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

medius mitochondrial markers the cytb and D‐Loop data sets separately and then on the cytb and D‐Loop data sets combined in a single analysis with two separate 2.4.1 | Genetic diversity and population structure partitions, implemented in beast 1.8.2 (Drummond, Suchard, Xie, & Rambaut, 2012), to reconstruct changes in the female effective pop‐ Sequences were aligned in Geneious 9.0.2 (Kearse et al.. [...] A visual output of the Geneland cluster results was of the chain was assessed in Tracer so that the effective sample size generated using the Clumpak server (Kopelman, Mayzel, Jakobsson, (ESS) of all parameters was >200 after removing at least 10% of the Rosenberg, & Mayrose, 2015). [...] However, the results of due to the presence of null alleles, as lower and mostly nonsignifi‐ the sex‐biased dispersal test suggested that males were the most cant FIS values were obtained when excluding the loci B29, PH3 and dispersive group with significantly higher FIS (nonsignificant with OLIVAL et AL. [...] Our molecular ancestral reconstruction dates tion of NiV spread supports this and shows a likely introduction to the origin of NiV in South Asia back to the year 1941 (95% HPD: Bangladesh from the India/Bangladesh border, and extensive move‐ 1,887–1,994) and is inferred geographically at the southern India/ ment of NiV strains within Bangladesh over the last few decades. [...] medius populations within the Nipah belt, with no evidence of geographic structure in NiV sequences, and This is the first study using a combined analysis of Pteropus medius clade I variants that were identical in the N gene were identified in and Nipah virus molecular analyses to understand the dynamics, several localities, indicating viral genetic mixing and homogenization.