{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:38:33Z","timestamp":1740184713262,"version":"3.37.3"},"reference-count":71,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2019,6,14]],"date-time":"2019-06-14T00:00:00Z","timestamp":1560470400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Genome Canada, Genome British Columbia, Genome Quebec"},{"name":"Large-Scale Applied Research","award":["#10106"],"award-info":[{"award-number":["#10106"]}]},{"name":"Resources and the Environment BioSurveillance of Forest Alien Enemies"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The genotype assignment problem consists of predicting, from the genotype of an individual, which of a known set of populations it originated from. The problem arises in a variety of contexts, including wildlife forensics, invasive species detection and biodiversity monitoring. Existing approaches perform well under ideal conditions but are sensitive to a variety of common violations of the assumptions they rely on.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this article, we introduce Mycorrhiza, a machine learning approach for the genotype assignment problem. Our algorithm makes use of phylogenetic networks to engineer features that encode the evolutionary relationships among samples. Those features are then used as input to a Random Forests classifier. The classification accuracy was assessed on multiple published empirical SNP, microsatellite or consensus sequence datasets with wide ranges of size, geographical distribution and population structure and on simulated datasets. It compared favorably against widely used assessment tests or mixture analysis methods such as STRUCTURE and Admixture, and against another machine-learning based approach using principal component analysis for dimensionality reduction. Mycorrhiza yields particularly significant gains on datasets with a large average fixation index (FST) or deviation from the Hardy-Weinberg equilibrium. Moreover, the phylogenetic network approach estimates mixture proportions with good accuracy.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Mycorrhiza is released as an easy to use open-source python package at github.com\/jgeofil\/mycorrhiza.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz476","type":"journal-article","created":{"date-parts":[[2019,6,6]],"date-time":"2019-06-06T11:11:17Z","timestamp":1559819477000},"page":"212-220","source":"Crossref","is-referenced-by-count":5,"title":["Mycorrhiza: genotype assignment using phylogenetic networks"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0352-6468","authenticated-orcid":false,"given":"Jeremy","family":"Georges-Filteau","sequence":"first","affiliation":[{"name":"School of Computer Science, McGill University , Montreal, QC, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4006-532X","authenticated-orcid":false,"given":"Richard C","family":"Hamelin","sequence":"additional","affiliation":[{"name":"Department of Forest and Conservation Sciences, The University of British Columbia , Vancouver, BC, Canada"},{"name":"D\u00e9partement des sciences du bois et de la for\u00eat, Universit\u00e9 Laval , Qu\u00e9bec, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9555-860X","authenticated-orcid":false,"given":"Mathieu","family":"Blanchette","sequence":"additional","affiliation":[{"name":"School of Computer Science, McGill University , Montreal, QC, Canada"}]}],"member":"286","published-online":{"date-parts":[[2019,6,14]]},"reference":[{"key":"2023013109502386700_btz476-B1","doi-asserted-by":"crossref","first-page":"1655","DOI":"10.1101\/gr.094052.109","article-title":"Fast model-based estimation of ancestry in unrelated individuals","volume":"19","author":"Alexander","year":"2009","journal-title":"Genome Res"},{"key":"2023013109502386700_btz476-B2","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/0001-8708(92)90061-O","article-title":"A canonical decomposition theory for metrics on a finite set","volume":"92","author":"Bandelt","year":"1992","journal-title":"Adv. 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Ecol"},{"key":"2023013109502386700_btz476-B38","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1016\/j.fsigen.2011.01.012","article-title":"Wildlife molecular forensics: identification of the Sardinian mouflon using STR profiling and the Bayesian assignment test","volume":"5","author":"Lorenzini","year":"2011","journal-title":"Forensic Sci. Int. Genet"},{"key":"2023013109502386700_btz476-B39","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1016\/j.tree.2004.12.004","article-title":"Assignment methods: matching biological questions with appropriate techniques","volume":"20","author":"Manel","year":"2005","journal-title":"Trends Ecol. Evol"},{"key":"2023013109502386700_btz476-B40","doi-asserted-by":"crossref","first-page":"10532","DOI":"10.1038\/ncomms10532","article-title":"Open access resources for genome-wide association mapping in rice","volume":"7","author":"McCouch","year":"2016","journal-title":"Nat. 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Appl"},{"key":"2023013109502386700_btz476-B51","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1093\/jhered\/esh074","article-title":"GENECLASS2: a software for genetic assignment and first-generation migrant detection","volume":"95","author":"Piry","year":"2004","journal-title":"J. Hered"},{"key":"2023013109502386700_btz476-B52","doi-asserted-by":"crossref","first-page":"98","DOI":"10.3389\/fgene.2013.00098","article-title":"An overview of STRUCTURE: applications, parameter settings, and supporting software","volume":"4","author":"Porras-Hurtado","year":"2013","journal-title":"Front. Genet"},{"year":"2018","author":"Porter","key":"2023013109502386700_btz476-B53"},{"key":"2023013109502386700_btz476-B54","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1093\/genetics\/155.2.945","article-title":"Inference of population structure using multilocus genotype data","volume":"155","author":"Pritchard","year":"2000","journal-title":"Genetics"},{"year":"2010","author":"Pritchard","key":"2023013109502386700_btz476-B55"},{"key":"2023013109502386700_btz476-B56","first-page":"20161762","article-title":"Global population divergence and admixture of the brown rat (Rattus norvegicus)","volume":"283","author":"Puckett","year":"2016","journal-title":"Proc. Biol. 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Manage"},{"key":"2023013109502386700_btz476-B63","doi-asserted-by":"crossref","first-page":"e1005896.","DOI":"10.1371\/journal.pgen.1005896","article-title":"Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting","volume":"12","author":"Sol\u00eds-Lemus","year":"2016","journal-title":"PLoS Genet"},{"key":"2023013109502386700_btz476-B121","first-page":"43","article-title":"Phylogenetics","author":"Semple","year":"2003","journal-title":"Oxford Lecture Series in Mathematics and its Applications"},{"key":"2023013109502386700_btz476-B64","first-page":"791","volume-title":"J. 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