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Schistosoma mansoni  is a parasitic fluke that infects millions of people in the developing world. This study presents the first application of population genomics to  S. mansoni  based on high-coverage resequencing data from 10 global isolates and an isolate of the closely-related  Schistosoma rodhaini , which infects rodents. Using population genetic tests, we document genes under directional and balancing selection in  S. mansoni  that may facilitate adaptation to the human host. Coalescence modeling reveals the speciation of  S. mansoni  and  S. rodhaini  as 107.5–147.6KYA, a period which overlaps with the earliest archaeological evidence for fishing in Africa. Our results indicate that  S. mansoni  originated in East Africa and experienced a decline in effective population size 20–90KYA, before dispersing across the continent during the Holocene. In addition, we find strong evidence that  S. mansoni  migrated to the New World with the 16–19 th  Century Atlantic Slave Trade.

Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection