Yong-Jin Won

Dispersal barriers and isolation among deep-sea mussel populations (Mytilidae: Bathymodiolus ) from eastern Pacific hydrothermal vents

Deep‐sea hydrothermal vent species are widely dispersed among habitat islands found along the global mid‐ocean ridge system. We examine factors that affect population structure, gene flow and isolation in vent‐endemic mussels of the genus Bathymodiolus from the eastern Pacific Ocean. Mussels were sampled from localities including the Galapagos Rift (GAR, 0°48′ N; 86°10′ W) and the East Pacific Rise (EPR, 13° N to 32° S latitude) across a maximum distance of 4900 km. The sampled range crossed a series of topographical features that interrupt linear aspects of the ridge system, and it encompassed regions of strong cross‐axis currents that could impede along‐axis dispersal of mussel larvae. Examinations of mitochondrial DNA sequences and allozyme variation revealed significant barriers to gene flow along the ridge axis. All populations from the GAR and EPR from 13° N to 11° S were homogeneous genetically and appeared to experience unimpeded high levels of interpopulational gene flow. In contrast, mussels from north and south of the Easter Microplate were highly divergent (4.4%), possibly comprising sister‐species that diverged after formation of the microplate ≈ 4.5 Ma. Strong cross‐axis currents associated with inflated bathymetry of the microplate region may reinforce isolation across this region.

Using nuclear haplotypes with microsatellites to study gene flow between recently separated Cichlid species

When populations or species have recently separated they often share genetic variation. However, it can be difficult to determine whether shared polymorphisms are the result of gene flow, the result of the persistence of variation in both populations since the time of common ancestry, or both of these factors. We have developed an empirical protocol for using loci that include unique nuclear DNA sequence haplotypes together with linked microsatellites or short tandem repeats (STRs). These ‘HapSTRs’ offer the potentially high resolution associated with the high mutation rate of STRs, together with the advantages of low homoplasy of unique sequence DNA. We also describe a new procedure for estimating the likelihood of HapSTR data under an Isolation with Migration model. An example using Cichlid fishes from Lake Malawi is described. The analysis suggests that the species have been exchanging genes since the time they began to diverge.

Cytonuclear disequilibrium in a hybrid zone involving deep-sea hydrothermal vent mussels of the genus Bathymodiolus

A hybrid zone involving the deep‐sea mussels, Bathymodiolus azoricus and B. puteoserpentis, was recently discovered at Broken Spur hydrothermal vent field (29°10′ N, 43°10′ W) along an intermediate segment of the Mid‐Atlantic Ridge axis. Examination of nuclear (allozymes) and cytoplasmic (mitochondrial DNA) gene markers in a new sample from Broken Spur revealed significant cytonuclear disequilibrium caused by an excess of the parental types (coupling phase) and a deficiency of recombinants (repulsion phase). An assignment test of individual multilocus genotypes also revealed an excess of parental genotypes in the admixed population. These results support the hypothesis that the Broken Spur mussel population comprises a nonequilibrium mixture of parental immigrants and hybrid individuals.

Postglacial range shift and demographic expansion of the marine intertidal snail Batillaria attramentaria

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 northwest Pacific. We applied phylogeographic and divergence population genetic approaches to mitochondrial COI sequences from B. attramentaria. To cover much of its distributional range, 197 individuals collected throughout Korea and 507 publically available sequences (mostly from Japan) were used. Finally, a Bayesian skyline plot (BSP) method was applied to reconstruct the demographic history of this species. We found four differentiated geographic groups around Korea, confirming the presence of two distinct, geographically subdivided haplogroups on the Japanese coastlines along the bifurcated routes of the warm Tsushima and Kuroshio Currents. These two haplogroups were estimated to have begun to split approximately 400,000 years ago. Population divergence analysis supported the hypothesis that the Yellow Sea was populated by a northward range expansion of a small fraction of founders that split from a southern ancestral population since the last glacial maximum (LGM: 26,000–19,000 years ago), when the southern area became re-submerged. BSP analyses on six geographically and genetically defined groups in Korea and Japan consistently demonstrated that each group has exponentially increased approximately since the LGM. This study resolved the phylogeography of B. attramentaria as a series of events connected over space and time; while paleoceanographic conditions determining the connectivity of neighboring seas in East Asia are responsible for the vicariance of this species, the postglacial sea-level rise and warming temperatures have played a crucial role in rapid range shifts and broad demographic expansions of its populations.

