Junghwa An

Mitochondrial genetic diversity and phylogenetic relationships of Siberian flying squirrel (Pteromys volans) populations

Abstract Siberian flying squirrel, an endangered species in South Korea, is distributed through major mountain regions of South Korea. The number of Siberian flying squirrel (Pteromys volans) in South Korea has decreased and their habitats are fragmented and isolated because of anthropogenic activities. So far no molecular genetic data has, however, been available for their conservation and management. To obtain better information concerning genetic diversity and phylogenetic relationships of the Siberian flying squirrel in South Korea, we examined 14 individuals from South Korea, 7 individuals from Russia, and 5 individuals from northeastern China along with previously published 29 haplotypes for 1,140 bp of the mtDNA cytochrome b gene. The 14 new individuals from South Korea had 7 haplotypes which were not observed in the regions of Russia and Hokkaido. The level of genetic diversity (0.616%) in the South Korean population was lower than that in eastern Russia (0.950%). The geographical distribution of mtDNA haplotypes and reduced median network confirmed that there are three major lineages of Siberian flying squirrel, occupying; Far Eastern, northern Eurasia, and the island of Hokkaido. The South Korean population only slightly distinct from the Eurasia, and eastern Russian population, and is part of the lineage Far Eastern. Based on these, we suggest that the South Korean population could be considered to belong to one partial ESU (Far Eastern) of three partial ESUs but a different management unit. However, the conservation priorities should be reconfirmed by nuclear genetic marker and ecological data.

Organization and variation of the mitochondrial DNA control region in five Caprinae species

The complete mitochondrial DNA (mtDNA) control region was analyzed from five species of the subfamily Caprinae; Naemorhedus caudatus, N. goral, Capra hircus, Capricornis swinhoei, and Capricornis crispus. Among these species, the control region ranged from 1,096 to 1,212 bp in length. Our results were compatible with the scheme of three domains (ETAS, Central, and CSB) within the control region. A + T < G + C was observed in all the domains. In the Korean gorals, of the 31 variable sites in the whole control region resulting in 15 haplotypes, 27 variable sites were in the ETAS domain. We found two to three tandem repeat in all five species examined in this study, three in N. caudatus and N. goral, two in Capra hircus and C. crispus, and one in C. swinhoei, respectively. All of these repeat units include two short sections of mirror symmetry (TACAT and ATGTA). Short mirror symmetries were well-resolved among five different species, although left domain has high substitution rates. By Kimura’s two parameter method, the genetic distances between the genera Naemorhedus and Capricornis were calculated and divergence time between Naemorhedus and Capricornis may be nearly 2Myr.

Subspecific Status of the Korean Tiger Inferred by Ancient DNA Analysis

The tiger population that once inhabited the Korean peninsula was initially considered a unique subspecies (Panthera tigris coreensis), distinct from the Amur tiger of the Russian Far East (P. t. altaica). However, in the following decades, the population of P. t. coreensis was classified as P. t. altaica and hence forth the two populations have been considered the same subspecies. From an ecological point of view, the classification of the Korean tiger population as P. t. altaica is a plausible conclusion. Historically, there were no major dispersal barriers between the Korean peninsula and the habitat of Amur tigers in Far Eastern Russia and northeastern China that might prevent gene flow, especially for a large carnivore with long-distance dispersal abilities. However, there has yet to be a genetic study to confirm the subspecific status of the Korean tiger. Bone samples from four tigers originally caught in the Korean peninsula were collected from two museums in Japan and the United States. Eight mitochondrial gene fragments were sequenced and compared to previously published tiger subspecies’ mtDNA sequences to assess the phylogenetic relationship of the Korean tiger. Three individuals shared an identical haplotype with the Amur tigers. One specimen grouped with Malayan tigers, perhaps due to misidentification or mislabeling of the sample. Our results support the conclusion that the Korean tiger should be classified as P. t. altaica, which has important implications for the conservation and reintroduction of Korean tigers.

Isolation and characterization of 12 microsatellite loci from Korean water deer (Hydropotes inermis argyropus) for population structure analysis in South Korea

The main goals of this study were to isolate microsatellites markers of Korean water deer (Hydropotes inermis argyropus) and understand the genetic status of the species in South Korea. Twelve new microsatellite loci were isolated and characterized to establish basic population genetic parameters for 45 H. i. argyropus specimens in South Korea. There were no significant regional or genetic structure differences between the mid-eastern and southwestern populations in South Korea according to the population genetic analyses. The number of alleles per locus ranged from two to 13 with an average of 6.08. Mean expected (HE) and observed heterozygosity (HO) were 0.622 and 0.533, respectively. Microsatellite variability was also not significant between the two regions (FST=0.012). These new markers should facilitate the future population genetics studies of Korean water deer and other closely related species.

A core set of microsatellite markers for conservation genetics studies of Korean goral (Naemorhedus caudatus) and its cross-species amplification in Caprinae species

In order to screen microsatellites for conservation genetics studies of the species, a total of 23 microsatellite loci from Korean goral (Naemorhedus caudatus), including 15 previously developed loci and 8 new loci in this study, were tested. Eleven microsatellites were screened and subjected to cross-species amplification using a test panel of four Caprinae species, Japanese serows (Capricornis crispus), Chinese gorals (Naemorhedus goral), Northern chamois (Rupicapra rupicapra) and domestic goats (Capra hircus). In addition, all eleven microsatellites (SY3A, SY12A, SY12B, SY48, SY58, SY71, SY76, SY84, SY84B, SY112, and SY129) satisfied the criteria to be a core set of microsatellites. This core set of microsatellites and cross-species amplification of Korean goral microsatellites were found to be helpful for high-resolution studies for conservation and management of Korean goral and other endangered Caprinae species.

