AbstractIxodid tick species function as important vectors of tick-borne diseases in Japan. In this study, we used genetic structure at two mitochondrial loci (cox1, 16S rRNA gene) to infer gene flow patterns of Ixodes ovatus and Haemaphysalis flava from Niigata Prefecture, Japan. We hypothesized that I. ovatus and H. flava have different population genetic structure because of their host mobility in different tick life stages despite sharing of hosts. Samples (n = 1 to 77) were collected in 29

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... I. ovatus) and 17 (H. flava) sampling locations across Niigata. For I. ovatus, pairwise FST and analysis of molecular variance (AMOVA) analyses of cox1 sequences indicated significant among-population differentiation. This was in contrast to H. flava, for which there were only two cases of significant pairwise differentiation and no overall structure. A Mantel test revealed isolation by distance and there was positive spatial autocorrelation of haplotypes in I. ovatus cox1 and 16S sequences, but non-significant results were observed in H. flava in both markers. Newly sampled I. ovatus grouped together with a published I. ovatus sequence from northern Japan and were distinct from two other I. ovatus groups that were reported from southern China. The three genetic groups (China 1, China 2, and Japan) in our data set suggest the potential for cryptic species within the lineage. While many factors can potentially account for the observed differences in genetic structure, including population persistence and large-scale patterns of range expansion, we propose that differences in the mobility of hosts of tick immature stages (small mammals in I. ovatus; birds in H. flava) may be driving the observed patterns.