</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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