Genetic Variation in Y-Chromosome Genes of Sika Deer (Cervus nippon) in Japan.

Sika deer (Cervus nippon) in Japan are classified into southern and northern groups. However, previous studies primarily relied on maternally inherited mitochondrial DNA (mtDNA). The paternally inherited Y-chromosome is useful for analyzing the contribution of males to the population genetic history of sika deer. In total, approximately 16 kb of partial sequences of four Y-chromosomal genes, Y-linked, sex-determining region Y, DEAD-box helicase 3 Y-linked, and Zinc finger protein Y-linked, were sequenced to investigate intraspecific variation. As a result, we identified nine intronic single nucleotide polymorphisms (SNPs) in 478 sika deer samples collected over the entire Japanese archipelago from Hokkaido to Kyushu. SNP genotyping revealed 10 distinct haplotypes (SYH1-SYH10). The most common haplotype (SYH1) was present in all populations and was the most abundant haplotype, identified in 80.3% of the sampled individuals. The remaining haplotypes were unique to a single locality. SYH1 was also central to all other haplotypes that diverged by a SNP, resulting in this haplotype being the core of a star-like cluster topography. We found that contrary to mtDNA patterns, there was no clear differentiation of Y-chromosome markers between the southern and the northern populations. Due to the female philopatry of sika deer, mtDNA may provide a highly structured differentiation of populations. On the other hand, the male-biased gene flow may provide a reduced differentiation of populations. Our findings revealed that the genetic structure of the Japanese sika deer is more complex than previously thought based on mtDNA-based phylogeographic studies.

Timing and distance of natal dispersal in Asian black bears.

Dispersal has important implications for population ecology and genetics of a species through redistribution of individuals. In most mammals, males leave their natal area before they reach sexual maturity, whereas females are commonly philopatric. Here, we investigate the patterns of natal dispersal in the Asian black bear (Ursus thibetanus) based on data from 550 bears (378 males, 172 females) captured or removed in Gunma and Tochigi prefectures on central Honshu Island, Japan in 2003-2018. We used genetic data and parentage analysis to investigate sex-biased differences in the distance of natal dispersal. We further investigated the age of dispersal using spatial autocorrelation analysis, that is, the change in the correlation between genetic and geographic distances in each sex and age group. Our results revealed that male dispersal distances (mean ± SE = 17.4 ± 3.5 km) were significantly farther than female distances (4.8 ± 1.7 km), and the results were not affected by years of mast failures, a prominent forage source for this population. Based on an average adult female home range radius of 1.8 km, 96% of the males and 50% of the females dispersed. In the spatial autocorrelation analysis, the changes in the relationship between genetic and geographic distances were more pronounced in males compared to females. Males seem to mostly disperse at age 3 regardless of mast productivity, and they gradually disperse far from their home range, but young and inexperienced males may return to their natal home range in years with poor food conditions. The results suggest that factors driving the dispersal process seem to be population structure-based instead of forage availability-based. In females, a significant genetic relationship was observed among all individuals in the group with a minimum age of 6 years within a distance of 2 km, which resulted in the formation of matrilineal assemblages.

Phylogeographic sympatry and isolation of the Eurasian badgers (Meles, Mustelidae, Carnivora): Implications for an alternative analysis using maternally as well as paternally inherited genes.

In the present study, to further understand the phylogenetic relationships among the Eurasian badgers (Meles, Mustelidae, Carnivora), which are distributed widely in the Palearctic, partial sequences of the mitochondrial DNA (mtDNA) control region (539-545 base-pairs) as a maternal genetic marker, and the sex-determining region on the Y-chromosome gene (SRY: 1052-1058 base-pairs), as a paternal genetic marker, were examined. The present study revealed ten SRY haplotypes from 47 males of 112 individuals of the Eurasian Continent and Japan. In addition, 39 mtDNA haplotypes were identified from those animals. From the phylogeography of both the uniparentally inherited genes, four lineages were recognized as Japanese, eastern Eurasian, Caucasian, and western Eurasian. The distribution patterns of the mtDNA lineages showed the existence of a sympatric zone between the eastern and western Eurasian lineages around the Volga River in western Russia. Furthermore, the present study suggested that in the Japanese badgers, the larger genetic differentiation of the Shikoku population was attributable to geographic history in the Japanese islands.

