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Recent work demonstrated the existence of hybrid microsatellite profiles in <jats:italic>Trypanosoma congolense<\/jats:italic>, a parasitic protozoan with detrimental effects on livestock productivity in sub\u2010Saharan Africa. Here, we present the first population genomic study of <jats:italic>T.\u00a0congolense<\/jats:italic>, revealing a remarkable number of single nucleotide polymorphisms (<jats:styled-content style=\"fixed-case\">SNP<\/jats:styled-content>s), small insertions\/deletions (indels) and gene deletions among 56 parasite genomes from ten African countries. One group of parasites from Zambia was particularly diverse, displaying a substantial number of heterozygous <jats:styled-content style=\"fixed-case\">SNP<\/jats:styled-content> and indel sites compared to <jats:italic>T.\u00a0congolense<\/jats:italic> parasites from the nine other sub\u2010Saharan countries. Genomewide 5\u2010kb phylogenetic analyses based on phased <jats:styled-content style=\"fixed-case\">SNP<\/jats:styled-content> data revealed that these parasites were the product of hybridization between phylogenetically distinct <jats:italic>T.\u00a0congolense<\/jats:italic> lineages. Other parasites within the same region in Zambia presented a mosaic of haplotypic ancestry and genetic variability, indicating that hybrid parasites persisted and recombined beyond the initial hybridization event. Our observations challenge traditional views of trypanosome population biology and encourage future research on the role of hybridization in spreading genes for drug resistance, pathogenicity and virulence.<\/jats:p>","DOI":"10.1111\/mec.14271","type":"journal-article","created":{"date-parts":[[2017,7,28]],"date-time":"2017-07-28T12:26:38Z","timestamp":1501244798000},"page":"6524-6538","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":59,"title":["Discovery and genomic analyses of hybridization between divergent lineages of <i>Trypanosoma congolense<\/i>, causative agent of Animal African Trypanosomiasis"],"prefix":"10.1111","volume":"26","author":[{"given":"Eliane","family":"Tihon","sequence":"first","affiliation":[{"name":"Department of Biomedical Sciences Institute of Tropical Medicine Antwerp Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hideo","family":"Imamura","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences Institute of Tropical Medicine Antwerp Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean\u2010Claude","family":"Dujardin","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences Institute of Tropical Medicine Antwerp Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Van Den Abbeele","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences Institute of Tropical Medicine Antwerp Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2542-5585","authenticated-orcid":false,"given":"Frederik","family":"Van den Broeck","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences Institute of Tropical Medicine Antwerp Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2017,8,24]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature09534"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.pt.2010.03.003"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0001-706X(00)00108-X"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0001211"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-294X.2004.02145.x"},{"key":"e_1_2_8_7_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0001828"},{"key":"e_1_2_8_8_1","doi-asserted-by":"publisher","DOI":"10.20506\/rst.34.2.2382"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0000961"},{"key":"e_1_2_8_10_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.281.5385.1986"},{"key":"e_1_2_8_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0304-4017(01)00609-4"},{"key":"e_1_2_8_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0304-4017(02)00164-4"},{"key":"e_1_2_8_13_1","doi-asserted-by":"publisher","DOI":"10.1099\/00221287-147-12-3231"},{"key":"e_1_2_8_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep06516"},{"key":"e_1_2_8_15_1","doi-asserted-by":"publisher","DOI":"10.1111\/1749-4877.12195"},{"key":"e_1_2_8_16_1","doi-asserted-by":"publisher","DOI":"10.4161\/fly.19695"},{"key":"e_1_2_8_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/0001-706X(92)90041-U"},{"key":"e_1_2_8_18_1","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2008-9-6-r103"},{"key":"e_1_2_8_19_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2307"},{"key":"e_1_2_8_20_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.drup.2008.10.002"},{"key":"e_1_2_8_21_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijpara.2004.11.009"},{"key":"e_1_2_8_22_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.806"},{"key":"e_1_2_8_23_1","doi-asserted-by":"publisher","DOI":"10.3390\/genes1010102"},{"key":"e_1_2_8_24_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.123430.111"},{"key":"e_1_2_8_25_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0002526"},{"key":"e_1_2_8_26_1","doi-asserted-by":"publisher","DOI":"10.1017\/S0031182000080112"},{"key":"e_1_2_8_27_1","first-page":"12","article-title":"Sleeping sickness survey in the Serengeti area (Tanzania) 1971. 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