{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,31]],"date-time":"2026-10-31T19:16:56Z","timestamp":1793474216299,"version":"4.5.0"},"reference-count":37,"publisher":"Wiley","issue":"6","license":[{"start":{"date-parts":[[2024,5,22]],"date-time":"2024-05-22T00:00:00Z","timestamp":1716336000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["310030_188883"],"award-info":[{"award-number":["310030_188883"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molecular Ecology Resources"],"published-print":{"date-parts":[[2024,8]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Admixture is a common biological phenomenon among populations of the same or different species. Identifying admixed tracts within individual genomes can provide valuable information to date admixture events, reconstruct ancestry\u2010specific demographic histories, or detect adaptive introgression, genetic incompatibilities, as well as regions of the genomes affected by (associative\u2010) overdominance. Although many local ancestry inference (LAI) methods have been developed in the last decade, their performance was accessed using large reference panels, which are rarely available for non\u2010model organisms or ancient samples. Moreover, the demographic conditions for which LAI becomes unreliable have not been explicitly outlined. Here, we identify the demographic conditions for which local ancestries can be best estimated using very small reference panels. Furthermore, we compare the performance of two LAI methods (RFMix and MOSAIC) with the performance of a newly developed approach (simpLAI) that can be used even when reference populations consist of single individuals. Based on simulations of various demographic models, we also determine the limits of these LAI tools and propose post\u2010painting filtering steps to reduce false\u2010positive rates and improve the precision and accuracy of the inferred admixed tracts. Besides providing a guide for using LAI, our work shows that reasonable inferences can be obtained from a single diploid genome per reference under demographic conditions that are not uncommon among past human groups and non\u2010model organisms.<\/jats:p>","DOI":"10.1111\/1755-0998.13981","type":"journal-article","created":{"date-parts":[[2024,5,22]],"date-time":"2024-05-22T10:45:33Z","timestamp":1716374733000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Assessing the limits of local ancestry inference from small reference panels"],"prefix":"10.1111","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1133-7130","authenticated-orcid":false,"given":"Sandra","family":"Oliveira","sequence":"first","affiliation":[{"name":"CMPG, Institute for Ecology and Evolution University of Bern  Berne Switzerland"},{"name":"Swiss Institute of Bioinformatics  Lausanne Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6624-5922","authenticated-orcid":false,"given":"Nina","family":"Marchi","sequence":"additional","affiliation":[{"name":"CMPG, Institute for Ecology and Evolution University of Bern  Berne Switzerland"},{"name":"Swiss Institute of Bioinformatics  Lausanne Switzerland"},{"name":"UMR7206 Eco\u2010Anthropologie, CNRS\u2010MNHN\u2010Universit\u00e9 Paris Cit\u00e9  Paris France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7507-6494","authenticated-orcid":false,"given":"Laurent","family":"Excoffier","sequence":"additional","affiliation":[{"name":"CMPG, Institute for Ecology and Evolution University of Bern  Berne Switzerland"},{"name":"Swiss Institute of Bioinformatics  Lausanne Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2024,5,22]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0605627103"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1086\/521987"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1007385"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2022.12.010"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bby112"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1006529"},{"key":"e_1_2_9_8_1","doi-asserted-by":"crossref","unstructured":"Edelman N. B. &Mallet J.(2021).Prevalence and Adaptive Impact of Introgression.https:\/\/doi.org\/10.1146\/annurev\u2010genet\u2010021821","DOI":"10.1146\/annurev-genet-021821-020805"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btab468"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bby044"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.113.160697"},{"key":"e_1_2_9_12_1","doi-asserted-by":"crossref","unstructured":"Hilmarsson H. Kumar A. S. Rastogi R. Bustamante C. D. Montserrat M. &Ioannidis A. G.(2021).High resolution ancestry deconvolution for next generation genomic data. BioRxiv.https:\/\/doi.org\/10.1101\/2021.09.19.460980","DOI":"10.1101\/2021.09.19.460980"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1073\/PNAS.1523951113"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/132.2.583"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010020\u20102487\u20102"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature13673"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2013.06.020"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2022.04.008"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.gde.2017.08.007"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.69016"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.1126\/SCIADV.ADH3822"},{"key":"e_1_2_9_22_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp197"},{"key":"e_1_2_9_23_1","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.112.145037"},{"key":"e_1_2_9_24_1","doi-asserted-by":"crossref","unstructured":"Pearson A. &Durbin R.(2023).Local ancestry inference for complex population histories. BioRxiv.https:\/\/doi.org\/10.1101\/2023.03.06.529121","DOI":"10.1101\/2023.03.06.529121"},{"key":"e_1_2_9_25_1","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms2140"},{"key":"e_1_2_9_26_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000519"},{"key":"e_1_2_9_27_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep12376"},{"key":"e_1_2_9_28_1","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.119.302139"},{"key":"e_1_2_9_29_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2007.09.022"},{"key":"e_1_2_9_30_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3295"},{"key":"e_1_2_9_31_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aao6266"},{"key":"e_1_2_9_32_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1227721"},{"key":"e_1_2_9_33_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.10090"},{"key":"e_1_2_9_34_1","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/127.3.627"},{"key":"e_1_2_9_35_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.072850.107"},{"key":"e_1_2_9_36_1","doi-asserted-by":"publisher","DOI":"10.1086\/504302"},{"key":"e_1_2_9_37_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12863\u2010020\u201000845\u20103"},{"key":"e_1_2_9_38_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859\u2010021\u201004350\u2010x"}],"container-title":["Molecular Ecology Resources"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/1755-0998.13981","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,30]],"date-time":"2024-07-30T10:49:35Z","timestamp":1722336575000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/1755-0998.13981"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,5,22]]},"references-count":37,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2024,8]]}},"alternative-id":["10.1111\/1755-0998.13981"],"URL":"https:\/\/doi.org\/10.1111\/1755-0998.13981","archive":["Portico"],"relation":{},"ISSN":["1755-098X","1755-0998"],"issn-type":[{"value":"1755-098X","type":"print"},{"value":"1755-0998","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,5,22]]},"assertion":[{"value":"2023-07-23","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-05-08","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-05-22","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e13981"}}