The impact of habitat fragmentation on genetic structure of the Japanese sika deer (Cervus nippon) in southern Kantoh, revealed by mitochondrial D-loop sequences

iSCNT embryo culture system for restoration of Cervus nippon hortulorum, presumed to be sika deer in the Korean Peninsula

Sika deer inhabiting South Korea became extinct when the last individual was captured on Jeju Island in Korea in 1920 owing to the Japanese seawater relief business, but it is believed that the same subspecies (Cervus nippon hortulorum) inhabits North Korea and the Russian Primorskaya state. In our study, mt-DNA was used to analyze the genetic resources of sika deer in the vicinity of the Korean Peninsula to restore the extinct species of continental deer on the Korean Peninsula. In addition, iSCNT was performed using cells to analyze the potential for restoration of extinct species. The somatic cells of sika deer came from tissues of individuals presumed to be Korean Peninsula sika deer inhabiting the neighboring areas of the Primorskaya state and North Korea. After sequencing 5 deer samples through mt-DNA isolation and PCR, BLAST analysis showed high matching rates for Cervus nippon hortulorum. This shows that the sika deer found near the Russian Primorsky Territory, inhabiting the region adjacent to the Korean Peninsula, can be classified as a subspecies of Cervus nippon hortulorum. The method for producing cloned embryos for species restoration confirmed that iSCNT-embryos developed smoothly when using porcine oocytes. In addition, the stimulation of endometrial cells and progesterone in the IVC system expanded the blastocyst cavity and enabled stable development of energy metabolism and morphological changes in the blastocyst. Our results confirmed that the individual presumed to be a continental deer in the Korean Peninsula had the same genotype as Cervus nippon hortulorum, and securing the individual's cell-line could restore the species through replication and produce a stable iSCNT embryo.

A historic religious sanctuary may have preserved ancestral genetics of Japanese sika deer (Cervus nippon)

Deer have been a major resource for human populations for thousands of years. Anthropogenic activities, such as hunting, have influenced the genetic structure and distribution of deer populations. In Japan, wild Japanese sika deer (Cervus nippon) have been hunted since ancient times but have also been historically protected as sacred animals in several sanctuaries. Sika deer have been protected for over a thousand years in the religious sanctuary around the Kasuga Taisha Shrine on the Kii Peninsula, located in the center of Japan. Here, we used short sequence repeats (SSR) and mitochondrial DNA (mtDNA) to investigate the genetic diversity, population structure, and demography of Japanese sika deer inhabiting the Kii Peninsula, Japan, and discuss possible anthropogenic influences. Using SSR, three distinct genetic groups were distinguished on the Kii Peninsula: an Eastern genetic group, a Western genetic group, and an isolated genetic group with individuals in the religious sanctuary of Kasuga Taisha Shrine in Nara city. The isolated genetic sanctuary group had only the mtDNA haplotype S4. The SSR genotype data suggested a newer divergence time of the genetic groups of the religious sanctuary than would have occurred as a result of Late Quaternary climate change. This time scale coincided with the establishment of the sanctuary with Kasuga Taisha Shrine. Thus, the religious protection conserved genetic variation over a thousand years.

Phylogeography of sika deer (Cervus nippon) inferred from mitochondrial cytochrome-b gene and microsatellite DNA

The genetic diversity and phylogenetic relationships of sika deer of different subspecies are uncertain. In order to explore the phylogenetic relationship of different sika deer subspecies, this study used a wider sample collection to analyze mitochondrial sequences and nuclear microsatellites of sika deer. The full lengths of cytochrome-b gene of 134 sika deer were sequenced, and 16 haplotypes were obtained. Based on phylogenetic and haplotype networks analysis, the sika deer was not clustered according to subspecies but was divided into four lineages. Lineage I includes individuals from C.n.kopschi, C.n.sichuanicus, and C.n.hortulorum subspecies; Lineage II includes individuals from C.n.hortulorum subspecies; Lineage III includes individuals from C.n.centralis, C.n.yakushime, C.n.mageshimae, and C.n.keramae subspecies, namely southern Japanese population; Lineage IV includes individuals from C.n.centralis and C.n.yesoensis subspecies, namely northern Japanese population. The microsatellite analysis showed that the sika deer in China and Japan originated independently. The three subspecies of China have significant genetic differentiation, while the three subspecies of Japan have no significant differentiation. This study provides reference for the research of genetic diversity and phylogenetic relationship of sika deer, and also provides scientific data for the evaluation, protection, and utilization of sika deer resources.

