Data from: Population genetics of fruit bat reservoir informs the dynamics, distribution, and diversity of Nipah virus

The structure and connectivity of wildlife host populations may influence
zoonotic disease dynamics, evolution, and therefore spillover risk to
people. Fruit bats in the genus Pteropus, or flying foxes, are the primary
natural reservoir for henipaviruses - a group of emerging paramyxoviruses
that threaten livestock and public health. In Bangladesh, Pteropus medius
is the reservoir for Nipah virus - and viral spillover has led to human
fatalities nearly every year since 2001. Here we use mitochondrial DNA and
nuclear microsatellite markers to measure the population structure,
demographic history, and phylogeography of P. medius in Bangladesh. We
combine this with a phylogeographic analysis of all known Nipah virus
sequences and strains currently available to better inform the dynamics,
distribution, and evolutionary history of Nipah virus. We show that P.
medius is primarily panmictic, but combined analysis of microsatellite and
morphological data shows evidence for differentiation of two populations
in Eastern Bangladesh, corresponding with a divergent strain of Nipah
virus also found in bats from Eastern Bangladesh. Our demographic analyses
indicate that a large, expanding population of flying foxes has existed in
Bangladesh since the Late Pleistocene, coinciding with human population
expansion in South Asia, suggesting repeated historical spillover of Nipah
virus likely occurred. We present the first evidence of mitochondrial
introgression, or hybridization, between P. medius and flying fox species
found in Southeast Asia (P. vampyrus and P. hypomelanus) which may help to
explain the distribution of Nipah virus strains across the region.