Comparative nucleotide diversity across North American and European populus species.
Identifieur interne : 002B55 ( Main/Exploration ); précédent : 002B54; suivant : 002B56Comparative nucleotide diversity across North American and European populus species.
Auteurs : Mohamed Ismail [Canada] ; Raju Y. Soolanayakanahally ; P R K. Ingvarsson ; Robert D. Guy ; Stefan Jansson ; Salim N. Silim ; Yousry A. El-KassabySource :
- Journal of molecular evolution [ 1432-1432 ] ; 2012.
Descripteurs français
- KwdFr :
- Amérique du Nord (MeSH), Données de séquences moléculaires (MeSH), Dynamique non linéaire (MeSH), Déséquilibre de liaison (génétique), Europe (MeSH), Facteurs temps (MeSH), Fréquence d'allèle (génétique), Gènes de plante (génétique), Génétique des populations (MeSH), Géographie (MeSH), Haplotypes (génétique), Locus génétiques (génétique), Modèles génétiques (MeSH), Nucléotides (génétique), Polymorphisme de nucléotide simple (génétique), Populus (génétique), Simulation numérique (MeSH), Spéciation génétique (MeSH), Spécificité d'espèce (MeSH), Variation génétique (MeSH).
- MESH :
- génétique : Déséquilibre de liaison, Fréquence d'allèle, Gènes de plante, Haplotypes, Locus génétiques, Nucléotides, Polymorphisme de nucléotide simple, Populus.
- Amérique du Nord, Données de séquences moléculaires, Dynamique non linéaire, Europe, Facteurs temps, Génétique des populations, Géographie, Modèles génétiques, Simulation numérique, Spéciation génétique, Spécificité d'espèce, Variation génétique.
English descriptors
- KwdEn :
- Computer Simulation (MeSH), Europe (MeSH), Gene Frequency (genetics), Genes, Plant (genetics), Genetic Loci (genetics), Genetic Speciation (MeSH), Genetic Variation (MeSH), Genetics, Population (MeSH), Geography (MeSH), Haplotypes (genetics), Linkage Disequilibrium (genetics), Models, Genetic (MeSH), Molecular Sequence Data (MeSH), Nonlinear Dynamics (MeSH), North America (MeSH), Nucleotides (genetics), Polymorphism, Single Nucleotide (genetics), Populus (genetics), Species Specificity (MeSH), Time Factors (MeSH).
- MESH :
- chemical , genetics : Nucleotides.
- geographic : Europe, North America.
- genetics : Gene Frequency, Genes, Plant, Genetic Loci, Haplotypes, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Populus.
- Computer Simulation, Genetic Speciation, Genetic Variation, Genetics, Population, Geography, Models, Genetic, Molecular Sequence Data, Nonlinear Dynamics, Species Specificity, Time Factors.
Abstract
Nucleotide polymorphisms in two North American balsam poplars (Populus trichocarpa Torr. & Gray and P. balsamifera L.; section Tacamahaca), and one Eurasian aspen (P. tremula L.; section Populus) were compared using nine loci involved in defense, stress response, photoperiodism, freezing tolerance, and housekeeping. Nucleotide diversity varied among species and was highest for P. tremula (θ(w) = 0.005, π(T) = 0.007) as compared to P. balsamifera (θ(w) = 0.004, π(T) = 0.005) or P. trichocarpa (θ(w) = 0.002, π(T) = 0.003). Across species, the defense and the stress response loci accounted for the majority of the observed level of nucleotide diversity. In general, the studied loci did not deviate from neutral expectation either at the individual locus (non-significant normalized Fay and Wu's H) or at the multi-locus level (non-significant HKA test). Using molecular clock analysis, section Tacamahaca probably shared a common ancestor with section Populus approximately 4.5 million year ago. Divergence between the two closely related balsam poplars was about 0.8 million years ago, a pattern consistent with an isolation-with-migration (IM) model. As expected, P. tremula showed a five-fold higher substitution rate (2 × 10(-8) substitution/site/year) compared to the North American species (0.4 × 10(-8) substitution/site/year), probably reflecting its complex demographic history. Linkage disequilibrium (LD) varied among species with a more rapid decay in the North American species (<400 bp) in comparison to P. tremula (≫400 bp). The similarities in nucleotide diversity pattern and LD decay of the two balsam poplar species likely reflects the recent time of their divergence.