Mobility of the forearm skeleton in the Asiatic black (Ursus thibetanus), brown (U. arctos) and polar (U. maritimus) bears.

In several primates and carnivores, pronation/supination angles of the forearm skeleton were examined, and it is thought that a larger angle is useful to acquire dexterous behaviors in feeding and/or life style, including climbing. In this study, the pronation/supination angles in Asiatic black, brown and polar bears were nondestructively examined. These specimens were classified as adult or non-adult. Three or four carcasses of each group of Asiatic black and brown bears were used for CT analysis, whereas only one adult polar bear was used. The forearms were positioned within the gantry of a CT scanner in both maximally supinated and pronated states. Extracted cross-sectional CT images of two positions were superimposed by overlapping the outlines of each ulna. The centroids of the radii were detected, and then the centroid of each radius and the midpoint of a line which connects between both ends of the surface of each radius facing the ulna, were connected by lines to measure the angle of rotation as an index of pronation/supination. In adult brown and polar bears, the angles were smaller as compared with the other groups (Asiatic black and non-adult brown bears). Asiatic black and non-adult brown bears can climb trees, whereas adult brown bears and polar bears cannot. This suggests that the pronation/supination angle is related to arboreal activity in Ursidae.

Origins and founder effects on the Japanese masked palm civet Paguma larvata (Viverridae, Carnivora), revealed from a comparison with its molecular phylogeography in Taiwan.

The source areas of the Japanese populations of the masked palm civet Paguma larvata (Viverridae, Carnivora), an alien species in Japan, have not been identified. In the present study, to reveal their origins and genetic features, we determined the full mitochondrial DNA cytochrome b sequences (1,140 base-pairs) of a total of 206 individuals of P. larvata from the Honshu and Shikoku islands of Japan (186 animals) and Taiwan (20 animals), and investigated their molecular phylogeography and the genetic relationships between populations in these countries. We found that each animal from Japan exhibited one of four haplotypes (JA1, JA2, JA4, and JA5), and that JA1 and JA4 were more frequent in eastern Honshu and Shikoku-central Honshu, respectively. By contrast, six haplotypes consisting of four new types (TW1, TW2, TW3, and TW4) and the previously reported two types (JA1 and JA4) were identified from 20 animals from native populations in Taiwan. Within Taiwan, one haplotype set (JA1, TW1, and TW2) was distributed in the western region, while a second (JA4, TW3, and TW4) was found in the eastern region; these regions are separated by high mountain ranges. Our comparison of haplotype distributions strongly demonstrated that the eastern Japanese populations originated from animals of western Taiwan, and that the western Japanese populations originated from those of eastern Taiwan. In addition, the lower genetic variability and particular distribution patterns of haplotypes in Japan showed founder effects, which may have resulted from multiple introductions of P. larvata to Japan from Taiwan.

A morphometric analysis of the Japanese macaque (Macaca fuscata) mandibular cheek teeth from the Torihama Shell-midden, Early Jomon Period, Fukui Prefecture, Japan.

We quantitatively examined the differences in the size and proportion of the Japanese macaque (Macaca fuscata) by comparing the Early Jomon specimens from Torihama shell-midden, Fukui Prefecture and modern specimens from Fukui Prefecture. The purpose of this study was to explore the temporal change in the proportion and size of teeth of the Japanese macaques based on the quantified data. The result of measurements of lower premolars and molars demonstrated that sexual dimorphism was evident only among the modern specimens where the females were significantly smaller than males. The size of male Torihama specimens was within the range of the modern population, whereas the size of the female Torihama specimens was significantly larger than the modern female population. The proportional pattern of premolars and molars for male and female Torihama specimens also differed. The results may suggest a possible difference in the degree of size reduction between males and females since the last glacial period.

Variation in mitochondrial DNA of Vietnamese pigs: relationships with Asian domestic pigs and Ryukyu wild boars.

Mitochondrial DNA (mtDNA) sequences (574 bp) of 30 Vietnamese pigs (large and small) were examined and compared with those of 61 haplotypes from wild boars and domestic pigs from various locations in Asia. The large Vietnamese pigs had genetic links to Ryukyu wild boars in southern Japan. The small Vietnamese pigs were closely related to other East Asian domestic pigs. These results indicate that Vietnamese pigs are genetically diverse and may be descendents of wild and domestic pigs from other regions of Asia.