• Animal Systematics, Evolution and Diversity
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• v.28 no.4
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• pp.279-290
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• 2012

Plecoglossus altivelis (ayu) is an amphidromous fish widely distributed in Northeastern Asia from the East China Sea to the northern Japanese coastal waters, encompassing the Korean Peninsula within its range. The shore lines of northeastern region in Asia have severely fluctuated following glaciations in the Quaternary. In the present study, we investigate the population genetic structure and historical demographic change of P. altivelis at a population level in East Asia. Analysis of molecular variance (AMOVA) based on 244 mitochondrial control region DNA sequences clearly showed that as the sampling scope extended to a larger geographic area, genetic differentiation began to become significant, particularly among Northeastern populations. A series of hierarchical AMOVA could detect the genetic relationship of three closely located islands between Korea and Japan that might have been tightly connected by the regional Tsushima current. Neutrality and mismatch distribution analyses revealed a strong signature of a recent population expansion of P. altivelis in East Asia, estimated at 126 to 391 thousand years ago during the late Pleistocene. Therefore it suggests that the present population of P. altivelis traces back to its approximate demographic change long before the last glacial maximum. This contrasts our a priori expectation that the most recent glacial event might have the most crucial effect on the present day demography of marine organisms through bottleneck and subsequent increase of effective population size in this region.

• Animal Systematics, Evolution and Diversity
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• v.29 no.2
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• pp.99-114
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• 2013

Phylogeographic and feeding ecological studies of seven terrestrial mustelid species (Carnivora, Mustelidae), the Japanese marten Martes melampus, the sable Martes zibellina, the Japanese badger Meles anakuma, the ermine or the stoat Mustela erminea, the Japanese weasel Mustela itatsi, the least weasel Mustela nivalis, and the Siberian weasel Mustela sibirica, representing four biogeographic patterns in the Japanese archipelagos (Hokkaido, Honshu-Shikoku-Kyushu, Tsushima, and Hokkaido-Honshu), were reviewed in order to clarify causes for the faunal assemblage processes of those mustelid species in Japan. Here, three main constraints were extracted as important factors on the mustelid assemblage. First, fundamental evolutionary differences maintained by niche conservatism in each ecologically diversified lineage ("evolutionary constraint") would enable the species to co-occur without any major problem (coexistence among Martes, Meles, and Mustela species). Second, "ecological constraints" would force two closely related species to be allopatric by competitive exclusion (Mu. itatsi and Mu. sibirica) or to be sympatric by resource partitions (Mu. erminea and Mu. nivalis). Third and most importantly, "geological constraints" would allow specific species to be embraced by a particular geographic region, primarily deciding which species co-occurs. The allopatric distribution of two Martes species in Japan would have been established by the strong effect of the geological separation in Tsugaru Strait. Elucidating both phylogeny and ecology of co-existing species in a community assemblage is important to know which species possess distinct lineage and which ecological traits are adapted to local environments, fulfilling the requirement of the field of conservation biology that endemism and adaptation should both be considered. The Japanese archipelagos would, therefore, provide valuable insight into the conservation for small carnivoran species.

• ALGAE
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• v.37 no.2
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• pp.123-133
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• 2022

Genetic diversity and distribution patterns of marine macroalgae are increasingly being documented in Southeast Asia. These studies show that there can be significant levels of genetic diversity and isolation between populations on either side of the Thai-Malay Peninsula. Bostrychia tenellla is a common filamentous red seaweed in the region and the entity is represented by at least two cryptic species. Despite being highly diverse and widespread, genetic variation and population structure of this species complex remains understudied, especially around the Thai-Malay Peninsula. We analyzed genetic diversity and inferred the phylogeographic pattern of specimens identified as B. tenella using the plastid RuBisCo spacer from samples from the Andaman Sea and the Gulf of Thailand. Our genetic analysis confirmed the occurrence of the two cryptic B. tenella species (B and C) along both coasts. Cryptic species B was more common in the area and displayed higher genetic diversity than species C. Historical demographic analyses indicated a stable population for species B, but more recent population expansion for species C. Our analyses also revealed that both cryptic species from the Andaman Sea possessed higher genetic diversity than those of the Gulf of Thailand. We also detected moderate to high levels of gene flow and weak phylogeographic structure of cryptic species B between the two coasts. In contrast, phylogeographic analysis showed genetic differences between populations of both cryptic species within the Andaman Sea. Overall, these results suggest that cryptic B. tenella species around Thai-Malay Peninsula may have undergone different demography histories, and their patterns of genetic diversity and phylogeography were likely caused by geological history and regional sea surface current circulation in the area.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.6
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• pp.902-912
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• 2020

