{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T08:25:32Z","timestamp":1740126332206,"version":"3.37.3"},"reference-count":36,"publisher":"Wiley","issue":"17","license":[{"start":{"date-parts":[[2018,8,24]],"date-time":"2018-08-24T00:00:00Z","timestamp":1535068800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/501100003130","name":"Fonds Wetenschappelijk Onderzoek","doi-asserted-by":"publisher","award":["1528117N"],"award-info":[{"award-number":["1528117N"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molecular Ecology"],"published-print":{"date-parts":[[2018,9]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>We recently published the first genomic diversity study of <jats:italic>Trypanosoma congolense<\/jats:italic>, a major aetiological agent of Animal African Trypanosomiasis. We demonstrated striking levels of <jats:styled-content style=\"fixed-case\">SNP<\/jats:styled-content> and indel diversity in the Eastern province of Zambia as a consequence of hybridization between divergent trypanosome lineages. We concluded that these and earlier findings in <jats:italic>T.\u00a0congolense<\/jats:italic> challenge the predominant clonal evolution (<jats:styled-content style=\"fixed-case\">PCE<\/jats:styled-content>) model. In a recent comment, Tibayrenc and Ayala claim that there are many features in <jats:italic>T.\u00a0congolense<\/jats:italic> supporting their theory of clonality. While we can follow the reasoning of the authors, we also identify major limitations in their theory and interpretations that resulted in incorrect conclusions. First, we argue that each <jats:italic>T.\u00a0congolense<\/jats:italic> subgroup should be analysed independently as they may represent different (sub)species rather than \u201cnear\u2010clades\u201d. Second, the authors neglect major findings of two robust population genetic studies on Savannah <jats:italic>T.\u00a0congolense<\/jats:italic> that provide clear evidence of frequent recombination. Third, we reveal additional events of introgressive hybridization in <jats:italic>T.\u00a0congolense<\/jats:italic> by analysing the maxicircle coding region using next\u2010generation sequencing analyses. At last, we pinpoint two important misinterpretations by the authors and show that there are no spatially and temporally widespread clones in <jats:italic>T.\u00a0congolense<\/jats:italic>. We stand by our earlier conclusions that the clonal framework is unlikely to accurately model the population structure of <jats:italic>T.\u00a0congolense<\/jats:italic>. Other theoretical frameworks such as Maynard Smith's epidemic model may better represent the complex ancestry seen in <jats:italic>T.\u00a0congolense<\/jats:italic>, where clones delimited in space and time arise against a background of recombination.<\/jats:p>","DOI":"10.1111\/mec.14809","type":"journal-article","created":{"date-parts":[[2018,8,24]],"date-time":"2018-08-24T07:39:25Z","timestamp":1535096365000},"page":"3425-3431","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Mitonuclear genomics challenges the theory of clonality in <i>Trypanosoma congolense<\/i>: Reply to Tibayrenc and Ayala"],"prefix":"10.1111","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2542-5585","authenticated-orcid":false,"given":"Frederik","family":"Van den Broeck","sequence":"first","affiliation":[{"name":"Biomedical Sciences Institute of Tropical Medicine Antwerp Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lisse J.M.","family":"Tavernier","sequence":"additional","affiliation":[{"name":"Biomedical Sciences Institute of Tropical Medicine Antwerp Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lieve","family":"Vermeiren","sequence":"additional","affiliation":[{"name":"Biomedical Sciences Institute of Tropical Medicine Antwerp Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean\u2010Claude","family":"Dujardin","sequence":"additional","affiliation":[{"name":"Biomedical Sciences Institute of Tropical Medicine Antwerp Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jan","family":"Van Den Abbeele","sequence":"additional","affiliation":[{"name":"Biomedical Sciences Institute of Tropical Medicine Antwerp Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2018,8,24]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti553"},{"key":"e_1_2_10_4_1","first-page":"409","article-title":"R: A language and environment for statistical computing","volume":"1","author":"R Development Core Team","year":"2015","journal-title":"R Foundation for Statistical Computing"},{"key":"e_1_2_10_5_1","first-page":"e18","article-title":"NOVOPlasty: de novo assembly of organelle genomes from whole genome data","volume":"45","author":"Dierckxsens N.","year":"2017","journal-title":"Nucleic Acids Research"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijpara.2007.03.002"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1051\/parasite\/2008153233"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00197-13"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.pt.2009.11.006"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.9.9.868"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1002453"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1111\/2041-210X.12410"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13071-015-1281-8"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.micro.59.030804.121325"},{"key":"e_1_2_10_16_1","doi-asserted-by":"publisher","DOI":"10.1038\/349029a0"},{"key":"e_1_2_10_17_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.90.10.4384"},{"key":"e_1_2_10_18_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.13186"},{"key":"e_1_2_10_19_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0001584"},{"key":"e_1_2_10_20_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0005564"},{"volume-title":"vegan: Community ecology package","year":"2017","author":"Oksanen J. 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