Population Structure, Admixture, and Migration Patterns of Japanese Sika Deer (Cervus nippon) Inhabiting Toyama Prefecture in Japan

Rapid expansion of sika deer, in both number and distribution, in the Japanese Archipelago has resulted in serious ecological disturbance. In the present study, the population structure and migration patterns of sika deer (Cervus nippon) among Toyama and adjacent Prefectures were investigated using 11 polymorphic microsatellite loci. Deviation from Hardy-Weinberg equilibrium was detected in both total and individual regional sika deer samples from Toyama Prefecture. Results of pairwise F_ST results, factorial correspondence analysis, and STRUCTURE analysis indicated that sika deer in Toyama are not genetically distinct from those in adjacent Prefectures. Bayesian STRUCTURE results suggested the existence of two distinct clusters. However, multiple lines of genetic structure and high admixture were detected across the populations located in the central region of Toyama Prefecture. Both contemporary and historical migration analyses showed that dispersal into Toyama Prefecture from neighboring prefectures was high, especially migration from the prefecture on the east into Toyama Prefecture, and bidirectional dispersion between Toyama Prefecture and the prefecture to the south. Knowledge of such genetic structures and population dynamics is required for appropriate management and conservation of sika deer populations in the Japanese Archipelago.

An initial record of a long-distance dispersal route of a male sika deer in central Japan

We conducted a global positioning system (GPS) tracking of a male sika deer (Cervus nippon) and his mother in the eastern foothills of the northern Japanese Alps, central Japan. Sika deer exhibited similar seasonal movement patterns; however, the male deer left his natal group at 11 months of age. At 15 months of age, the male deer settled in the neighboring mountain, which was 74 km away from his natal range. This is the first record of long-distance (>50 km) natal dispersal of the sika deer. Our findings might help to explain the expanding distribution of the sika deer.

Genetic Population Structure of Sika Deer, Cervus nippon, Derived from Multiple Origins, Around Toyama Prefecture of Japan

Recently, expansion of the number and distribution of sika deer, Cervus nippon, in the Japanese Archipelago has resulted in the disturbance of indigenous gene pools and ecosystems. There are also concerns that the artificial introduction of sika deer to certain areas may aggravate this situation. In order to contribute to the conservation of ecosystems, I examined the current state of genetic disturbance and dispersal routes in the sika deer populations around Toyama Prefecture, one of the main areas of expanding sika deer distribution. Of 12 haplotypes detected by mitochondrial DNA D-loop sequence analysis, 10 were found to belong to a previously detected sika deer group in northern Japan, although the remaining two haplotypes corresponded to the southern Japanese sika deer group. The latter two haplotypes were detected at especially high frequencies in the southern area of Toyama Prefecture, suggesting that these haplotypes may derive from artificially introduced individuals. Occurrence patterns of indigenous haplotypes around Toyama Prefecture revealed immigration into Toyama Prefecture through different routes, mainly in the east and south-west. The genetic results presented here may have application in predicting future dispersal routes, as well as aid in the establishment of effective measures for management of sika deer.

The inter-relationship between dietary and environmental properties and tooth wear: comparisons of mesowear, molar wear rate, and hypsodonty index of extant Sika deer populations

In reference to the evolutionary trend of increasing cheek tooth height in herbivorous ungulates, the causes of dental abrasion have long been debated. Interspecific comparisons of extant ungulates have revealed that both phytoliths in grass and external abrasive matter may play important roles. Using analysis of extant sika deer living in various environments and showing continuous latitudinal variation in food habits from northern grazing to southern browsing, we quantitatively evaluated the influence of dietary and environmental properties on three dental variables: mesowear score (MS), molar wear rate, and M3 hypsodonty index. We used 547 skulls and 740 mandibles from 16 populations of sika deer to obtain the dental measurements. We found that only graminoid proportion in diet correlated with MS and the molar wear rate, implying that phytoliths in grass abrade dental tissues. In contrast, annual precipitation in habitat was not correlated with any of the dental variables. We also found a significant correlation between the molar wear rate (selective pressure for high-crowned molars) and the M3 hypsodonty index of extant sika deer, implying an evolutionary increment in molar height corresponding to the molar wear rate. Our intraspecific comparative analyses provide further support for use of mesowear analysis as a paleodiet estimation method; it not only reveals staple food types (graminoids or dicots) but also implies regional or seasonal variation in the diet of the species.

