Yong-Jin Won

• Ewha Womans University

The cellular and molecular mechanisms governing sexual reproduction are conserved across eukaryotes. Nevertheless, hybridization can disrupt these mechanisms, leading to asexual reproduction, often accompanied by polyploidy. In this study, we investigate how ploidy level and ratio of parental genomes in hybrids affect their reproductive mode. We an...

The introduced Asian mud-tidal gastropod Batillaria attramentaria has been reported to quickly dominate its new habitat, Elkhorn Slough, USA, which has a different osmotic condition from its native habitat. This species has also been reported to have a substantial impact on the ecosystem of the new habitat. In this study, we compared the gene expre...

Batillaridae is a common gastropod family that occurs abundantly in the shallow coastal zone of the intertidal mudflats of the northwest Pacific Ocean, Australasia, and North America. In this family, Batillaria attramentaria is known for its biological invasion and colonization in estuarine and intertidal zones. It can endure and adapt the harsh in...

The cellular and molecular mechanisms governing sexual reproduction are highly conserved across eukaryotes. Nevertheless, hybridization can disrupt such machinery leading to asexual reproduction. To investigate how hybridization and polyploidization affect gametogenesis and reproductive outcomes of asexual hybrids, we conducted a comprehensive stud...

The cellular and molecular mechanisms governing sexual reproduction are highly conserved across eukaryotes. Nevertheless, hybridization can disrupt such machinery leading to asexual reproduction. To investigate how hybridization and polyploidization affect gametogenesis and reproductive outcomes of asexual hybrids, we conducted a comprehensive stud...

The hairy snails of the genus Alviniconcha are representative deep-sea hydrothermal vent animals distributed across the Western Pacific and Indian Ocean. Out of six known species in the genus Alviniconcha, only one nominal species of A. marisindica was found in the Indian Ocean from the Carlsberg Ridge (CR), Central Indian Ridge (CIR) to the northe...

The mytilid mussel Bathymodiolus thermophilus lives in the deep-sea hydrothermal vent regions due to its relationship with chemosynthetic symbiotic bacteria. It is well established that symbionts reside in the gill bacteriocytes of the mussel and can utilize hydrogen sulfide, methane, and hydrogen from the surrounding environment. However, it is ob...

The population divergence process of deep-sea vent invertebrates is driven by both biotic (e.g., dispersal during the larval stage) and abiotic factors such as deep-ocean currents, depth, and the geological setting of vents. However, little is known regarding the divergence of hydrothermal vent microorganisms. Therefore, our study sought to investi...

The mytilid mussel Bathymodiolus thermophilus lives in the deep-sea hydrothermal vent regions due to its symbiotic relationship with chemosynthetic Gammaproteobacteria species which reside inside specialized gill cells. The symbionts in the gill bacteriocytes oxidize the reduced sulfur amply available in the vent environment. Here we sequenced and...

Anthropogenic habitat alteration can rapidly disturb native fish species by hybridization with introduced species. In Korea, the construction of water conduits has unilaterally introduced the allopatrically separated fish species Cobitis tetralineata from the Seomjin River to the Dongjin River where its sister species C. nalbanti inhabits. To asses...

Vertical transmission of bacterial endosymbionts is accompanied by virtually irreversible gene loss that results in a progressive reduction in genome size. While the evolutionary processes of genome reduction have been well described in some terrestrial symbioses, they are less understood in marine systems where vertical transmission is rarely obse...

This article describes the experimental locomotor data used to study the general and adaptive responses to salt stress of the northern Pacific intertidal gastropod Batillaria attramentaria. The data were obtained from a series of 30-day experiments on snails acclimated to different salinity regimes. Snails were collected from coastal areas on the e...

Plasticity in salt tolerance can be crucial for successful biological invasions of novel habitats by marine gastropods. The intertidal snail Batillaria attramentaria, which is native to East Asia but invaded the western shores of North America from Japan 80 years ago, provides an opportunity to examine how environmental salinity may shape behaviora...