Objective: Mongolia is one of a few countries that supports over 25 million goats, but genetic diversity, demographic history, and the origin of goat populations in Mongolia have not been well studied. This study was conducted to assess the genetic diversity, phylogenetic status and population structure of Mongolian native goats, as well as to discuss their origin together with other foreign breeds from different countries using hypervariable region 1 (HV1) in mtDNA. Methods: In this study, we examined the genetic diversity and phylogenetic status of Mongolian native goat populations using a 452 base-pair long fragment of HVI of mitochondrial DNA from 174 individuals representing 12 populations. In addition, 329 previously published reference sequences from different regions were included in our phylogenetic analyses. Results: Investigated native Mongolian goats displayed relatively high genetic diversities. After sequencing, we found a total of 109 polymorphic sites that defined 137 haplotypes among investigated populations. Of these, haplotype and nucleotide diversities of Mongolian goats were calculated as 0.997±0.001 and 0.0283±0.002, respectively. These haplotypes clearly clustered into four haplogroups (A, B, C, and D), with the predominance of haplogroup A (90.8%). Estimates of pairwise differences (Fst) and the analysis of molecular variance values among goat populations in Mongolia showed low genetic differentiation and weak geographical structure. In addition, Kazakh, Chinese (from Huanghuai and Leizhou), and Arabian (Turkish and Baladi breeds) goats had smaller genetic differentiation compared to Mongolian goats. Conclusion: In summary, we report novel information regarding genetic diversity, population structure, and origin of Mongolian goats. The findings obtained from this study reveal that abundant haplogroups (A to D) occur in goat populations in Mongolia, with high levels of haplotype and nucleotide diversity.

• Korean Journal of Plant Taxonomy
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• v.45 no.3
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• pp.254-261
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• 2015

Genetic variations of Abies koreana and Abies nephrolepis were assessed using two mitochondrial DNA regions (nad5 intron 4 and nad5 intron 1) for 16 natural populations to understand their phylogeographical history. Seven polymorphic sites of the two combined regions resulted in the resolution of four haplotypes (M1-M4). The average gene diversity within the population ($H_S$) was 0.098, the total gene diversity ($H_T$) was 0.620, and the interpopulation differentiation was $G_{ST}=0.841$, $N_{ST}=0.849$. The populations were divided into three groups (northern area, central area, southern area) according to their geographic locations. The populations of the northern and southern areas were mostly fixed for M1 and M2, respectively. The populations of the central area showed the highest levels of gene diversity ($H_T=0.654$) due to introgression from the northern area and southern area. The presence of a single mtDNA haplotype in the southern area suggests that current widespread populations have expanded to the central area from a specific refugium population after the last glacial period.

• Molecules and Cells
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• v.28 no.5
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• pp.423-430
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• 2009

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.

• Fisheries and Aquatic Sciences
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• v.27 no.3
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• pp.145-158
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• 2024

Life history characteristics, habitat landscape, and historical events are believed to have shaped the patterns of genetic variation in many taxa. The bony lip barb, Osteohilus vittatus, represent a potamodromous fish that complete all life cycle in freshwater and is widely distributed in Southeast Asia. It usually lives in small rivers and other freshwater habitats, and movement between habitats for either food or reproduction has been typical. These life history characteristics may promote gene flow, leading to less structured populations. However, many freshwater habitats are fragmented, which restricts gene flow. We investigate how this interplay has shaped patterns of genetic variation and phylogeographic structure within this species in the Sundaland, a biodiversity hotspot with a complex geological history, using mitochondrial cytochrome oxidase I (mtCOI) as a genetic marker. Forty-six mtCOI sequences of 506 bp long were collected from ten localities, eight geographically isolated and two connected. The sequences were used for population genetic and phylogeographic analyses. Our results showed a low genetic diversity within populations but high between populations. There was a deep phylogeographic structure among geographically isolated populations but a lack of such structure in the connected habitats. Among geographically isolated populations, sequence divergence was revealed, ranging from 1.8% between Java and Sumatra populations to 12.2% between Malaysia and Vietnam. An indication of structuring was also observed among localities that are geographically closer but without connectivity. We conclude that despite high dispersal capacity, the joint effects of historical events, long-term geographic isolation associated with sea level oscillation during the Pleistocene, and restricted gene flow related to lack of habitat connectivity have shaped the phylogeographic structure within the O. vittatus over the Sundaland.

• Korean Journal of Environmental Biology
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• v.38 no.4
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• pp.650-657
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• 2020

We conducted a phylogeographic analysis of Korean endemic Zacco koreanus populations inhabiting the East-flowing river (Gangneung Yeongokcheon; GY, Yangyang Namdaecheon; YN), the Han River (Seomgang; SG, Soksacheon; SS), and the Nakdong River(Gilancheon; GA) using the mitochondrial DNA cytochrome oxidase I (COI) gene (619 bp). Population genetic analysis was further performed to assess the population connectivity for the GY river where there is a large number of human-made artificial weirs with several fishways. The phylogeographic analysis revealed that while the populations of the East-flowing river and those of the Han River formed a monophyletic lineage, the Nakdong River individuals represented a distinct lineage with 3.7-4.2% (mean=4.0%) genetic distance from the other lineages. The population genetic analysis of the GY showed that a mid-stream population harbored relatively higher mitochondrial diversity relative to up- and down-stream populations, and there was no genetic differentiation between these three populations. The latter findings might suggest high genetic connectivity between the populations via genetic flow along the fishways. However, an analysis using faster-evolving genetic markers, such as microsatellites, is needed to confirm the findings of high population connectivity. Our study suggests the possibility of the presence of cryptic species in Z. koreanus in the Nakdong River basin. However, further study with more individual samples as well as additional markers or even more advanced genomic tools is required to test our hypothesis. Ecological or phenotypic analyses should be conducted to test whether the observed Nakdong River lineage represents a different or cryptic species, or simply hidden, but excessive, intraspecific diversity.