Loter: A Software Package to Infer Local Ancestry for a Wide Range of Species.
Identifieur interne : 000D96 ( Main/Exploration ); précédent : 000D95; suivant : 000D97Loter: A Software Package to Infer Local Ancestry for a Wide Range of Species.
Auteurs : Thomas Dias-Alves [France] ; Julien Mairal [France] ; Michael G B. Blum [France]Source :
- Molecular biology and evolution [ 1537-1719 ] ; 2018.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Populus.
- Haplotypes, Humains, Logiciel, Techniques génétiques.
English descriptors
- KwdEn :
- MESH :
- genetics : Populus.
- Genetic Techniques, Haplotypes, Humans, Software.
Abstract
Admixture between populations provides opportunity to study biological adaptation and phenotypic variation. Admixture studies rely on local ancestry inference for admixed individuals, which consists of computing at each locus the number of copies that originate from ancestral source populations. Existing software packages for local ancestry inference are tuned to provide accurate results on human data and recent admixture events. Here, we introduce Loter, an open-source software package that does not require any biological parameter besides haplotype data in order to make local ancestry inference available for a wide range of species. Using simulations, we compare the performance of Loter to HAPMIX, LAMP-LD, and RFMix. HAPMIX is the only software severely impacted by imperfect haplotype reconstruction. Loter is the less impacted software by increasing admixture time when considering simulated and admixed human genotypes. For simulations of admixed Populus genotypes, Loter and LAMP-LD are robust to increasing admixture times by contrast to RFMix. When comparing length of reconstructed and true ancestry tracts, Loter and LAMP-LD provide results whose accuracy is again more robust than RFMix to increasing admixture times. We apply Loter to individuals resulting from admixture between Populus trichocarpa and Populus balsamifera and lengths of ancestry tracts indicate that admixture took place ∼100 generations ago. We expect that providing a rapid and parameter-free software for local ancestry inference will make more accessible genomic studies about admixture processes.
DOI: 10.1093/molbev/msy126
PubMed: 29931083
PubMed Central: PMC6107063
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Loter: A Software Package to Infer Local Ancestry for a Wide Range of Species.</title><author><name sortKey="Dias Alves, Thomas" sort="Dias Alves, Thomas" uniqKey="Dias Alves T" first="Thomas" last="Dias-Alves">Thomas Dias-Alves</name><affiliation wicri:level="3"><nlm:affiliation>CNRS, TIMC-IMAG UMR 5525, Univ. Grenoble Alpes, Grenoble, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CNRS, TIMC-IMAG UMR 5525, Univ. Grenoble Alpes, Grenoble</wicri:regionArea><placeName><region type="region">Auvergne-Rhône-Alpes</region><region type="old region">Rhône-Alpes</region><settlement type="city">Grenoble</settlement></placeName></affiliation></author><author><name sortKey="Mairal, Julien" sort="Mairal, Julien" uniqKey="Mairal J" first="Julien" last="Mairal">Julien Mairal</name><affiliation wicri:level="3"><nlm:affiliation>CNRS, Institute of Engineering Univ. Grenoble Alpes, LJK, Univ. Grenoble Alpes, Inria, Grenoble, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CNRS, Institute of Engineering Univ. Grenoble Alpes, LJK, Univ. Grenoble Alpes, Inria, Grenoble</wicri:regionArea><placeName><region type="region">Auvergne-Rhône-Alpes</region><region type="old region">Rhône-Alpes</region><settlement type="city">Grenoble</settlement></placeName></affiliation></author><author><name sortKey="Blum, Michael G B" sort="Blum, Michael G B" uniqKey="Blum M" first="Michael G B" last="Blum">Michael G B. Blum</name><affiliation wicri:level="3"><nlm:affiliation>CNRS, TIMC-IMAG UMR 5525, Univ. Grenoble Alpes, Grenoble, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CNRS, TIMC-IMAG UMR 5525, Univ. Grenoble Alpes, Grenoble</wicri:regionArea><placeName><region type="region">Auvergne-Rhône-Alpes</region><region type="old region">Rhône-Alpes</region><settlement type="city">Grenoble</settlement></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2018">2018</date><idno type="RBID">pubmed:29931083</idno><idno type="pmid">29931083</idno><idno type="doi">10.1093/molbev/msy126</idno><idno type="pmc">PMC6107063</idno><idno type="wicri:Area/Main/Corpus">000D80</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000D80</idno><idno type="wicri:Area/Main/Curation">000D80</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000D80</idno><idno type="wicri:Area/Main/Exploration">000D80</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Loter: A Software Package to Infer Local Ancestry for a Wide Range of Species.