Given their recent switch to a vertically-transmitted intracellular lifestyle, the chemosynthetic bacteria associated with deep-sea vesicomyid clams are an excellent model system to study the processes underlying reductive genome evolution. In this study, we provide the first estimates of the relative contributions of drift, recombination and selec...

The morphologically similar populations of the Korean freshwater spined loach recently described as a new species Cobitis nalbanti (Actinopterygii: Cypriniformes: Cobitidae) inhabit the rivers and streams on the Korean Peninsula that flow into the Yellow Sea and the Korea Strait. These shallow sea areas have experienced recurrent sea-level rises an...

We describe a new vent mussel species, Gigantidas vrijenhoeki n. sp., from material collected at a depth of 2022 m in the newly discovered Onnuri Vent Field (OVF) during the 2018 expedition to the Central Indian Ridge. This large modioliform mussel thrives around diffusive vents in aggregation with another dominant hydrothermal vent mussel, Bathymo...

This article contains supplementary data from the research paper entitled “A newly discovered Gigantidas bivalve mussel from the Onnuri Vent Field on the northern Central Indian Ridge” [1], describes a new mussel species within the subfamily Bathymodiolinae named Gigantidas vrijenhoeki. Data are comprised of two parts: 1) shell image and molecular...

Salinity is one of the most crucial environmental factors that structures biogeographic boundaries of aquatic organisms, affecting distribution, abundance, and behavior. However, the association between behavior and gene regulation underlying acclimation to changes in salinity remains poorly understood. In this study, we investigated the effects of...

Genomic introgression through interspecific hybridization has been observed in some species of the freshwater fish family Cobitidae. Within this family, a Cobitis hankugensis–Iksookimia longicorpa diploid–triploid hybrid species complex on the Korean peninsula is unique in displaying hybridogenesis, a unisexual reproduction mode that allows hybrids...

Biological invasion of the intertidal gastropod Batillaria attramentaria from Japanese shoreline to the west seashore of the USA was documented about 100 years ago. This offers a valuable opportunity to study how changes in environmental salinity shape behavioral and genomic evolution of the snail. In this study, we investigated the effects of biot...

The recent discovery of two new species of kiwaid squat lobsters on hydrothermal vents in the Pacific Ocean and in the Pacific sector of the Southern Ocean has prompted a re-analysis of Kiwaid biogeographical history. Using a larger alignment with more fossil calibrated nodes than previously, we consider the precise relationship between Kiwaidae, C...

List of primers used in this study. (DOCX)

Predominant habitats as reported in publications–or observed during specimen collection—along with habitat designation in Beast 2.4.3 discrete trait analyses. (DOCX)

Maximum likelihood tree topology (best ML tree) of a nine-partition anomuran crustacean dataset generated in IQ-TREE 1.5.4. Node support numbers represent ML bootstrap percentages from 1000 non-parametric bootstrap replicates. (TIFF)

Supplementary materials and methods. (DOCX)

Classification, sampling locations/provenance and voucher ID of the species and GenBank accession numbers of genes used in this study. 'X' denotes missing data. GenBank accession numbers in bold are new sequences from this study and italicised numbers are existing genbank sequences that have been extended. (DOCX)

Gblocks 0.91 scheme for excising poorly or ambiguously aligned portions of rRNA sequences. (DOCX)

Substitution models used in this study as determined by PartitionFinder 2.1.1. (DOCX)

Output from Beast 2.4.3 analyses showing divergence date estimates and % probability of habitat assignment for key nodes within Chirostyloidea and Kiwaidae. (DOCX)

Maximum likelihood tree topology with the ultrafast bootstrap approximation method of a nine-partition anomuran crustacean dataset generated in IQ-TREE 1.5.4. Node support numbers represent ultrafast approximate bootstrap percentages from 100,000 replicates. (TIFF)

Maximum likelihood tree topology (best ML tree) of a fourteen-partition anomuran crustacean dataset generated in IQ-TREE 1.5.4. Node support numbers represent ML bootstrap percentages from 1000 non-parametric bootstrap replicates. (TIFF)

Maximum likelihood tree topology with the ultrafast bootstrap approximation method of a fourteen-partition anomuran crustacean dataset generated in IQ-TREE 1.5.4. Node support numbers represent ultrafast approximate bootstrap percentages from 100,000 replicates. (TIFF)

Species inhabiting deep-sea hydrothermal vents are strongly influenced by the geological setting, as it provides the chemical-rich fluids supporting the food web, creates the patchwork of seafloor habitat, and generates catastrophic disturbances that can eradicate entire communities. The patches of vent habitat host a network of communities (a meta...

