Ho Young Suk

Harnessing the Power of Genomics to Secure the Future of Seafood

Best use of scientific knowledge is required to maintain the fundamental role of seafood in human nutrition. While it is acknowledged that genomic-based methods allow the collection of powerful data, their value to inform fisheries management, aquaculture, and biosecurity applications remains underestimated. We review genomic applications of relevance to the sustainable management of seafood resources, illustrate the benefits of, and identify barriers to their integration. We conclude that the value of genomic information towards securing the future of seafood does not need to be further demonstrated. Instead, we need immediate efforts to remove structural roadblocks and focus on ways that support integration of genomic-informed methods into management and production practices. We propose solutions to pave the way forward.

Complete Mitochondrial Genomes of Carcinoscorpius rotundicauda and Tachypleus tridentatus (Xiphosura, Arthropoda) and Implications for Chelicerate Phylogenetic Studies

Horseshoe crabs (order Xiphosura) are often referred to as an ancient order of marine chelicerates and have been considered as keystone taxa for the understanding of chelicerate evolution. However, the mitochondrial genome of this order is only available from a single species, Limulus polyphemus. In the present study, we analyzed the complete mitochondrial genomes from two Asian horseshoe crabs, Carcinoscorpius rotundicauda and Tachypleus tridentatus to offer novel data for the evolutionary relationship within Xiphosura and their position in the chelicerate phylogeny. The mitochondrial genomes of C. rotundicauda (15,033 bp) and T. tridentatus (15,006 bp) encode 13 protein-coding genes, two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes. Overall sequences and genome structure of two Asian species were highly similar to that of Limulus polyphemus, though clear differences among three were found in the stem-loop structure of the putative control region. In the phylogenetic analysis with complete mitochondrial genomes of 43 chelicerate species, C. rotundicauda and T. tridentatus were recovered as a monophyly, while L. polyphemus solely formed an independent clade. Xiphosuran species were placed at the basal root of the tree, and major other chelicerate taxa were clustered in a single monophyly, clearly confirming that horseshoe crabs composed an ancestral taxon among chelicerates. By contrast, the phylogenetic tree without the information of Asian horseshoe crabs did not support monophyletic clustering of other chelicerates. In conclusion, our analyses may provide more robust and reliable perspective on the study of evolutionary history for chelicerates than earlier analyses with a single Atlantic species.

Population genetic structure and colonization history of short ninespine sticklebacks (Pungitius kaibarae).

The contemporary distribution and genetic structure of a freshwater fish provide insight into its historical geodispersal and geographical isolation following Quaternary climate changes. The short ninespine stickleback, Pungitius kaibarae, is a small gasterosteid fish occurring in freshwater systems on the Korean Peninsula and in southeast Russia. On the Korean Peninsula, P. kaibarae populations are distributed in three geographically separated regions: the NE (northeast coast), SE (southeast coast), and a limited area in the ND (Nakdong River). In this study, we used mitochondrial loci and microsatellites to investigate the evolutionary history of P. kaibarae populations by assessing their pattern of genetic structure. Our analyses revealed a marked level of divergence among three regional populations, suggesting a long history of isolation following colonization, although ND individuals showed relatively higher genetic affinity to populations from SE than those from NE. The populations from NE showed a great degree of interpopulation differentiation, whereas populations from SE exhibited only weak genetic structuring. Upon robust phylogenetic analysis, P. kaibarae formed a monophyletic group with Russian P. sinensis and P. tymensis with strong node confidence values, indicating that P. kaibarae populations on the Korean Peninsula originated from the southward migration of its ancestral lineage around the middle Pleistocene.

