Hang Lee

Genetic evidence of illegal trade in protected whales links Japan with the US and South Korea

We report on genetic identification of ‘whale meat’ purchased in sushi restaurants in Los Angeles, CA (USA) in October 2009 and in Seoul, South Korea in June and September 2009. Phylogenetic analyses of mtDNA cytochrome b sequences confirmed that the products included three species of whale currently killed in the controversial scientific whaling programme of Japan, but which are protected from international trade: the fin, sei and Antarctic minke. The DNA profile of the fin whale sold in Seoul established a match to products purchased previously in Japan in September 2007, confirming unauthorized trade between these two countries. Following species identification, these products were handed over to the appropriate national or local authorities for further investigation. The illegal trade of products from protected species of whales, presumably taken under a national permit for scientific research, is a timely reminder of the need for independent, transparent and robust monitoring of any future whaling.

The robust phylogeny of Korean wild boar (Sus scrofa coreanus) using partial D-loop sequence of mtDNA.

In order to elucidate the precise phylogenetic relationships of Korean wild boar (Sus scrofa coreanus), a partial mtDNA D-loop region (1,274 bp, NC_000845 nucleotide positions 16576-1236) was sequenced among 56 Korean wild boars. In total, 25 haplotypes were identified and classified into four distinct subgroups (K1 to K4) based on Bayesian phylogenetic analysis using Markov chain Monte Carlo methods. An extended analysis, adding 139 wild boars sampled worldwide, confirmed that Korean wild boars clearly belong to the Asian wild boar cluster. Unexpectedly, the Myanmarese/Thai wild boar population was detected on the same branch as Korean wild boar subgroups K3 and K4. A parsimonious median-joining network analysis including all Asian wild boar haplotypes again revealed four maternal lineages of Korean wild boars, which corresponded to the four Korean wild boar subgroups identified previously. In an additional analysis, we supplemented the Asian wild boar network with 34 Korean and Chinese domestic pig haplotypes. We found only one haplotype, C31, that was shared by Chinese wild, Chinese domestic and Korean domestic pigs. In contrast to our expectation that Korean wild boars contributed to the gene pool of Korean native pigs, these data clearly suggest that Korean native pigs would be introduced from China after domestication from Chinese wild boars.

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.

Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly

BackgroundThere are three main dietary groups in mammals: carnivores, omnivores, and herbivores. Currently, there is limited comparative genomics insight into the evolution of dietary specializations in mammals. Due to recent advances in sequencing technologies, we were able to perform in-depth whole genome analyses of representatives of these three dietary groups.ResultsWe investigated the evolution of carnivory by comparing 18 representative genomes from across Mammalia with carnivorous, omnivorous, and herbivorous dietary specializations, focusing on Felidae (domestic cat, tiger, lion, cheetah, and leopard), Hominidae, and Bovidae genomes. We generated a new high-quality leopard genome assembly, as well as two wild Amur leopard whole genomes. In addition to a clear contraction in gene families for starch and sucrose metabolism, the carnivore genomes showed evidence of shared evolutionary adaptations in genes associated with diet, muscle strength, agility, and other traits responsible for successful hunting and meat consumption. Additionally, an analysis of highly conserved regions at the family level revealed molecular signatures of dietary adaptation in each of Felidae, Hominidae, and Bovidae. However, unlike carnivores, omnivores and herbivores showed fewer shared adaptive signatures, indicating that carnivores are under strong selective pressure related to diet. Finally, felids showed recent reductions in genetic diversity associated with decreased population sizes, which may be due to the inflexible nature of their strict diet, highlighting their vulnerability and critical conservation status.ConclusionsOur study provides a large-scale family level comparative genomic analysis to address genomic changes associated with dietary specialization. Our genomic analyses also provide useful resources for diet-related genetic and health research.

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.

Identification of species and sex of Korean Roe Deer (Capreolus pygargus tianschanicus) using SRY and CYTB genes

Abstract The nucleotide sequences of a male‐specific marker sex determining region Y (SRY) gene and a mitochondrial cytochrome B (CYTB) gene were characterized and analyzed to establish a molecular method for identification of species and sex of Korean roe deer (Capreolus pygargus tianschanicus). Similarity search result of SRY sequences showed very similar result to those reported in Moose (Alces alces) and Reindeer (Rangifer tarandus), both of which had 95.9% similarity in identity. CYTB genes were very similar to those reported in Siberian roe deer (C. pygargus pygargus) which had 98.6% similarity and not to European roe deer (C. capreolus), suggesting that the DNA samples tested were of Siberian roe deer lineage. Polymerase chain reaction (PCR)‐based sex typing successfully discriminated between carcasses of male and female roe deer. Males had SRY band on agarose gels and females did not. The result of this molecular sex typing provided similar information with that obtained by genital organ observation. Therefore, this molecular method using male specific marker SRY and mitochondrial CYTB genes would be very useful for identification of the species and sex of the carcass remains of roe deer.