We investigated whether tetraploidy in Iksookimia yongdokensis adds more species specific variation in its early life history characteristics. To this end, morphological and temporal characteristics were analysed using artificial fertilisation and laboratory culture, and the results were compared to seventeen other species of the family Cobitidae....

It remains a challenge in evolutionary genetics to elucidate how beneficial mutations arise and propagate in a population and how selective pressures on mutant alleles are structured over space and time. By identifying "sweeping haplotypes (SHs)" that putatively carry beneficial alleles and are increasing (or have increased) rapidly in frequency, a...

The genus Iksookimia contains six species of primary freshwater fishes that are endemic to South Korea. Previous phylogenetic studies, based on DNA sequence data from three or fewer loci, have suggested non-monophyly of the genus, providing inconsistent resolutions of the relationships of Iksookimia. Our coalescent and concatenation-based phylogene...

The Taebaek Mountains in South Korea serves as the most apparent biogeographic barrier for South Korean freshwater fishes, resulting in two distinct ichthyofaunal assemblages on the eastern (East/Japan Sea slope) and western (Yellow Sea and Korea Strait slopes) sides of the mountain range. Of nearly 100 species of native primary freshwater fishes i...

Ichthyofauna and fish community were investigated at 17 representative stations of the Dongjin River drainage system from spring to fall in 2014. The survey resulted in a list of 53 species belonging to 14 families structured into 4 distinctive parts along the river: uppermost-stream, upper-stream, mid-stream, and lower-stream. Comparison of specie...

Background Chemolithoautotrophic primary production sustains dense invertebrate communities at deep-sea hydrothermal vents and hydrocarbon seeps. Symbiotic bacteria that oxidize dissolved sulfur, methane, and hydrogen gases nourish bathymodiolin mussels that thrive in these environments worldwide. The mussel symbionts are newly acquired in each gen...

Cobitis nalbanti, new species, is described from the South Korean Han and Geum Rivers, draining to the Yellow Sea. It differs from its congeners by having a wide, ovoid lamina circularis; rounded scales with a large, slightly-displaced focal zone; a relatively long, protruded snout; the suborbital spine not reaching the center of the eye; the mandi...

The habitat, age and spawning characteristics of the Korean eastern spined loach, Iksookimia yongdokensis, were investigated to obtain baseline data for its ecological characteristics in the Chuksancheon (stream), Yeongdeok-gun, Gyeongsangbuk-do, Korea. The difference between the habitats of juveniles (0 +) and 1~4 year old loaches was that juvenil...

The sexually reproducing fish, Poeciliopsis monacha (Actinopterygii, Cyprinodontiformes, Poeciliidae), is the maternal ancestor of six hybrid biotypes that reproduce clonally. The gene content and order of its 16,818 bp mitochondrial genome is virtually identical with that of other sexually reproducing poeciliid fishes, providing no evidence for a...

Background The Equator and Easter Microplate regions of the eastern Pacific Ocean exhibit geomorphological and hydrological features that create barriers to dispersal for a number of animals associated with deep-sea hydrothermal vent habitats. This study examined effects of these boundaries on geographical subdivision of the vent polychaete Alvinel...

A new species of deep-sea yeti crab, Kiwa araonae, is described from a hydrothermal vent field, Mujin (“Misty Harbor”), at a depth of about 2000 m on the Australian-Antarctic Ridge (AAR), Southern Ocean. The Mujin vent field (62°11.79′S), in a large, unexplored gap in the Circum-Antarctic Ridge system, is the most southern record for a yeti crab to...