Pseudo but actually genuine: Rhodeus pseudosericeus provides insight into the phylogeographic history of the Amur bitterling

Geographic isolation and colonization events have been considered complimentary historical processes in shaping the contemporary structure of regional biotas and taxonomic diversity. Accordingly, insight regarding vicariance and geodispersal might be gained by the analysis of phylogenetic pattern of related but geographically isolated taxa. Here, we examined endangered Rhodeus pseudosericeus in the Korean Peninsula based on mitochondrial cytochrome b sequences to provide information regarding the evolutionary origin of Amur-European bitterlings, Rhodeus sericeus and Rhodeus amarus. Our data and the contemporary distribution of R. pseudosericeus indicate that founding individuals have colonized the western coast of the Korean Peninsula via the paleo-Huang He River and since been subdivided into populations isolated by drainage formation. Our phylogenetic analyses indicated that it was likely R. pseudosericeus had a sister relationship to the R. sericeus–amarus complex, indicating that the R. sericeus–amarus clade originated from the dispersal of either R. pseudosericeus or its ancestral lineage. The geodispersal scenario based on our phylogenetic analyses supports the previous hypothesis that the Amur River likely created confluences with some tributaries of the paleo-Huang He River. Overall, the present study offers new insight into the taxonomic entity of R. pseudosericeus and a more comprehensive understanding of the phylogeographic history of R. sericeus and European bitterling lineages.

Microsatellite variation in colonizing populations of yellow-legged Asian hornet, Vespa velutina nigrithorax, in South Korea

Introduction of exotic species poses a tremendous challenge to the preservation of original biodiversity and productivity in natural ecosystems. The yellow‐legged Asian hornet Vespa velutina nigrithorax, which is native to tropical/subtropical areas in Indo‐China, was identified in 2003 for the first time in South Korea and has established itself in a short period of time. Population genetic study of invasive species may provide exceptional opportunities to test evolutionary theory as well as patterns of colonization from the beginning of the process. Here, the genetic variability of this invasive hornet was examined using seven microsatellites to estimate the propagule pressure and to expect the spreading pathway of this invasive hornet across its range. Overall, there was a significant loss of genetic diversity in its invaded ranges compared to its native range, suggesting that this invasive hornet was introduced via a very small number of propagules. Our results also support that this invasive hornet has experienced a severe bottleneck, as a large reduction was mainly observed in the number of alleles but not in heterozygosity. No significant genetic structuring among populations was found. This study provides baseline information about the current demographic status of the invaded populations, which will help governing agencies prevent further invasions and manage native ecosystems.

Dynamic influence of patch size on occupancy of woodland birds

Throughout the long history of landscape ecology, scientists have devoted substantial efforts to understand potential forest patch size and isolation effects on the abundance and diversity of woodland species. Which bird species flourish or perish as a response to forest fragmentation may compose fundamental information for the reserve design and landscape management in a region. Here, we designed a bird survey of the urban forest areas in Dangjin city located on South Koreas west coast to test (1) if bird species richness follows the pattern predicted by species-area relationship and (2) if there is seasonal variation in the pattern. As expected, patch area was the most significant variable explaining patch occupancy of resident and summering woodland birds in every season. Our data about the number of dominant vegetation suggest that larger areas contain greater habitat heterogeneity and more diverse niches. About half of the resident species did not appear to be area-sensitive and were categorized as edge species. On the other hand, many summering species showed strong area-sensitivity, potentially avoiding small patches that are almost entirely edge habitats in urban landscape. Our results suggest that lots of contemporary forest edges, fragmented by agricultural or urban development, do not any more function for feeding or nesting places for those species.

Exploring the Utility of Partial Cytochrome c Oxidase Subunit 1 for DNA Barcoding of Gobies