Development of 10 microsatellite loci from the Korean Ratsnake (Elaphe schrenckii) and its application across Elaphe species from South Korea, Russia, and China

We have developed 10 microsatellite loci from the Korean ratsnake Elaphe schrenckii. Polymorphism of each locus was assessed in 25 unrelated individuals for E. schrenckii from South Korea, 10 E. anomala and 10 E. schrenckii from China, and 10 E. schrenckii from Russia. E. anomala, a closely related species to E. schrenckii in China. The number of alleles per locus varied from 1–9 (mean 4.4) for Korean populations, 2–7 (mean 3.9) for Chinese E. anomala, 1–7 (mean 4.0) for Chinese E. schrenckii, and 1–4 (mean 2.5) for Russian E. schrenckii. The average expected heterozygosity was 0.500, 0.534, 0.487, and 0.338 for E. schrenckii from South Korea, E. anomala from China, E. schrenckii from China, and E. schrenckii from Russia, respectively. The microsatellite markers used in this study may be applied to other Elaphe species for population analysis, eliminating the time-consuming task of finding new loci. These selected markers are useful for assessing population structure, intraspecific variation, and conservation and management of E. schrenckii.

Genetic diversity and population structure of the long-tailed goral, Naemorhedus caudatus , in South Korea

The long-tailed goral, Naemorhedus caudatus, is an internationally endangered species. This species is distributed throughout Northeastern Asia including Northeastern China, the Russian Far East and the Korean peninsula. The population size of long-tailed gorals is currently decreasing in South Korea, and thus effective conservation of the animal is urgently needed. Although the evolution and phylogeny of this animal have been studied, population genetic studies are needed to design effective conservation and management strategies. To evaluate the present status of genetic diversity and genetic structure of long-tailed gorals in South Korea, we investigated genetic variability among 68 goral individuals from different regions, including 11 captive zoo animals, at 12 microsatellite loci. The level of genetic diversity was moderate in wild goral populations, but lower in the captive group. The goral population from the lower northeast region of South Korea was distinct from the upper northeast population, probably due to the natural climatic and geographic conditions. The genetic characteristics of the captive group were more similar to those of the upper northeast population than the lower northeast, confirming that the zoo animals originated in the Seorak Mountain range. Direct translocations between the upper and lower northeast populations are not currently recommended considering the natural population structure and the moderate levels of genetic diversity in the two populations. This study highlights the importance of genetic information in designing effective conservation strategies and translocations of endangered animals, including the Korean goral.

The mitochondrial genome of the long-billed plover, Charadrius placidus (Charadriiformes: Charadriidae)

Abstract The present study provides the first full mitochondrial genome sequence of a long-billed plover from South Korea. This mitogenome is 16,895 bp in length and consists of 13 protein-coding genes, 2 ribosomal-RNA genes, 22 transfer-RNA genes, and a non-coding control region. Overall, base composition was: A, 31.4%; C, 31.1%; G, 13.8%; and T, 23.8%. A frameshift mutation in the ND3 gene was identified and a tandem repeat (AACA) was observed in the D-loop region. The phylogenetic analysis based on concatenated coding genes indicated Charadriidae’s monophyly. These results contribute to further understanding of long-billed plover phylogenetic relationships and species identification.

Complete mitochondrial genome of Siberian musk deer Moschus moschiferus (Artiodactyla: Moschidae) and phylogenetic relationship with other moschus species

Abstract The Siberian musk deer, Moschus moschiferus, is an Endangered species in South Korea due to its decreasing population size caused by illegal hunting and habitat destruction. In this study, the complete mitochondrial genome of M. moschiferus was determined using next-generation sequencing. Total length of its mitogenome is 16,356 bp in length, encoding 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region. Its AT contents are 62.4%, which are higher than its GC contents (37.7%) (A, 34.1%; C, 24.9%; G, 12.8%; and T, 28.3%). Phylogenetic relationship of genus Moschus showed topologies similar to those reported in previous studies. Sequence comparison between two M. moschiferus from South Korea indicated high sequence variations with 122 nucleotide differences. These results provide useful information necessary for further phylogenetic studies of Moschus species.

Complete mitochondrial genome sequence of Emberiza sulphurata (Emberizidae: Emberiza)

Abstract The Japanese yellow bunting (Emberiza sulphurata) is considered to be an endangered species. Here, the complete mitochondrial genome of E. sulphurata (16,797 bp in length) was determined. The genome consists of 37 genes (13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes) and one control region (D-loop), and so is highly similar in architecture to the typical vertebrate mtDNA genome. The base composition of the mtDNA was A (29.9%), C (32.6%), G (14.5%), and T (23.0%), so the percentage of A and T (52.9%) was slightly higher than that of G and C. All the genes in E. sulphurata were encoded on the H-strand, except for the genes for the ND6 subunit and eight tRNAs, which were encoded on the L-stand. Phylogenetic analysis using Emberizidae mitogenomes revealed that E. sulphurata was grouped into the family Emberizidae and that E. spodocephala is the most closely related species.