To estimate the degree of crossbreeding between Japanese wild boars and crossbred Inobuta in Wakayama prefecture, we examined haplotypes of mitochondrial DNA (mtDNA) and genotypes of the nuclear glucosephosphate isomerase-processed pseudogene (GPIP) in tissue samples obtained from 176 wild boars over a 3-year period. Five different haplotypes (J10, J15, J21, J22 and J23) and 3 GPIP alleles (GPIP1, GPIP3a and GPIP3b) were detected. These genetic profiles were classified as Japanese wild boar lineage without the genetic markers typical of Inobuta. The present genetic profile of wild boars, consisting of mtDNA haplotypes and GPIP genotypes, is a useful tool for studying the genetic structure of the local feral population.

To examine the genetic origin of Ryukyu wild boar, we sequenced mitochondrial DNA (mtDNA: 574-bp) from Vietnamese wild boar and Vietnamese indigenous domestic pigs and compared these sequences with the mtDNA of Ryukyu wild boar by phylogenetic analysis. Numerous Vietnamese wild boars were genetically related to Ryukyu wild boar, suggesting that descendants of the ancestors of Ryukyu wild boar still inhabit Vietnam. The mtDNA sequences of Vietnamese indigenous domestic pigs are extremely diverse and are thought to have contributed to the diversity of mtDNA among East Asian domestic pigs.

We used variation in the mitochondrial DNA (mtDNA) control region (D-loop) to examine the genetic structure of the sika deer (Cervus nippon) population on the Boso Peninsula, central Japan. A total of four haplotypes was found. In order to examine whether or not artificial barriers such as roads, dams, and golf courses affect the spatial heterogeneity of mtDNA haplotypes, we implemented two exclusive spatial analyses (SAMOVA and network analysis based on Monmonier’s algorithm) for searching genetic discontinuities between artificial barriers. Prior to the analyses, the whole distribution area was divided into meaningful eight blocks. Analysis of molecular variance (AMOVA) detected significant spatial heterogeneity in the constitution of the haplotypes among the blocks. The subsequent spatial analyses detected some significant spatial discontinuities on borders of the blocks. In particular, the largest discontinuity was observed in the area including motorway Line 81, but the traffic density of Line 81 is generally not very heavy compared to other major roads. These findings suggest that roads could be one of major barriers to hamper migration of sika deer to some extent, but other potential factors such as the location of food resources and/or the history of bottleneck event are also likely to more or less contribute to configure the present patterns of haplotype distribution.