Gobiids are hyperdiverse compared with other teleost groups, with about 2,000 species occurring in marine, freshwater, and blackish habitats, and they show a remarkable variety of morphologies and ecology. Testing the effectiveness of DNA barcodes on species that have emerged as a result of radiation remains a major challenge in evolutionary biology. Here, we used the cytochrome c oxidase subunit 1 (COI) sequences from 144 species of gobies and related species to evaluate the performance of distance-based DNA barcoding and to conduct a phylogenetic analysis. The average intra-genus genetic distance was considerably higher than that obtained in previous studies. Additionally, the interspecific divergence at higher taxonomic levels was not significantly different from that at the intragenus level, suggesting that congeneric gobies possess substantial interspecific sequence divergence in their COI gene. However, levels of intragenus divergence varied greatly among genera, and we do not provide sufficient evidence for using COI for cryptic species delimitation. Significantly more nucleotide changes were observed at the third codon position than that at the first and the second codons, revealing that extensive variation in COI reflects synonymous changes and little protein level variation. Despite clear signatures in several genera, the COI sequences did resolve genealogical relationships in the phylogenetic analysis well. Our results support the validity of COI barcoding for gobiid species identification, but the utilization of more gene regions will assist to offer a more robust gobiid species phylogeny.

Complete mitochondrial genome of endangered Rhodeus pseudosericeus and its implications for the reconstruction of phylogenetic relationship among Acheilognathinae species

Abstract Rhodeus pseudosericeus is a native bitterling to the Korean Peninsula and found in very limited areas with small census size. Here, its complete mitochondrial genome was analyzed to provide novel data for the reconstruction of phylogenetic relationship among Acheilognathinae species. The genome was a 16,574 bp long consisting of 1 putative control region, 2 rRNA genes, 22 tRNA and 13 protein-coding genes. The gene arrangement was completely identical to those observed in other Acheilognathinae species as well as in other cyprinid species. In our phylogenetic analyses, three major genera of Acheilognathinae indepedently formed monophyletic groups in the tree reconstructed based on the whole genome sequences, whereas Rhodeus was not recovered as a single monophyly when solely considering protein-coding genes, indicating that the taxonomic reevaluation is still required in this subfamily.

The mechanisms leading to ontogenetic diet shift in a microcanivore, Pterogobius elapoides (Gobiidae)

Abstract A variety of fish species undergo an ontogenetic change in prey selectivity, and several potentially interacting factors, including nutrient requirement, microhabitat change, and foraging ability, may account for the occurrence of the shift. Here we examine the foraging ecology and ontogenetic diet shift of a micro-carnivorous goby, Pterogobius elapoides (serpentine goby), dominant component of fish assemblage in shallow rocky areas off the coast in Korea and Japan. Although most other gobies are primarily benthic carnivores, P. elapoides is a semipelagic fish; however, little is known about how those species change their foraging tactics with growth. In our diet analyses, the most common diet was pelagic copepods and benthic amphipods, and diet shift was observed from pelagic to benthic with growth. The ontogenetic diet shift seems to be the result of the preference for energetically more profitable prey in larger-size classes as well as the results of different prey availability due to among-habitat variation in diet. However, differential food preference does not appear to affect individual scope for searching food. Several factors such as predation pressures and interspecific resource partitioning might contribute to the changes in diet observed among size classes, which were included in our ongoing tests.

Human-mediated processes affecting distribution and genetic structure of Squalidus multimaculatus, a freshwater cyprinid with small spatial range

ABSTRACT Endemic species typically have a narrow niche breadth, and are likely more vulnerable to extinction than more widespread taxa. Squalidus multimaculatus is a small cyprinid endemic to the Korean Peninsula, and its reported geographical range was restricted to several small rivers located along the southeast coast. Several populations of S. multimaculatus have supposedly been subject to a variety of recent anthropogenic actions. Here, we analyzed the pattern of genetic diversity within and among populations of S. multimaculatus using nine microsatellite loci to quantify the relative contributions of human-mediated processes to the contemporary distribution and genetic structure. Overall, low levels of genetic diversity were exhibited in the populations of S. multimaculatus. Genetic differentiations among populations were not completely represented by their geographical proximity, likely resulting from the low intrapopulation genetic variability and anthropogenic transplants. The most conspicuous outcome of the anthropogenic activities was the introgression of alleles from a closely related species, S. gracilis majimae. Our study showed that anthropogenic transplanting, even with only a small number of individuals, can challenge our conservation goal to maintain the species integrity that has long been shaped in evolutionary processes.