Dybowski's sika deer (Cervus nippon hortulorum): genetic divergence between natural primorian and introduced Czech populations

Dybowski's sika deer (Cervus nippon hortulorum) originally inhabited the majority of the Primorsky Krai in Far Eastern Russia, north-eastern China, and Korean Peninsula. At present, only the Russian population seems to be stable, even though this taxon is still classified as endangered by the Russian Federation. Almost 100 years ago, this subspecies, among others, was imported to several European countries including the Czech Republic. We used both mitochondrial (mtDNA; the cytochrome b gene and the control region) and nuclear DNA markers to examine the actual taxonomic status of modern Czech Dybowski's sika population and to compare the genetic diversity between the introduced and the native populations. Altogether, 124 Czech samples and 109 Primorian samples were used in the analyses. Within the samples obtained from individuals that were all morphologically classified as Dybowski's sika, we detected mtDNA haplotypes of Dybowski's sika (84 samples), as well as those belonging to other sika subspecies: northern Japanese sika (25 samples), southern Japanese sika (6 samples), and south-eastern Chinese sika (8 samples). Microsatellite analysis revealed a certain level of heterozygote deficiency and a high level of inbreeding in both populations. The high number of private alleles, factorial correspondence analysis, and Bayesian clustering analysis indicate a high level of divergence between both populations. The large degree of differentiation and the high number of population-specific alleles could be a result of a founder effect, could be a result of a previously suggested bottleneck within the Primorian population, and could also be affected by the crossbreeding of captive individuals with other sika subspecies.

Genetic variation and population structure of the Japanese sika deer (Cervus nippon) in the Tohoku District based on mitochondrial D-loop sequences

The sika deer (Cervus nippon) once inhabited the entire Tohoku District, the northeastern part of the main island of Japan. Currently, they are isolated as three discontinuous populations on Mt. Goyo, the Oshika Peninsula, and Kinkazan Island. To assess the genetic diversity and relationships among the sika deer populations in the Tohoku District, we analyzed the mitochondrial DNA D-loop sequences from 177 individuals. We detected a total of five haplotypes. Three haplotypes were present in the population from Mt. Goyo at a haplotype diversity of 0.235 ± 0.061, two haplotypes in the population from the Oshika Peninsula at 0.171 ± 0.064, and only one haplotype was detected in the population from the Kinkazan Island. A significant genetic differentiation was observed among all population pairs. Collectively, our data supports the observed population bottlenecks in the past. Four of the five haplotypes were specific to one of the three populations, whereas only one haplotype was shared between the Mt. Goyo and the Oshika Peninsula populations. This common haplotype may indicate a common ancestral population in the Tohoku District. Conversely, the D-loop haplotypes were completely different among the Kinkazan Island and Oshika Peninsula populations. The lack of a shared haplotype indicates that female gene flow between the two populations is very limited and that the 0.6 km strait acts as a strong barrier.

Ability of wildlife overpasses to provide connectivity and prevent genetic isolation

We reviewed research on wildlife overpasses in the context of their genetic effectiveness to provide connectivity between population patches that have been isolated by road construction. The potential ecological consequences of such habitat fragmentation include reduction of gene flow between subpopulations and hence an increase in genetic differentiation and a decrease in genetic diversity. Among the solutions to provide connectivity between patches isolated by roads, wildlife overpasses are one of the most expensive alternatives. Despite the high costs associated with their construction, most of the studies assessing their use by wildlife remain observational, reporting evidence for passage use but few data on the number of individual crossings. Moreover, the use itself of wildlife overpasses does not appear sufficient to assess their effectiveness from a genetic viewpoint because a minimum number of individuals is required to assure gene flow between population patches and because the spatiotemporal dimension of individual movements and demographic parameters of subpopulations must be considered. So far, there is no evidence that wildlife overpasses do or do not efficiently address genetic issues. This lack of data is probably due to the fact that few mitigation efforts have implemented monitoring programs that incorporate sufficient experimental designs into pre- and postconstruction evaluation. To assess the genetic effectiveness of wildlife overpasses, long-term monitoring programs, including fieldwork and genetic analyses, are needed.

Genetic diversity and population structure of Scottish Highland red deer (Cervus elaphus) populations: a mitochondrial survey

The largest population of red deer (Cervus elaphus) in Europe is found in Scotland. However, human impacts through hunting and introduction of foreign deer stock have disturbed the population's genetics to an unknown extent. In this study, we analysed mitochondrial control region sequences of 625 individuals to assess signatures of human and natural historical influence on the genetic diversity and population structure of red deer in the Scottish Highlands. Genetic diversity was high with 74 haplotypes found in our study area (115 x 87 km). Phylogenetic analyses revealed that none of the individuals had introgressed mtDNA from foreign species or subspecies of deer and only suggested a very few localized red deer translocations among British localities. A haplotype network and population analyses indicated significant genetic structure (Phi(ST)=0.3452, F(ST)=0.2478), largely concordant with the geographical location of the populations. Mismatch distribution analysis and neutrality tests indicated a significant population expansion for one of the main haplogroups found in the study area, approximately dated c. 8200 or 16 400 years ago when applying a fast or slow mutation rate, respectively. Contrary to general belief, our results strongly suggest that native Scottish red deer mtDNA haplotypes have persisted in the Scottish Highlands and that the population retains a largely natural haplotype diversity and structure in our study area.