A Six Nuclear Gene Phylogeny of Citrus (Rutaceae) Taking into Account Hybridization and Lineage Sorting
Identifieur interne : 000F78 ( Main/Exploration ); précédent : 000F77; suivant : 000F79A Six Nuclear Gene Phylogeny of Citrus (Rutaceae) Taking into Account Hybridization and Lineage Sorting
Auteurs : Chandrika Ramadugu [États-Unis] ; Bernard E. Pfeil [Australie, Suède] ; Manjunath L. Keremane [États-Unis] ; Richard F. Lee [États-Unis] ; Ivan J. Maureira-Butler [Chili] ; Mikeal L. Roose [États-Unis]Source :
- PLoS ONE [ 1932-6203 ] ; 2013.
Abstract
Genus
(1) We generated phylogenetic trees using haplotype sequences of six low copy nuclear genes. (2) Published simple sequence repeat data were re-analyzed to study population structure and the results were compared with the phylogenetic trees constructed using sequence data and coalescence simulations. (3) To distinguish between hybridization and incomplete lineage sorting, we developed and utilized a coalescence simulation approach. In other studies, species trees have been inferred despite the possibility of hybridization having occurred and used to generate null distributions of the effect of lineage sorting alone (by coalescent simulation). Since this is problematic, we instead generate these distributions directly from observed gene trees. Of the six trees generated, we used the most resolved three to detect hybrids. We found that 11 of 33 samples appear to be affected by historical hybridization. Analysis of the remaining three genes supported the conclusions from the hybrid detection test.
We have identified or confirmed probable hybrid origins for several
Url:
DOI: 10.1371/journal.pone.0068410
PubMed: 23874615
PubMed Central: 3713030
Affiliations:
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Pfeil</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Commonwealth Scientific and Industrial Research Organisation Plant Industry, Canberra, Australian Capital Territory, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Commonwealth Scientific and Industrial Research Organisation Plant Industry, Canberra, Australian Capital Territory</wicri:regionArea><wicri:noRegion>Australian Capital Territory</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>DBES, Gothenburg University, Gothenburg, Sweden</addr-line></nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea>DBES, Gothenburg University, Gothenburg</wicri:regionArea><wicri:noRegion>Gothenburg</wicri:noRegion></affiliation></author><author><name sortKey="Keremane, Manjunath L" sort="Keremane, Manjunath L" uniqKey="Keremane M" first="Manjunath L." last="Keremane">Manjunath L. Keremane</name><affiliation wicri:level="2"><nlm:aff id="aff4"><addr-line>United States Department of Agriculture–Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>United States Department of Agriculture–Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Lee, Richard F" sort="Lee, Richard F" uniqKey="Lee R" first="Richard F." last="Lee">Richard F. Lee</name><affiliation wicri:level="2"><nlm:aff id="aff4"><addr-line>United States Department of Agriculture–Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>United States Department of Agriculture–Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Maureira Butler, Ivan J" sort="Maureira Butler, Ivan J" uniqKey="Maureira Butler I" first="Ivan J." last="Maureira-Butler">Ivan J. Maureira-Butler</name><affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>Agriaquaculture Nutritional Genomic Center, Centro de Genómica Nutricional Agroacuícola, Genomics and Bioinformatics Unit, Temuco, Chile</addr-line></nlm:aff><country xml:lang="fr">Chili</country><wicri:regionArea>Agriaquaculture Nutritional Genomic Center, Centro de Genómica Nutricional Agroacuícola, Genomics and Bioinformatics Unit, Temuco</wicri:regionArea><wicri:noRegion>Temuco</wicri:noRegion></affiliation></author><author><name sortKey="Roose, Mikeal L" sort="Roose, Mikeal L" uniqKey="Roose M" first="Mikeal L." last="Roose">Mikeal L. Roose</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Botany and Plant Sciences, University of California Riverside, Riverside, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Botany and Plant Sciences, University of California Riverside, Riverside, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23874615</idno><idno type="pmc">3713030</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3713030</idno><idno type="RBID">PMC:3713030</idno><idno type="doi">10.1371/journal.pone.0068410</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">001149</idno><idno type="wicri:Area/Pmc/Curation">001148</idno><idno type="wicri:Area/Pmc/Checkpoint">000B71</idno><idno type="wicri:Area/Ncbi/Merge">001356</idno><idno type="wicri:Area/Ncbi/Curation">001356</idno><idno type="wicri:Area/Ncbi/Checkpoint">001356</idno><idno type="wicri:Area/Main/Merge">000F83</idno><idno type="wicri:Area/Main/Curation">000F78</idno><idno type="wicri:Area/Main/Exploration">000F78</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A Six Nuclear Gene Phylogeny of <italic>Citrus</italic> (Rutaceae) Taking into Account Hybridization and Lineage Sorting</title><author><name sortKey="Ramadugu, Chandrika" sort="Ramadugu, Chandrika" uniqKey="Ramadugu C" first="Chandrika" last="Ramadugu">Chandrika Ramadugu</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Botany and Plant Sciences, University of California Riverside, Riverside, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Botany and Plant Sciences, University of California Riverside, Riverside, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Pfeil, Bernard E" sort="Pfeil, Bernard E" uniqKey="Pfeil B" first="Bernard E." last="Pfeil">Bernard E. Pfeil</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Commonwealth Scientific and Industrial Research Organisation Plant Industry, Canberra, Australian Capital Territory, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Commonwealth Scientific and Industrial Research Organisation Plant Industry, Canberra, Australian