</title><author><name sortKey="Dias Alves, Thomas" sort="Dias Alves, Thomas" uniqKey="Dias Alves T" first="Thomas" last="Dias-Alves">Thomas Dias-Alves</name><affiliation wicri:level="3"><nlm:affiliation>CNRS, TIMC-IMAG UMR 5525, Univ. Grenoble Alpes, Grenoble, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CNRS, TIMC-IMAG UMR 5525, Univ. Grenoble Alpes, Grenoble</wicri:regionArea><placeName><region type="region">Auvergne-Rhône-Alpes</region><region type="old region">Rhône-Alpes</region><settlement type="city">Grenoble</settlement></placeName></affiliation></author><author><name sortKey="Mairal, Julien" sort="Mairal, Julien" uniqKey="Mairal J" first="Julien" last="Mairal">Julien Mairal</name><affiliation wicri:level="3"><nlm:affiliation>CNRS, Institute of Engineering Univ. Grenoble Alpes, LJK, Univ. Grenoble Alpes, Inria, Grenoble, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CNRS, Institute of Engineering Univ. Grenoble Alpes, LJK, Univ. Grenoble Alpes, Inria, Grenoble</wicri:regionArea><placeName><region type="region">Auvergne-Rhône-Alpes</region><region type="old region">Rhône-Alpes</region><settlement type="city">Grenoble</settlement></placeName></affiliation></author><author><name sortKey="Blum, Michael G B" sort="Blum, Michael G B" uniqKey="Blum M" first="Michael G B" last="Blum">Michael G B. Blum</name><affiliation wicri:level="3"><nlm:affiliation>CNRS, TIMC-IMAG UMR 5525, Univ. Grenoble Alpes, Grenoble, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CNRS, TIMC-IMAG UMR 5525, Univ. Grenoble Alpes, Grenoble</wicri:regionArea><placeName><region type="region">Auvergne-Rhône-Alpes</region><region type="old region">Rhône-Alpes</region><settlement type="city">Grenoble</settlement></placeName></affiliation></author></analytic><series><title level="j">Molecular biology and evolution</title><idno type="eISSN">1537-1719</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Genetic Techniques (MeSH)</term><term>Haplotypes (MeSH)</term><term>Humans (MeSH)</term><term>Populus (genetics)</term><term>Software (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Haplotypes (MeSH)</term><term>Humains (MeSH)</term><term>Logiciel (MeSH)</term><term>Populus (génétique)</term><term>Techniques génétiques (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genetic Techniques</term><term>Haplotypes</term><term>Humans</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Haplotypes</term><term>Humains</term><term>Logiciel</term><term>Techniques génétiques</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Admixture between populations provides opportunity to study biological adaptation and phenotypic variation. Admixture studies rely on local ancestry inference for admixed individuals, which consists of computing at each locus the number of copies that originate from ancestral source populations. Existing software packages for local ancestry inference are tuned to provide accurate results on human data and recent admixture events. Here, we introduce Loter, an open-source software package that does not require any biological parameter besides haplotype data in order to make local ancestry inference available for a wide range of species. Using simulations, we compare the performance of Loter to HAPMIX, LAMP-LD, and RFMix. HAPMIX is the only software severely impacted by imperfect haplotype reconstruction. Loter is the less impacted software by increasing admixture time when considering simulated and admixed human genotypes. For simulations of admixed Populus genotypes, Loter and LAMP-LD are robust to increasing admixture times by contrast to RFMix. When comparing length of reconstructed and true ancestry tracts, Loter and LAMP-LD provide results whose accuracy is again more robust than RFMix to increasing admixture times. We apply Loter to individuals resulting from admixture between Populus trichocarpa and Populus balsamifera and lengths of ancestry tracts indicate that admixture took place ∼100 generations ago. We expect that providing a rapid and parameter-free software for local ancestry inference will make more accessible genomic studies about admixture processes.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29931083</PMID><DateCompleted><Year>2020</Year><Month>02</Month><Day>20</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>06</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1537-1719</ISSN><JournalIssue CitedMedium="Internet"><Volume>35</Volume><Issue>9</Issue><PubDate><Year>2018</Year><Month>09</Month><Day>01</Day></PubDate></JournalIssue><Title>Molecular biology and evolution</Title><ISOAbbreviation>Mol Biol Evol</ISOAbbreviation></Journal><ArticleTitle>Loter: A Software Package to Infer Local Ancestry for a Wide Range of Species.