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.

Genetic diversity and demographic history of introduced sika deer on the Delmarva Peninsula

The introduction of non-native species can have long-term effects on native plant and animal communities. Introduced populations are occasionally not well understood and offer opportunities to evaluate changes in genetic structure through time and major population changes such as bottleneck and or founder events. Invasive species can often evolve rapidly in new and novel environments, which could be essential to their long-term success. Sika deer are native to East Asia, and their introduction and establishment to the Delmarva Peninsula, USA, is poorly documented, but probably involved ≥1 founder and/or bottleneck events. We quantified neutral genetic diversity in the introduced population and compared genetic differentiation and diversity to the presumed source population from Yakushima Island, Japan, and a captive population of sika deer in Harrington, Delaware, USA. Based on the data from 10 microsatellite DNA loci, we observed reduced genetic variation attributable to founder events, support for historic hybridization events, and evidence that the population did originate from Yakushima Island stocks. Estimates of population structure through Bayesian clustering and demographic history derived from approximate Bayesian computation (ABC), were consistent with the hypothesized founder history of the introduced population in both timing and effective population size (approximately five effective breeding individuals, an estimated 36 generations ago). Our ABC results further supported a single introduction into the wild happening before sika deer spread throughout the Delmarva. We conclude that free-ranging sika deer on Delmarva are descended from ca. five individuals introduced about 100 years ago from captive stocks of deer maintained in the United Kingdom. Free-ranging sika deer on Delmarva have lost neutral diversity due to founder and bottleneck events, yet populations have expanded in recent decades and show no evidence of abnormalities associated with inbreeding. We suggest management practices including increasing harvest areas and specifically managing sika deer outside of Maryland.

Paternity determination of captive bottlenose dolphins (Tursiops truncatus) using microsatellite DNA analysis

We applied previously published PCR primer pairs to amplify alleles at three polymorphic microsatellite loci to determine the genetic relationship of 6 bottlenose dolphins (Tursiops truncatus) that were living together in a Japanese aquarium. The three microsatellite loci were sufficient to determine the haplotype relationships of the six dolphins, which represented three different generations. It was confirmed that this genotyping method is simple and economical for assessing, establishing and maintaining genetic diversity in captive populations and will become a very effective technique for ex situ conservation in aquariums and zoos.

Bottleneck effects on the sika deer Cervus nippon population in Hokkaido, revealed by ancient DNA analysis

The population size of the sika deer Cervus nippon on Hokkaido Island of Japan had been remarkably reduced because of heavy hunting pressure since the beginning of Meiji Period and effects of heavy snow in 1879 and 1881. After that, the number of sika deer in Hokkaido has increased gradually due to the protection by the Hokkaido government. In the present study, in order to investigate the bottleneck effects, we analyzed ancient mitochondrial DNA (mtDNA) on sika deer bones excavated from archaeological sites just before Meiji Period. On 86 of 113 bones from 13 archaeological sites of Ainu Culture Period (17-19th centuries), 602 base-pair fragments of the mtDNA control region were successfully sequenced. Consequently, we found three new haplotypes (g-, h- and i-types) which had not been identified in modern sika deer. In addition, four haplotypes (a-, b-, c- and d-types) identified from modern sika deer were also found in the archaeological deer. The new haplotypes and previously reported hapoltypes from sika deer of Hokkaido were phylogenetically much closer to each other, compared with those of modern sika deer from Honshu, Kyushu and the Chinese continent. Geographical distribution patterns of haplotypes of the ancient population were different from those of the modern population in Hokkaido. Our findings indicated that their genetic diversity was reduced through the bottleneck and that population structures of sika deer were changed widely in Hokkaido due to genetic drift.

Efficiency of semi-automated fluorescent multiplex PCRs with 11 microsatellite markers for genetic studies of deer populations

Thirty bovine and eight ovine microsatellite primer pairs were tested on four tropical deer species: Eld's and Swamp deer (highly threatened) and Rusa and Vietnamese Sika deer (economically important). Thirty markers gave an amplified product in all four species (78.9%). The number of polymorphic microsatellite markers varied among the species from 14 in Eld's deer (47%) to 20 in Swamp deer (67%). Among them, 11 microsatellite loci were multiplexed in three polymerase chain reactions (PCRs) and labelled with three different fluorochromes that can be loaded in one gel-lane. To test the efficiency of the multiplex, primary genetic studies (mean number of alleles, expected heterozygosities and Fis values) were carried out on four deer populations. Parentage exclusion probability and probability of identity were computed and discussed on a Swamp deer population. These multiplexes PCRs were also tested on several other deer species and subspecies. The aim of this study is to establish a tool useful for genetic studies of population structure and diversity in four tropical deer species which with few modifications can be applied to other species of the genus Cervus.