Identification of cichlid fishes from Lake Malawi using computer vision.

Background 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 adaptive speciation and taxonomic classification, such high diversity could serve as a foundation for automation of species identification of cichlids. Methodology/Principal Finding Here we demonstrate a method for automatic classification of the Lake Malawi cichlids based on computer vision and geometric morphometrics. For this end we developed a pipeline that integrates multiple image processing tools to automatically extract informative features of color and stripe patterns from a large set of photographic images of wild cichlids. The extracted information was evaluated by statistical classifiers Support Vector Machine and Random Forests. Both classifiers performed better when body shape information was added to the feature of color and stripe. Besides the coloration and stripe pattern, body shape variables boosted the accuracy of classification by about 10%. The programs were able to classify 594 live cichlid individuals belonging to 12 different classes (species and sexes) with an average accuracy of 78%, contrasting to a mere 42% success rate by human eyes. The variables that contributed most to the accuracy were body height and the hue of the most frequent color. Conclusions Computer vision showed a notable performance in extracting information from the color and stripe patterns of Lake Malawi cichlids although the information was not enough for errorless species identification. Our results indicate that there appears an unavoidable difficulty in automatic species identification of cichlid fishes, which may arise from short divergence times and gene flow between closely related species.

Genomic replacement of native Cobitis lutheri with introduced C. tetralineata through a hybrid swarm following the artificial connection of river systems

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 has unidirectionally introduced C. tetralineata into the native habitat of C. lutheri, and then these species have hybridized in the main stream section of the Dongjin River. According to the divergence population genetic analyses of DNA sequence data, the two species diverged about 3.3 million years ago, which is interestingly coincident with the unprecedented paleoceanographic change that caused isolations of the paleo-river systems in northeast Asia due to sea-level changes around the late Pliocene. Multilocus genotypic data of nine microsatellites and three nuclear loci revealed an extensively admixed structure in the hybrid zone with a high proportion of various post-F1 hybrids. Surprisingly, pure native C. lutheri was absent in the hybrid zone in contrast to the 7% of pure C. tetralineata. Such a biased proportion must have resulted from the dominant influence of continually introducing C. tetralineata on the native C. lutheri which has no supply of natives from other tributaries to the hybrid zone due to numerous low-head dams. In addition, mating experiments indicated that there is no discernible reproductive isolation between them. All the results suggest that the gene pool of native C. lutheri is being rapidly replaced by that of continually introducing C. tetralineata through a hybrid swarm for the last 80 years, which will ultimately lead to the genomic extinction of natives in this hybrid zone.

Cobitis nalbanti , a new species of spined loach from South Korea, and redescription of Cobitis lutheri (Teleostei: Cobitidae)

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 mandibular barbel not reaching the anterior edge of the eye; usually 12-14 dark brown blotches in the fourth Gambettas zone; a single elongated black spot on the upper part of the caudal-fin base; the only streak on the head running from the tip of the snout to the nape, across the eye; 2n=48-51 and NF=66. Cobitis nalbanti was previously identified as C. lutheri. Morphological analysis of C. lutheri shows that it is distinct in having a short obtuse snout, the suborbital spine reaching the center of the eye, the mandibular barbel reaching the anterior edge of the eye, usually less than 12 dark brown blotches in the fourth Gambettas zone, two spots at the caudal-fin base, several dark streaks on the head, and 2n=50, NF=70. A lectotype is selected for C. lutheri. Cobitis lutheri has a wide distribution in the Amur River basin, several rivers flowing into the Sea of Japan (East Sea), and in the northern part of Sakhalin Island.