Complete mitochondrial genome of a Steller sea lion Eumetopias jubatus (Carnivora, Otariidae)

The Steller sea lion (Eumetopias jubatus Schreber, 1776; Mammalia, Carnivora, Otariidae) is one of the most endangered species (IUCN 2009; Ministry of Environment of Korea 2004). The population of the Steller sea lion has dramatically declined during the past five decades worldwide (Trites and Donnelly 2003). Thus, it is very important for the systematic conservation of the endangered species to characterize the mitochondrial genomes, a technique that has been usefully employed in the fields of population genetics, phylogeography, species identification, and DNA barcoding (Tunez et al. 2006; Yoo et al. 2006; Koyama et al. 2008; Phillips et al. 2009). In the present study, the nearly complete mitochondrial genome (16,310 bp; GenBank accession number GU475464) of E. jubatus collected from Pohang, South Korea, was sequenced except for the ca. 330 bp downstream region of the control region not sequenced possibly due to the poly-G track. Its characteristics are presented in Table I. It is the second (nearly) complete mitochondrial genome sequenced from this species (Arnason et al. 2002). Although eight nearly complete mitochondrial genome sequences had been deposited directly in GenBank (AB300601–AB3006018), ca. 500 bp of the control region had not been sequenced. Overall characteristics including the mitochondrial genome organization and the gene arrangement pattern were identical to the typical vertebrate mitochondrial genome. The complete mitochondrial genome consists of 13 protein-coding, 22 tRNA, and 2 rRNA genes and one control region. Except for the seven tRNA genes and ND6, all other mitochondrial genes are encoded on the heavy strand. The overall base composition of the heavy strand is 33.51% A, 25.78% T, 26.96% C, and 13.75% G, with an AT content of 59.29%. The AT content was higher than the GC content, as generally shown in other vertebrate mitochondrial genomes (e.g. Bahn et al. 2009; Jang et al. 2009; Woo et al. 2009). Compared with that of Arnason et al. (2002), all 13 protein-coding and two rRNA genes have identical gene lengths and high nucleotide sequence similarities, ranging from 99 to 100%, and the control region is most variable with at least 3% sequence differences. All 21 tRNA genes can fold into a typical cloverleaf secondary structure except for tRNA, which lacks a dihydrouridine arm. The 12S and 16S rRNA genes are located between tRNA and tRNA (963 bp), and between tRNA and tRNA (UUR) (1577bp), respectively. Except for ND2 and ND3 (ATA start codon) and ND5 (ATC start codon), all protein-coding genes initiate with ATG. CO3, ND3, and ND4 end with an incomplete stop codon only with a single “T”. We expect that the present result will contribute to the preservation of genetic resources of endangered

Korea Barcode of Life Database System (KBOL)

A major concern regarding the collection and storage of biodiversity information is the inefficiency of conventional taxonomic approaches in dealing with a large number of species. This inefficiency has increased the demand for automated, rapid, and reliable molecular identification systems and large-scale biological databases. DNA-based taxonomic approaches are now arguably a necessity in biodiversity studies. In particular, DNA barcoding using short DNA sequences provides an effective molecular tool for species identification. We constructed a large-scale database system that holds a collection of 5531 barcode sequences from 2429 Korean species. The Korea Barcode of Life database (KBOL, http://koreabarcode.org) is a web-based database system that is used for compiling a high volume of DNA barcode data and identifying unknown biological specimens. With the KBOL system, users can not only link DNA barcodes and biological information but can also undertake conservation activities, including environmental management, monitoring, and detecting significant organisms.

Isolation of Mycobacterium bovis from Free-Ranging Wildlife in South Korea

Abstract We demonstrate Mycobacterium bovis infection in wild boar (Sus scrofa) in South Korea. During 2012–15, we attempted to isolate M. bovis from 847 wild animals, mainly Korean water deer (Hydropotes inermis argyropus), raccoon dogs (Nyctereutes procyonoides), and wild boar, from 11 regions in South Korea. We isolated M. bovis from three of 118 wild boar (2.5%) captured in Gyeonggi Province, where bovine tuberculosis (bTB) outbreaks have also occurred in livestock. Spoligotypes and mycobacterial interspersed repetitive units–variable number tandem repeats types of these M. bovis isolates (SB0140 and SB1040, 4-2-3-3-7-5-5-4-4-3-4-3 and 5-2-3-3-7-5-5-4-3-10-5-2; MIRU4, MIRU16, MIRU27, MIRU31, ETR-A, ETR-B, ETR-C, QUB11b, QUB26, QUB3336, VNTR2401, and VNTR3171) have also been identified from farmed livestock such as cattle (Bos taurus coreanae), Formosan sika deer (Cervus nippon taiouanus), and American elk (Cervus canadensis) in the country. In South Korea, bTB appears to be endemic in livestock, and there are numerous opportunities for contact between wild boar and livestock due to high population densities and broad activity ranges. Our results support the hypothesis that M. bovis is transmitted between domestic and wild animals.

Discrimination of animal species using polymorphisms of the nuclear gene zinc finger protein 238.

We screened 3750 single exonic genes listed in the intronless genes in the eukaryotes (SEGE) database and performed bioinformatic analyses to identify candidate genes for new species-specific markers. A set of PCR primers for the conserved regions of ZNF238 was developed and used to amplify the 823 bp DNA fragment. We compared nucleotide variations of the PCR products among 20 species plus two subspecies of animals, which led to the identification of interspecies nucleotide variations. To establish a simple method for the analysis of species-specific DNA polymorphisms using ZNF238, we developed a PCR-RFLP method using HhaI and HpyCH4IV restriction enzymes for 13 species. For the remaining species, the direct sequencing of PCR products provided additional SNPs, enabling precise species classification. As a result, we report here that a new nuclear DNA marker, ZNF238, can be used to increase the accuracy of species identification among euteleostomi (bony vertebrates).