Schistosoma mansoni raw genotype calls from exome data

Schistosoma mansoni, a snail-vectored, blood fluke that infects humans,
was introduced into the Americas from Africa during the Trans-Atlantic
slave trade. As this parasite shows strong specificity to the snail
intermediate host, we expected that adaptation to S. American Biomphalaria
spp. snails would result in population bottlenecks and strong signatures
of selection. We scored 475,081 single nucleotide variants (SNVs) in 143
S. mansoni from the Americas (Brazil, Guadeloupe, and Puerto Rico) and
Africa (Cameroon, Niger, Senegal, Tanzania, and Uganda), and used these
data to ask: (i) Was there a population bottleneck during colonization?
(ii) Can we identify signatures of selection associated with colonization?
And (iii) what were the source populations for colonizing parasites? We
found a 2.4-2.9-fold reduction in diversity and much slower decay in
linkage disequilibrium (LD) in parasites from East to West Africa.
However, we observed similar nuclear diversity and LD in West Africa and
Brazil, suggesting no strong bottlenecks and limited barriers to
colonization. We identified five genome regions showing selection in the
Americas, compared with three in West Africa and none in East Africa,
which we speculate may reflect adaptation during colonization. Finally, we
infer that unsampled African populations from central African regions
between Benin and Angola, with contributions from Niger, are likely the
major source(s) for Brazilian S. mansoni. The absence of a bottleneck
suggests that this is a rare case of a serendipitous invasion, where S.
mansoni parasites were preadapted to the Americas and were able to
establish with relative ease.