{"doi":"10.1093/sysbio/syaa084","title":"The Multilocus Multispecies Coalescent: A Flexible New Model of Gene Family Evolution","abstract":"<jats:title>Abstract</jats:title>\n                  <jats:p>Incomplete lineage sorting (ILS), the interaction between coalescence and speciation, can generate incongruence between gene trees and species trees, as can gene duplication (D), transfer (T), and loss (L). These processes are usually modeled independently, but in reality, ILS can affect gene copy number polymorphism, that is, interfere with DTL. This has been previously recognized, but not treated in a satisfactory way, mainly because DTL events are naturally modeled forward-in-time, while ILS is naturally modeled backward-in-time with the coalescent. Here, we consider the joint action of ILS and DTL on the gene tree/species tree problem in all its complexity. In particular, we show that the interaction between ILS and duplications/transfers (without losses) can result in patterns usually interpreted as resulting from gene loss, and that the realized rate of D, T, and L becomes nonhomogeneous in time when ILS is taken into account. We introduce algorithmic solutions to these problems. Our new model, the multilocus multispecies coalescent, which also accounts for any level of linkage between loci, generalizes the multispecies coalescent (MSC) model and offers a versatile, powerful framework for proper simulation, and inference of gene family evolution. [Gene duplication; gene loss; horizontal gene transfer; incomplete lineage sorting; multispecies coalescent; hemiplasy; recombination.]</jats:p>","journal":"Systematic Biology","year":2021,"id":45531,"datarank":0.8956815648375938,"base_score":3.1780538303479458,"endowment":3.1780538303479458,"self_citation_contribution":0.47670807455219194,"citation_network_contribution":0.41897349028540176,"self_endowment_contribution":0.47670807455219194,"citer_contribution":0.41897349028540176,"corpus_percentile":null,"corpus_rank":null,"citation_count":23,"citer_count":18,"citers_with_citation_signal":13,"citers_with_endowment":13,"datacite_reuse_total":3,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":208461,"name":"Celine Scornavacca","orcid":null,"position":1,"is_corresponding":false},{"id":87975,"name":"Nicolas Galtier","orcid":"0000-0002-0479-4878","position":2,"is_corresponding":false},{"id":212563,"name":"Yao-Ban Chan","orcid":null,"position":3,"is_corresponding":false},{"id":212562,"name":"Qiuyi Li","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":3.1780538303479458,"endowment":3.1780538303479458,"datacite_reuse_total":3,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"33169795","pmcid":null,"openalex_id":"https://openalex.org/W3093602888","authors":[],"funders":[{"funder_name":"Agence Nationale de la Recherche","grant_id":"ANR-19-CE45-0012 f","title":null},{"funder_name":"French National Research Agency (ANR)","grant_id":"ANR-19-CE45-0012","title":"Combining Combinatorial Algorithms and Sequence-Based Phylogeny Reconstruction Methods to Infer Meaningful Explicit Phylogenetic Networks"}],"total_grants":2,"fwci":0.8946,"citation_percentile":0.7296549,"influential_citations":0,"citation_trend":[{"year":2018,"count":1},{"year":2020,"count":1},{"year":2021,"count":4},{"year":2022,"count":4},{"year":2023,"count":2},{"year":2024,"count":2},{"year":2025,"count":3},{"year":2026,"count":6}],"oa_status":"hybrid","license":"other-oa","oa_locations":[{"url":"https://academic.oup.com/sysbio/article-pdf/70/4/822/38664021/syaa084.pdf","host_type":"journal"},{"url":"https://academic.oup.com/sysbio/article-pdf/70/4/822/38664021/syaa084.pdf","host_type":"publisher"},{"url":"http://academic.oup.com/sysbio/advance-article-pdf/doi/10.1093/sysbio/syaa084/36232416/syaa084.pdf","host_type":"publisher"},{"url":"http://academic.oup.com/sysbio/article-pdf/70/4/822/38664021/syaa084.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/sysbio/syaa084","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/33169795","host_type":"repository"},{"url":"https://hal.science/hal-02972075","host_type":"repository"},{"url":"https://doi.org/10.1101/2020.05.07.081836","host_type":""},{"url":"https://hal.archives-ouvertes.fr/hal-02972075/file/bioarxiv.pdf","host_type":""},{"url":"https://dx.doi.org/10.1093/sysbio/syaa084","host_type":""},{"url":"https://dx.doi.org/10.1101/2020.05.07.081836","host_type":""},{"url":"https://hal.science/hal-02972075v1/document","host_type":""},{"url":"https://hal.science/hal-02972075v1","host_type":""},{"url":"http://dx.doi.org/10.1101/2020.05.07.081836","host_type":""},{"url":"https://doi.org/https://doi.org/10.1093/sysbio/syaa084","host_type":""}],"fields_of_study":["Genomics and Phylogenetic Studies","Chromosomal and Genetic Variations","Genetic diversity and population structure","Computer Simulation","Evolution, Molecular","Gene Duplication","Gene Transfer, Horizontal","Genetic Speciation","Models, Genetic","Multigene Family","Phylogeny"],"mesh_terms":["Computer Simulation","Multigene Family","Models, Genetic","Phylogeny","Evolution, Molecular","Gene Duplication","Gene Transfer, Horizontal","Genetic Speciation"],"keywords":["Coalescent theory","Biology","Gene duplication","Coalescence (physics)","Gene","Lineage (genetic)","Horizontal gene transfer","Tree (set theory)","Evolutionary biology","Genetics","Computational biology","Phylogenetics","Mathematics","Combinatorics","hemiplasy","[SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]","[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics","Gene Transfer, Horizontal","Models, Genetic","Genetic Speciation","incomplete lineage sorting","Phylogenetics and taxonomy","612","gene loss","recombination","Evolution, Molecular","multispecies coalescent","Multigene Family","[SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy","[SDV.GEN.GPO] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]","Computer Simulation","[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]","Phylogeny","[INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]"],"sdg_mappings":[{"sdg_number":14,"sdg_label":"14. 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