Differential patterns of diversity at neutral and adaptive loci in endangered Rhodeus pseudosericeus populations.

Given the fact that threatened species are often composed of isolated small populations, spatial continuity or demography of the populations may be major factors that have shaped the species' genetic diversity. Thus, neutral loci have been the most commonly-used markers in conservation genetics. However, the populations under the influence of different environmental factors may have evolved in response to different selective pressures, which cannot be fully reflected in neutral genetic variation. Rhodeus pseudosericeus, a bitterling species (Acheilognathidae; Cypriniformes) endemic to the Korean Peninsula, are only found in some limited areas of three rivers, Daecheon, Han and Muhan, that flow into the west coast. Here, we genotyped 24 microsatellite loci and two loci (DAB1 and DAB3) of MHC class II peptide-binding ß1 domain for 222 individuals collected from seven populations. Our microsatellite analysis revealed distinctive differentiation between the populations of Daecheon and Muhan Rivers and the Han River populations, and populations were structured into two subgroups within the Han River. Apparent positive selection signatures were found in the peptide-binding residues (PBRs) of the MHC loci. The allelic distribution of MHC showed a degree of differentiation between the populations of Daecheon and Muhan Rivers and the Han River populations, partially similar to the results obtained for microsatellites, however showed rather complex patterns among populations in the Han River. Considering the apparent differences in the distribution of supertypes obtained based on the physicochemical differences induced by the polymorphisms of these PBRs, the differentiation in DAB1 between the two regional groups may result in the differences in immune function. No differentiation between these two regions was observed in the supertyping of DAB3, probably indicating that only DAB1 was associated with the response to locally specialized antigenic peptides.

Evidence of an ancient connectivity and biogeodispersal of a bitterling species, Rhodeus notatus, across the Korean Peninsula.

The modern-day distribution of freshwater fishes throughout multiple rivers is likely the result of past migration during times when currently separate drainages were once connected. Here, we used mitochondrial and microsatellite analyses for 248 individuals of Rhodeus notatus collected from seven different rivers to obtain better understand historical gene flow of freshwater fish on the Korean Peninsula. Based on our phylogenetic analyses, this Korean species originated through the paleo-Yellow River from China and first colonized near the west coast. These genetic data also provided evidence of estuary coalescences among the rivers flowing to the west and southwest coast on well-developed continental shelf. In addition, the pattern of population structure revealed the biogeodispersal route from the west coast to the south coast. It could be inferred that massive migration was not involved in the formation of southern populations, since the signature of historical genetic drift was clearly observed. Our study is the first genetic attempt to confirm hypotheses describing the migration of freshwater species towards the end of East Asia, which have previously been developed using only geological reasoning.

Genetic and phylogenetic structure of Hynobius quelpaertensis, an endangered endemic salamander species on the Korean Peninsula.

BACKGROUND: The Korean Peninsula is a small but unique area showing great endemic Hynobius diversity with H. quelpaertensis, H. yangi, H. unisacculus and three species candidates (HC1, HC3 and HC4). H. quelpaertensis is distributed in the southern part and in Jeju Island, while the remaining species have extremely narrow distributions. OBJECTIVES: To examine the genetic structure of H. quelpaertensis and the phylogenetic placement in Hynobius. METHODS: Three mitochondrial and six microsatellite loci were genotyped for 204 Hynobius quelpaertensis, three H. leechii, three H. yangi, three HC1, two H. unisacculus, three HC3, three HC4 and ten Japanses H. lichenatus. RESULTS: A high level of mitochondrial diversity was found in H. quelpaertensis. Our mitochondrial data showed evidence of a historical link between inland and Jeju Island despite the signature of founder effect likely experienced by the early island populations. However, our microsatellite analysis showed the fairly clear signature of isolation history between in- and island populations. Upon phylogenetic analysis, H. quelpaertensis, H. unisacculus and HC1 formed a cluster, whereas H. yangi belonged to a separate cluster. HC3 and HC4 were clustered with either H. quelpaertensis or H. yangi depending on the locus used. CONCLUSION: Our results show at least partially the historical imprints engraved by dispersal of Korean endemic Hynobius during Pleistocene, potentially providing a fundamental basis in determining the conservation units and finding management strategies for these species.