Capital Territory</wicri:regionArea><wicri:noRegion>Australian Capital Territory</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>DBES, Gothenburg University, Gothenburg, Sweden</addr-line></nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea>DBES, Gothenburg University, Gothenburg</wicri:regionArea><wicri:noRegion>Gothenburg</wicri:noRegion></affiliation></author><author><name sortKey="Keremane, Manjunath L" sort="Keremane, Manjunath L" uniqKey="Keremane M" first="Manjunath L." last="Keremane">Manjunath L. Keremane</name><affiliation wicri:level="2"><nlm:aff id="aff4"><addr-line>United States Department of Agriculture–Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>United States Department of Agriculture–Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Lee, Richard F" sort="Lee, Richard F" uniqKey="Lee R" first="Richard F." last="Lee">Richard F. Lee</name><affiliation wicri:level="2"><nlm:aff id="aff4"><addr-line>United States Department of Agriculture–Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>United States Department of Agriculture–Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Maureira Butler, Ivan J" sort="Maureira Butler, Ivan J" uniqKey="Maureira Butler I" first="Ivan J." last="Maureira-Butler">Ivan J. Maureira-Butler</name><affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>Agriaquaculture Nutritional Genomic Center, Centro de Genómica Nutricional Agroacuícola, Genomics and Bioinformatics Unit, Temuco, Chile</addr-line></nlm:aff><country xml:lang="fr">Chili</country><wicri:regionArea>Agriaquaculture Nutritional Genomic Center, Centro de Genómica Nutricional Agroacuícola, Genomics and Bioinformatics Unit, Temuco</wicri:regionArea><wicri:noRegion>Temuco</wicri:noRegion></affiliation></author><author><name sortKey="Roose, Mikeal L" sort="Roose, Mikeal L" uniqKey="Roose M" first="Mikeal L." last="Roose">Mikeal L. Roose</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Botany and Plant Sciences, University of California Riverside, Riverside, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Botany and Plant Sciences, University of California Riverside, Riverside, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Genus <italic>Citrus</italic> (Rutaceae) comprises many important cultivated species that generally hybridize easily. Phylogenetic study of a group showing extensive hybridization is challenging. Since the genus <italic>Citrus</italic> has diverged recently (4–12 Ma), incomplete lineage sorting of ancestral polymorphisms is also likely to cause discrepancies among genes in phylogenetic inferences. Incongruence of gene trees is observed and it is essential to unravel the processes that cause inconsistencies in order to understand the phylogenetic relationships among the species.</p></sec><sec><title>Methodology and Principal Findings</title><p>(1) We generated phylogenetic trees using haplotype sequences of six low copy nuclear genes. (2) Published simple sequence repeat data were re-analyzed to study population structure and the results were compared with the phylogenetic trees constructed using sequence data and coalescence simulations. (3) To distinguish between hybridization and incomplete lineage sorting, we developed and utilized a coalescence simulation approach. In other studies, species trees have been inferred despite the possibility of hybridization having occurred and used to generate null distributions of the effect of lineage sorting alone (by coalescent simulation). Since this is problematic, we instead generate these distributions directly from observed gene trees. Of the six trees generated, we used the most resolved three to detect hybrids. We found that 11 of 33 samples appear to be affected by historical hybridization. Analysis of the remaining three genes supported the conclusions from the hybrid detection test.</p></sec><sec><title>Conclusions</title><p>We have identified or confirmed probable hybrid origins for several <italic>Citrus</italic> cultivars using three different approaches–gene phylogenies, population structure analysis and coalescence simulation. Hybridization and incomplete lineage sorting were identified primarily based on differences among gene phylogenies with reference to null expectations via coalescence simulations. We conclude that identifying hybridization as a frequent cause of incongruence among gene trees is critical to correctly infer the phylogeny among species of <italic>Citrus</italic>.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Barrett, Hc" uniqKey="Barrett H">HC Barrett</name></author><author><name sortKey="Rhodes, Am" uniqKey="Rhodes A">AM Rhodes</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mabberley, Dj" uniqKey="Mabberley D">DJ Mabberley</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Scora, Rw" uniqKey="Scora R">RW Scora</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tanaka, T" uniqKey="Tanaka T">T Tanaka</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Swingle, Wt" uniqKey="Swingle W">WT 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Keremane</name><name sortKey="Lee, Richard F" sort="Lee, Richard F" uniqKey="Lee R" first="Richard F." last="Lee">Richard F. Lee</name><name sortKey="Roose, Mikeal L" sort="Roose, Mikeal L" uniqKey="Roose M" first="Mikeal L." last="Roose">Mikeal L. Roose</name></country><country name="Australie"><noRegion><name sortKey="Pfeil, Bernard E" sort="Pfeil, Bernard E" uniqKey="Pfeil B" first="Bernard E." last="Pfeil">Bernard E. Pfeil</name></noRegion></country><country name="Suède"><noRegion><name sortKey="Pfeil, Bernard E" sort="Pfeil, Bernard E" uniqKey="Pfeil B" first="Bernard E." last="Pfeil">Bernard E. Pfeil</name></noRegion></country><country name="Chili"><noRegion><name sortKey="Maureira Butler, Ivan J" sort="Maureira Butler, Ivan J" uniqKey="Maureira Butler I" first="Ivan J." last="Maureira-Butler">Ivan J. Maureira-Butler</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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