</ArticleTitle><Pagination><MedlinePgn>2318-2326</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/molbev/msy126</ELocationID><Abstract><AbstractText>Admixture between populations provides opportunity to study biological adaptation and phenotypic variation. Admixture studies rely on local ancestry inference for admixed individuals, which consists of computing at each locus the number of copies that originate from ancestral source populations. Existing software packages for local ancestry inference are tuned to provide accurate results on human data and recent admixture events. Here, we introduce Loter, an open-source software package that does not require any biological parameter besides haplotype data in order to make local ancestry inference available for a wide range of species. Using simulations, we compare the performance of Loter to HAPMIX, LAMP-LD, and RFMix. HAPMIX is the only software severely impacted by imperfect haplotype reconstruction. Loter is the less impacted software by increasing admixture time when considering simulated and admixed human genotypes. For simulations of admixed Populus genotypes, Loter and LAMP-LD are robust to increasing admixture times by contrast to RFMix. When comparing length of reconstructed and true ancestry tracts, Loter and LAMP-LD provide results whose accuracy is again more robust than RFMix to increasing admixture times. We apply Loter to individuals resulting from admixture between Populus trichocarpa and Populus balsamifera and lengths of ancestry tracts indicate that admixture took place ∼100 generations ago. We expect that providing a rapid and parameter-free software for local ancestry inference will make more accessible genomic studies about admixture processes.</AbstractText><CopyrightInformation>© The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Dias-Alves</LastName><ForeName>Thomas</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>CNRS, TIMC-IMAG UMR 5525, Univ. Grenoble Alpes, Grenoble, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mairal</LastName><ForeName>Julien</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>CNRS, Institute of Engineering Univ. Grenoble Alpes, LJK, Univ. Grenoble Alpes, Inria, Grenoble, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Blum</LastName><ForeName>Michael G B</ForeName><Initials>MGB</Initials><AffiliationInfo><Affiliation>CNRS, TIMC-IMAG UMR 5525, Univ. Grenoble Alpes, Grenoble, France.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><Acronym>ERC_</Acronym><Agency>European Research Council</Agency><Country>International</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D023362">Evaluation Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Mol Biol Evol</MedlineTA><NlmUniqueID>8501455</NlmUniqueID><ISSNLinking>0737-4038</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D005821" MajorTopicYN="Y">Genetic Techniques</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006239" MajorTopicYN="N">Haplotypes</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">admixture</Keyword><Keyword MajorTopicYN="Y">local ancestry</Keyword><Keyword MajorTopicYN="Y">optimization</Keyword><Keyword MajorTopicYN="Y">population genetics</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>6</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>2</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2018</Year><Month>6</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">29931083</ArticleId><ArticleId IdType="pii">5040668</ArticleId><ArticleId IdType="doi">10.1093/molbev/msy126</ArticleId><ArticleId IdType="pmc">PMC6107063</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>PLoS Genet. 2016 Feb 10;12(2):e1005847</Citation><ArticleIdList><ArticleId IdType="pubmed">26863142</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Ecol. 2016 Jun;25(11):2427-42</Citation><ArticleIdList><ArticleId IdType="pubmed">26825293</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Genet. 2013 May;9(5):e1003477</Citation><ArticleIdList><ArticleId IdType="pubmed">23671421</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Genet. 2017 Apr 4;13(4):e1006644</Citation><ArticleIdList><ArticleId IdType="pubmed">28376121</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2013 Sep;23(9):1514-21</Citation><ArticleIdList><ArticleId IdType="pubmed">23861382</ArticleId></ArticleIdList></Reference><Reference><Citation>Am J Hum Genet. 2006 Apr;78(4):629-44</Citation><ArticleIdList><ArticleId IdType="pubmed">16532393</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 2003 Dec;165(4):2213-33</Citation><ArticleIdList><ArticleId IdType="pubmed">14704198</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2009 Jun 15;25(12):i213-21</Citation><ArticleIdList><ArticleId IdType="pubmed">19477991</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Genet. 