Polymorphism of MHC class IIB in an acheilognathid species, Rhodeus sinensis shaped by historical selection and recombination.

BACKGROUND: Rhodeus sinensis is a bitterling species occurring throughout the numerous freshwater systems on the East Asia. Here, we analyzed the diversity of the MHC class IIB (DAB) genes from this species, which may offer meaningful insights into evolutionary processes in this species as well as other bitterlings. RESULTS: Using cDNA and gDNA samples from 50 individuals, we discovered classical 140 allelic sequences that could be allocated into either DAB1 (Rhsi-DAB1) or DAB3 (Rhsi-DAB3). DAB sequences completely lacking the intron, but identical or similar to Rhsi-DAB1, were also discovered from our gDNA samples, and this intron loss likely originated from the retrotransposition events of processed mDNA. The ß1 domain was the most polymorphic in both Rhsi-DAB1 and -DAB3. Putative peptide biding residues (PBRs) in Rhsi-DAB1, but not in Rhsi-DAB3, exhibited a significant dN/dS, presumably indicating that different selection pressures have acted on those two DABs. Recombination between different alleles seemed to have contributed to the increase of diversity in Rhsi-DABs. Upon phylogenetic analysis, Rhsi-DAB1 and -DAB3 formed independent clusters. Several alleles from other species of Cypriniformes were embedded in the clade of Rhsi-DAB1, whereas Rhsi-DAB3 clustered with alleles from the wider range of taxa (Cyprinodontiformes), indicating that these two Rhsi-DABs have taken different historical paths. CONCLUSIONS: A great deal of MHC class IIB allelic diversity was found in R. sinensis, and gene duplication, selection and recombination may have contributed to this diversity. Based on our data, it is presumed that such historical processes have commonly or differently acted on the polymorphism of Rhsi-DAB1 and -DAB3.

Taxonomic characterization of Tanakia species (Acheilognathidae) using DNA barcoding analyses.

Tanakia is a bitterling genus with six species found in Far East Asia. Our aim was to construct the standard DNA barcode database available for the identification of six Tanakia species by comparing the range of intra- and inter-specific genetic distances, identifying the phylogenetic placement of each Tanakia species and providing the unique barcode characteristics that are specific to each species, using cytochrome oxidase I (COI) and cytochrome b (cyt b). Both loci failed to create a perfect barcoding gap between the ranges of inter- and intra-specific genetic distances, though interspecific COI distances were sufficiently greater than intraspecific values with only a few exceptions. In our phylogenetic analyses, T. koreensis and T. signifer did not form a monophyletic cluster of haplotypes in both loci. COI provided clear nucleotide characteristics that distinguish each species, whereas relatively fewer informative sites were found within the range of cyt b. Overall, COI could be regarded as appropriate species identification solution in Tanakia. Our analyses yielded some taxonomic issues that need the further investigation, and are expected to be helpful in the examination for the conservation status of Tanakia species that are on the verge of being endangered.

The complete mitochondrial genomes of three geographical lineages in short ninespine stickleback (Pungitius kaibarae) complex and their phylogenetic implication.

The short ninespine stickleback, Pungitius kaibarae, is a small gasterosteid species complex containing three geographical lineages: ND, NE and SE. Here, complete mitochondrial genomes of these three lineages were analyzed to estimate the genetic differentiation among them and to identify their phylogenetic placement in genus Pungitius. Although the overall genome structure was identical among those three lineages, the genome sizes were slightly different from each other, ranging from 16,489 to 16,500 bp. Upon robust phylogenetic tree inferred by Bayesian algorithm, ND and SE showed relatively higher affinity, and those three lineages formed a monophyletic group with Russian P. tymensis, clearly supporting previous studies.