DOI: 10.1007/s00239-012-9504-5
PubMed: 22562720
Affiliations:
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Soolanayakanahally</name></author><author><name sortKey="Ingvarsson, P R K" sort="Ingvarsson, P R K" uniqKey="Ingvarsson P" first="P R K" last="Ingvarsson">P R K. Ingvarsson</name></author><author><name sortKey="Guy, Robert D" sort="Guy, Robert D" uniqKey="Guy R" first="Robert D" last="Guy">Robert D. Guy</name></author><author><name sortKey="Jansson, Stefan" sort="Jansson, Stefan" uniqKey="Jansson S" first="Stefan" last="Jansson">Stefan Jansson</name></author><author><name sortKey="Silim, Salim N" sort="Silim, Salim N" uniqKey="Silim S" first="Salim N" last="Silim">Salim N. Silim</name></author><author><name sortKey="El Kassaby, Yousry A" sort="El Kassaby, Yousry A" uniqKey="El Kassaby Y" first="Yousry A" last="El-Kassaby">Yousry A. 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Nucleotide diversity varied among species and was highest for P. tremula (θ(w) = 0.005, π(T) = 0.007) as compared to P. balsamifera (θ(w) = 0.004, π(T) = 0.005) or P. trichocarpa (θ(w) = 0.002, π(T) = 0.003). Across species, the defense and the stress response loci accounted for the majority of the observed level of nucleotide diversity. In general, the studied loci did not deviate from neutral expectation either at the individual locus (non-significant normalized Fay and Wu's H) or at the multi-locus level (non-significant HKA test). Using molecular clock analysis, section Tacamahaca probably shared a common ancestor with section Populus approximately 4.5 million year ago. Divergence between the two closely related balsam poplars was about 0.8 million years ago, a pattern consistent with an isolation-with-migration (IM) model. As expected, P. tremula showed a five-fold higher substitution rate (2 × 10(-8) substitution/site/year) compared to the North American species (0.4 × 10(-8) substitution/site/year), probably reflecting its complex demographic history. Linkage disequilibrium (LD) varied among species with a more rapid decay in the North American species (<400 bp) in comparison to P. tremula (≫400 bp). The similarities in nucleotide diversity pattern and LD decay of the two balsam poplar species likely reflects the recent time of their divergence.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22562720</PMID><DateCompleted><Year>2013</Year><Month>03</Month><Day>18</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1432-1432</ISSN><JournalIssue CitedMedium="Internet"><Volume>74</Volume><Issue>5-6</Issue><PubDate><Year>2012</Year><Month>Jun</Month></PubDate></JournalIssue><Title>Journal of molecular evolution</Title><ISOAbbreviation>J Mol Evol</ISOAbbreviation></Journal><ArticleTitle>Comparative nucleotide diversity across North American and European populus species.</ArticleTitle><Pagination><MedlinePgn>257-72</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00239-012-9504-5</ELocationID><Abstract><AbstractText>Nucleotide polymorphisms in two North American balsam poplars (Populus trichocarpa Torr. & Gray and P. balsamifera L.; section Tacamahaca), and one Eurasian aspen (P. tremula L.; section Populus) were compared using nine loci involved in defense, stress response, photoperiodism, freezing tolerance, and housekeeping. Nucleotide diversity varied among species and was highest for P. tremula (θ(w) = 0.005, π(T) = 0.007) as compared to P. balsamifera (θ(w) = 0.004, π(T) = 0.005) or P. trichocarpa (θ(w) = 0.002, π(T) = 0.003). Across species, the defense and the stress response loci accounted for the majority of the observed level of nucleotide diversity. In general, the studied loci did not deviate from neutral expectation either at the individual locus (non-significant normalized Fay and Wu's H) or at the multi-locus level (non-significant HKA test). Using molecular clock analysis, section Tacamahaca probably shared a common ancestor with section Populus approximately 4.5 million year ago. Divergence between the two closely related balsam poplars was about 0.8 million years ago, a pattern consistent with an isolation-with-migration (IM) model. As expected, P. tremula showed a five-fold higher substitution rate (2 × 10(-8) substitution/site/year) compared to the North American species (0.4 × 10(-8) substitution/site/year), probably reflecting its complex demographic history. Linkage disequilibrium (LD) varied among species with a more rapid decay in the North American species (<400 bp) in comparison to P. tremula (≫400 bp). The similarities in nucleotide diversity pattern and LD decay of the two balsam poplar species likely reflects the recent time of their divergence.