2009 Jun;5(6):e1000519</Citation><ArticleIdList><ArticleId IdType="pubmed">19543370</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Commun. 2014;5:3163</Citation><ArticleIdList><ArticleId IdType="pubmed">24495941</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Ecol. 2016 Jun;25(11):2443-53</Citation><ArticleIdList><ArticleId IdType="pubmed">27106273</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Rev Genet. 2011 Jun 28;12(8):523-8</Citation><ArticleIdList><ArticleId IdType="pubmed">21709689</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Ecol. 2016 Jun;25(11):2337-60</Citation><ArticleIdList><ArticleId IdType="pubmed">26836441</ArticleId></ArticleIdList></Reference><Reference><Citation>Am J Hum Genet. 2013 Aug 8;93(2):278-88</Citation><ArticleIdList><ArticleId IdType="pubmed">23910464</ArticleId></ArticleIdList></Reference><Reference><Citation>Cell. 2014 May 8;157(4):785-94</Citation><ArticleIdList><ArticleId IdType="pubmed">24813606</ArticleId></ArticleIdList></Reference><Reference><Citation>Sci Rep. 2016 Jan 28;6:20048</Citation><ArticleIdList><ArticleId IdType="pubmed">26818889</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 2012 Jun;191(2):607-19</Citation><ArticleIdList><ArticleId IdType="pubmed">22491189</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Rev Genet. 2011 Sep 16;12(10):703-14</Citation><ArticleIdList><ArticleId IdType="pubmed">21921926</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Genet. 2014 Jun 26;10(6):e1004410</Citation><ArticleIdList><ArticleId IdType="pubmed">24967630</ArticleId></ArticleIdList></Reference><Reference><Citation>Am J Hum Genet. 2007 Nov;81(5):1084-97</Citation><ArticleIdList><ArticleId IdType="pubmed">17924348</ArticleId></ArticleIdList></Reference><Reference><Citation>Am J Hum Genet. 2008 Feb;82(2):290-303</Citation><ArticleIdList><ArticleId IdType="pubmed">18252211</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2012 May 15;28(10):1359-67</Citation><ArticleIdList><ArticleId IdType="pubmed">22495753</ArticleId></ArticleIdList></Reference><Reference><Citation>Am J Hum Genet. 2015 Jan 8;96(1):37-53</Citation><ArticleIdList><ArticleId IdType="pubmed">25529636</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2010 Sep 2;467(7311):52-8</Citation><ArticleIdList><ArticleId IdType="pubmed">20811451</ArticleId></ArticleIdList></Reference><Reference><Citation>Am J Hum Genet. 2004 May;74(5):979-1000</Citation><ArticleIdList><ArticleId IdType="pubmed">15088269</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Genet. 2017 Mar;49(3):470-475</Citation><ArticleIdList><ArticleId IdType="pubmed">28135247</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2002 May 28;99(11):7335-9</Citation><ArticleIdList><ArticleId IdType="pubmed">12032283</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2008 Apr;18(4):668-75</Citation><ArticleIdList><ArticleId IdType="pubmed">18353809</ArticleId></ArticleIdList></Reference><Reference><Citation>Trends Ecol Evol. 2008 Dec;23(12):686-94</Citation><ArticleIdList><ArticleId IdType="pubmed">18845358</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Genet. 2017 Jan 3;13(1):e1006529</Citation><ArticleIdList><ArticleId IdType="pubmed">28045893</ArticleId></ArticleIdList></Reference><Reference><Citation>Heredity (Edinb). 2013 Dec;111(6):474-85</Citation><ArticleIdList><ArticleId IdType="pubmed">23860234</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>France</li></country><region><li>Auvergne-Rhône-Alpes</li><li>Rhône-Alpes</li></region><settlement><li>Grenoble</li></settlement></list><tree><country name="France"><region name="Auvergne-Rhône-Alpes"><name sortKey="Dias Alves, Thomas" sort="Dias Alves, Thomas" uniqKey="Dias Alves T" first="Thomas" last="Dias-Alves">Thomas Dias-Alves</name></region><name sortKey="Blum, Michael G B" sort="Blum, Michael G B" uniqKey="Blum M" first="Michael G B" last="Blum">Michael G B. Blum</name><name sortKey="Mairal, Julien" sort="Mairal, Julien" uniqKey="Mairal J" first="Julien" last="Mairal">Julien Mairal</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/PoplarV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000D96 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000D96 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= PoplarV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:29931083
|texte= Loter: A Software Package to Infer Local Ancestry for a Wide Range of Species.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:29931083" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PoplarV1
| This area was generated with Dilib version V0.6.37. |  |