The Australian-Antarctic Ridge (AAR) is one of the largest unexplored regions of the global mid-ocean ridge system. Here, we report a multi-year effort to locate and characterize hydrothermal activity on two 1st-order segments of the AAR: KR1 and KR2. To locate vent sites on each segment, we used profiles collected by Miniature Autonomous Plume Rec...

The present study was conducted to determine the full rpoB and eight house-keeping gene sequences of 78 and 35, respectively, avian pathogenic E. coli (APEC) strains. Phylogenetic comparison with 66 E. coli and Shigella strains from GenBank and EMBL was also conducted. Based on the full rpoB sequence, 50 different rpoB sequence types (RSTs) were id...

Figure S1. Neighbor-joining tree of twenty unique haplotypes of COI (619 bp) from Korean Batillaria attramentaria. Batillaria multiformis was used as an outgroup.

Figure S2. The marginal posterior-probability distributions for population-demographic parameters of (A) population sizes, (B) migration rates, and (C) divergence times of IMa2 analyses with three populations of today: Yellow Sea (YS) group, South Sea (SS) group, and Jeju Island (JI) group, as described in figure 3..

To address the impacts of past climate changes, particularly since the last glacial period, on the history of the distribution and demography of marine species, we investigated the evolutionary and demographic responses of the intertidal batillariid gastropod, Batillaria attramentaria, to these changes, using the snail as a model species in the nor...

Abstract The complete mitochondrial genome of Ridgeia piscesae (Polychaeta, Siboglinidae), one of the dominant taxa in deep-sea hydrothermal vents, is reported here for the first time. The R. piscesae mitogenome is 15,002 bp in total length and includes 13 protein-coding gene sequences, small and large rRNA sequences and 22 tRNA sequences. All gene...

River connections via artificial canals will bring about secondary contacts between previously isolated fish species. Here, we present a genetic consequence of such a secondary contact between Cobitis fish species, C. lutheri in the Dongjin River, and C. tetralineata in the Seomjin River in Korea. The construction of water canals about 80 years ago...

Phylogenetic trees of haplotypes from the Dongjin River and nonhybridized allopatric populations of two Cobitis species of (A) Cytochrome b, (B) Ptr, (C) ENC1, and (D) SH3PX3 genes, based on unrooted neighbor- joining method. Dark and light gray shading rectangular boxes represent T-type and L-type group, respectively. Hybrid_Hap, Haplotypes from t...

Table S1. Values of Tajima's D and Fu's Fs, and their P-values in four loci (Cyt b, ENC1, Ptr and SH3PX3 genes). Table S2. Pairwise FST values among the Cobitis lutheri and C. tetralineata populations from nonhybridized allopatric localities (locality 1, 2, and 3 for C. lutheri; locality 7 and 8 for C. tetralineata) using the multilocus genotypic d...

Histogram of the number of individuals sorted by the type of Cyt b gene and hybrid classes. F2, F2 hybrids; B1, backcrosses with pure Cobitis tetralineata; P1, pure C. tetralineata.

The explosively radiating evolution of cichlid fishes of Lake Malawi has yielded an amazing number of haplochromine species estimated as many as 500 to 800 with a surprising degree of diversity not only in color and stripe pattern but also in the shape of jaw and body among them. As these morphological diversities have been a central subject of ada...

The dwarf loach, Kichulchoia brevifasciata, is a primary freshwater fish endemic to South Korea (Republic of Korea). Due to its limited geographic range, special habitat requirements, and scarcity, this species has been considered one of the most endangered cobitid loaches in the world. Gene tree and species tree reconstruction derived from mitocho...

Abstract We sequenced 16,971 bp of the linear mitochondrial DNA of the moon jellyfish Aurelia sp. nov. and characterized it by comparing with Aurelia aurita. They had 13 protein-coding genes (PCGs), 16S rRNA and 12S rRNA with three tRNAs (tRNA-Leu, tRNA-Ser(TGA), tRNA-Met). Both have another two PCGs, orf969 and orf324 with telomeres at both ends....