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ismail</LastName><ForeName>Mohamed</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Forest Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada. mohamed.ismail@agr.menofia.edu.eg</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Soolanayakanahally</LastName><ForeName>Raju Y</ForeName><Initials>RY</Initials></Author><Author ValidYN="Y"><LastName>Ingvarsson</LastName><ForeName>Pär K</ForeName><Initials>PK</Initials></Author><Author ValidYN="Y"><LastName>Guy</LastName><ForeName>Robert D</ForeName><Initials>RD</Initials></Author><Author ValidYN="Y"><LastName>Jansson</LastName><ForeName>Stefan</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Silim</LastName><ForeName>Salim N</ForeName><Initials>SN</Initials></Author><Author ValidYN="Y"><LastName>El-Kassaby</LastName><ForeName>Yousry A</ForeName><Initials>YA</Initials></Author></AuthorList><Language>eng</Language><DataBankList 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UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2012</Year><Month>05</Month><Day>06</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>J Mol Evol</MedlineTA><NlmUniqueID>0360051</NlmUniqueID><ISSNLinking>0022-2844</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009711">Nucleotides</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D003198" MajorTopicYN="N">Computer Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005060" MajorTopicYN="N" Type="Geographic">Europe</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005787" MajorTopicYN="N">Gene Frequency</DescriptorName><QualifierName UI="Q000235" 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MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015810" MajorTopicYN="N">Linkage Disequilibrium</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008957" MajorTopicYN="N">Models, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017711" MajorTopicYN="N">Nonlinear Dynamics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009656" MajorTopicYN="N" Type="Geographic">North America</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009711" MajorTopicYN="N">Nucleotides</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013045" MajorTopicYN="N">Species Specificity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013997" MajorTopicYN="N">Time Factors</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2011</Year><Month>04</Month><Day>06</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2012</Year><Month>04</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2012</Year><Month>5</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2012</Year><Month>5</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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</li></region><settlement><li>Vancouver</li></settlement><orgName><li>Université de la Colombie-Britannique</li></orgName></list><tree><noCountry><name sortKey="El Kassaby, Yousry A" sort="El Kassaby, Yousry A" uniqKey="El Kassaby Y" first="Yousry A" last="El-Kassaby">Yousry A. El-Kassaby</name><name sortKey="Guy, Robert D" sort="Guy, Robert D" uniqKey="Guy R" first="Robert D" last="Guy">Robert D. Guy</name><name sortKey="Ingvarsson, P R K" sort="Ingvarsson, P R K" uniqKey="Ingvarsson P" first="P R K" last="Ingvarsson">P R K. Ingvarsson</name><name sortKey="Jansson, Stefan" sort="Jansson, Stefan" uniqKey="Jansson S" first="Stefan" last="Jansson">Stefan Jansson</name><name sortKey="Silim, Salim N" sort="Silim, Salim N" uniqKey="Silim S" first="Salim N" last="Silim">Salim N. Silim</name><name sortKey="Soolanayakanahally, Raju Y" sort="Soolanayakanahally, Raju Y" uniqKey="Soolanayakanahally R" first="Raju Y" last="Soolanayakanahally">Raju Y. Soolanayakanahally</name></noCountry><country name="Canada"><region name="Colombie-Britannique "><name sortKey="Ismail, Mohamed" sort="Ismail, Mohamed" uniqKey="Ismail M" first="Mohamed" last="Ismail">Mohamed Ismail</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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