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Recent research has revealed that viable hybrids and introgressed lineages between <jats:italic>Schistosoma<\/jats:italic> spp. are prevalent across Africa and beyond, including those with zoonotic potential. However, it remains unclear whether these hybrid lineages represent recent hybridization events, suggesting hybridization is ongoing, and\/or whether they represent introgressed lineages derived from ancient hybridization events. In human schistosomiasis, investigation is hampered by the inaccessibility of adult-stage worms due to their intravascular location, an issue which can be circumvented by post-mortem of livestock at abattoirs for <jats:italic>Schistosoma<\/jats:italic> spp. of known zoonotic potential. To characterise the composition of naturally-occurring schistosome hybrids, we performed whole-genome sequencing of 21 natural livestock infective schistosome isolates. To facilitate this, we also assembled a <jats:italic>de novo<\/jats:italic> chromosomal-scale draft assembly of <jats:italic>Schistosoma curassoni<\/jats:italic>. Genomic analyses identified isolates of <jats:italic>S<\/jats:italic>. <jats:italic>bovis<\/jats:italic>, <jats:italic>S<\/jats:italic>. <jats:italic>curassoni<\/jats:italic> and hybrids between the two species, all of which were early generation hybrids with multiple generations found within the same host. These results show that hybridization is an ongoing process within natural populations with the potential to further challenge elimination efforts against schistosomiasis.<\/jats:p>","DOI":"10.1371\/journal.ppat.1010706","type":"journal-article","created":{"date-parts":[[2022,8,8]],"date-time":"2022-08-08T17:38:12Z","timestamp":1659980292000},"page":"e1010706","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":32,"title":["Genomic evidence of contemporary hybridization between Schistosoma species"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2017-6623","authenticated-orcid":true,"given":"Duncan J.","family":"Berger","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elsa","family":"L\u00e9ger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Geetha","family":"Sankaranarayanan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariama","family":"S\u00e8ne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolas D.","family":"Diouf","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muriel","family":"Rabone","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aidan","family":"Emery","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fiona","family":"Allan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James A.","family":"Cotton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Berriman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joanne P.","family":"Webster","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,8,8]]},"reference":[{"issue":"3","key":"ppat.1010706.ref001","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1038\/nrg3644","article-title":"Genomics and the origin of species","volume":"15","author":"O Seehausen","year":"2014","journal-title":"Nat Rev Genet"},{"issue":"5","key":"ppat.1010706.ref002","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/j.tree.2005.02.010","article-title":"Hybridization as an invasion of the genome","volume":"20","author":"J. 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