Genomic data reveal a North-South split and introgression history of blood fluke populations across Africa

The human parasitic fluke, Schistosoma haematobium hybridizes with the
livestock parasite S. bovis in the laboratory, but the frequency of
hybridization in nature is unclear. Here, we analyze 34.6 million single
nucleotide variants in 162 samples from 18 African countries, revealing a
sharp genetic discontinuity between northern and southern S. haematobium.
We find no evidence for recent hybridization. Instead the data reveal
admixture events that occurred 257-879 generations ago in northern S.
haematobium populations. Fifteen introgressed S. bovis genes are
approaching fixation in northern S. haematobium with four genes
potentially driving adaptation. Further, we identify 19 regions that are
resistant to introgression; these are enriched on the sex chromosomes.
These results (i) suggest strong barriers to gene flow between these
species, (ii) indicate that hybridization may be less common than
currently envisaged, but (iii) reveal profound genomic consequences of
rare interspecific hybridization between schistosomes of medical and
veterinary importance.