<p>Ordinary Least Squares model and ANOVA results.</p>

ITS/<i>cox1</i> genotyping suggested extensive recent hybridization and zoonotic infection. Among parasites from humans, 10.1% carried both <i>S. curassoni</i> and <i>S. haematobium</i> ITS, consistent with F1 or early generation hybrids, 21% had livestock schistosome markers at both <i>cox1</i> and ITS suggesting zoonotic infection, while 13.7% carried <i>S. bovis cox1</i> alongside mixed <i>S. curassoni</i> and <i>S. haematobium</i> ITS, suggesting more complex ancestry.

Genome sequencing revealed a very different picture. All parasites from humans formed a tight cluster regardless of ITS or <i>cox1</i> genotype, while all worms from cattle were well differentiated. We found no schistosomes containing 50% livestock parasite ancestry consistent with F1s.

Instead, we observed regionally varying levels of <i>S. bovis</i> introgression, with modest levels in southern Nigeria (mean = 4.9%) and low levels in northern Nigeria (mean = 0.06%). These results demonstrate that: (i) two-locus genotyping is uninformative for detecting zoonotic infection or recent hybridization between <i>S. haematobium</i> and livestock schistosomes and (ii) previous data generated using this approach requires reinterpretation.

These findings reveal the limitations of widely-used approaches for documenting zoonotic infection and hybridization between <i>S. haematobium</i> and livestock schistosome species.</p></div>