Abstract We sequenced 16,775 bp of the linear mitochondrial DNA of the jellyfish Chrysaora quinquecirrha and characterized them. C. quinquecirrha has 13 protein-coding genes (PCGs), 16S rRNA and 12S rRNA with 3 tRNAs (tRNA-Leu, tRNA-Ser(TGA), tRNA-Met) as shown in Aurelia sp. nov. Both have another two PCGs such as helicase and orf363 with telomere...

Background The inhabitants of deep-sea hydrothermal vents occupy ephemeral island-like habitats distributed sporadically along tectonic spreading-centers, back-arc basins, and volcanically active seamounts. The majority of vent taxa undergo a pelagic larval phase, and thus varying degrees of geographical subdivision, ranging from no impedance of di...

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 in...

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...

The phylum Cnidaria is comprised of remarkably diverse and ecologically significant taxa, such as the reef-forming corals, and occupies a basal position in metazoan evolution. The origin of this phylum and the most recent common ancestors (MRCAs) of its modern classes remain mostly unknown, although scattered fossil evidence provides some insights...

This article documents the addition of 299 microsatellite marker loci and nine pairs of single-nucleotide polymorphism (SNP) EPIC primers to the Molecular Ecology Resources (MER) Database. Loci were developed for the following species: Alosa pseudoharengus, Alosa aestivalis, Aphis spiraecola, Argopecten purpuratus, Coreoleuciscus splendidus, Garra...

Mitochondrial genomes of many nonbilaterian animals show high diversity of genome size and gene content, revealing many intergenic regions (IGRs), diverse repeats and additional genes. Here we present a new complete mitogenome of the cnidarian sea fan species, Calicogorgia granulosa (Anthozoa: Octocorallia) and its novel genomic features. The 20,24...

In a species with a large distribution relative to its dispersal capacity, geographic variation in traits may be explained by gene flow, selection, or the combined effects of both. Studies of genetic diversity using neutral molecular markers show that patterns of isolation by distance (IBD) or barrier effect may be evident for geographic variation...

DNA barcoding of Bryozoa or "moss animals" has hardly advanced and lacks reference sequences for correct species identification. To date only a small number of cytochrome c oxidase subunit I (COI) sequences from 82 bryozoan species have been deposited in the National Center for Biotechnology Information (NCBI) GenBank and Barcode of Life Data Syste...

This article documents the addition of 238 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Alytes dickhilleni, Arapaima gigas, Austropotamobius italicus, Blumeria graminis f. sp. tritici, Cobitis lutheri, Dendroctonus ponderosae, Glossina morsitans morsitans, Haplophilus subterr...

We sequenced the whole mitochondrial genome of Dendronephthya gigantea (Anthozoa: Octocorallia: Nephteidae), the first mitochondrial genome sequence report in the Family Nephtheidae. The mitochondrial genome of D. gigantea was 18,842 bp in length, and contained 14 protein coding genes (atp6 and 8, cox1-3, cytb, nd1-6 and 4L, and msh1), two ribosoma...

This article documents the addition of 411 microsatellite marker loci and 15 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Acanthopagrus schlegeli, Anopheles lesteri, Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergi...

The short-eared owl (Asia flammeus), which lives in open wetland habitats, has been threatened and become endangered in South Korea due to the destruction and loss of its habitats. However, the diet of the short-eared owl remains to be studied. The prey of the short-eared owl was monitored using molecular methods as an alternative tool. A total of...

Lepomis macrochirus from the family Centrarchidae, commonly known as Bluegill sunfish, is an introduced freshwater fish in Korea that thrives in lakes, ponds, reservoirs and rivers. Since its introduction into Korea in 1969, Lepomis macrochirus has rapidly dispersed out and increased in number almost all over the freshwater ecosystems in Korea. Con...

In ecological character displacement, traits involved in reproductive isolation may not evolve in arbitrary directions when changes in these traits are by-products of adaptation to an ecological niche. In reproductive character displacement, however, selection acts directly on reproductive characters to enhance the degree of reproductive isolation...

Title: Descriptive statistics of morphological characters in G. fultoni and G. vernalis. The values in a cell are mean ± standard deviation. See the Method for definitions of morphological characters. See Table 1 for sample sizes.