Yong‐Jin Won

Ewha Womans University

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Robert C. Vrijenhoek

Monterey Bay Aquarium Research Institute

Ajit Kumar Patra

Indian Institute of Technology Kharagpur

Sook‐Jin Jang

Inha University

Eunji Park

University of British Columbia

Si-Yeong Jun

Ewha Womans University

Sook Jin Jang

Inha University

Phuong‐Thao Ho

Ewha Womans University

Yujin Chung

Kyonggi University

Sook-Jin Jang

Inha University

Maëva Perez

Hong Kong Baptist University

Cooperative Institutions

Ewha Womans University

Woods Hole Oceanographic Institution

Korea Institute of Ocean Science and Technology

Monterey Bay Aquarium Research Institute

Rutgers, The State University of New Jersey

Seoul National University

University of Washington

Korea Polar Research Institute

Ewha Womans University Medical Center

Scripps Institution of Oceanography

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Identification of Cichlid Fishes from Lake Malawi Using Computer Vision

PLoS ONE (2013)

Deokjin Joo Ye-seul Kwan Jongwoo Song Catarina Pinho Jody Hey

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.

Cichlid

Identification

10.1371/journal.pone.0077686

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Citations (19)

Deep-sea Hydrothermal Vents: Ecology and Evolution

Journal of Ecology and Environment (2006)

Yong‐Jin Won

Chemosynthesis

10.5141/jefb.2006.29.2.175

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Citations (1)

Additional file 5: Table S5. of Geographical structure of endosymbiotic bacteria hosted by Bathymodiolus mussels at eastern Pacific hydrothermal vents

Figshare (2017)

Phuong‐Thao Ho Eunji Park Soon Hyung Hong Eunhye Kim Kangchon Kim

Genetic diversity indices of symbiont 16S rRNA gene from 45 individuals of host Bathymodiolus mussels in the EPR and PAR. (XLSX 13Â kb)

Table (database)

10.6084/m9.figshare.c.3791164_d5

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Citations (0)

Additional file 6: Table S7. of Geographical structure of endosymbiotic bacteria hosted by Bathymodiolus mussels at eastern Pacific hydrothermal vents

Figshare (2017)

Phuong‐Thao Ho Eunji Park Soon Hyung Hong Eunhye Kim Kangchon Kim

Genetic diversity indices of symbiont protein-coding genes from 72 individuals of host Bathymodiolus mussels in the EPR, GAR, and PAR (based on 1% error correction criterion for the 454 pryosequencing raw data). (XLSX 48Â kb)

Table (database)

10.6084/m9.figshare.c.3791164_d6

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Characterization of Symbiont Populations in Life-History Stages of Mussels From Chemosynthetic Environments

Biological Bulletin (2005)

Jennifer L. Salerno Stephen A. Macko Steve J. Hallam Monika Bright Yong‐Jin Won

The densities of chemoautotrophic and methanotrophic symbiont morphotypes were determined in life- history stages (post-larvae, juveniles, adults) of two species of mussels (Bathymodiolus azoricus and B. heckerae) from deep-sea chemosynthetic environments (the Lucky Strike hydrothermal vent and the Blake Ridge cold seep) in the Atlantic Ocean. Both symbiont morphotypes were observed in all specimens and in the same relative proportions, regardless of life-history stage. The relative abundance of symbiont morphotypes, determined by transmission electron microscopy, was different in the two species: chemoautotrophs were dominant (13:1–18:1) in B. azoricus from the vent site; methanotrophs were dominant (2:1–3:1) in B. heckerae from the seep site. The ratio of CH4:H2S is proposed as a determinant of the relative abundance of symbiont types: where CH4:H2S is less than 1, as at the Lucky Strike site, chemoautotrophic symbionts dominate; where CH4:H2S is greater than 2, as at the seep site, methanotrophs dominate. Organic carbon and nitrogen isotopic compositions of B. azoricus (δ13C = −30‰; δ15N = −9‰) and B. heckerae (δ13C = −56‰; δ15N = −2‰) varied little among life-history stages and provided no record of a larval diet of photosynthetically derived organic material in the post-larval and juvenile stages.

Chemosynthesis

Cold seep

Petroleum seep

10.2307/3593123

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Citations (71)

A regulatory hydrogenase gene cluster observed in the thioautotrophic symbiont of Bathymodiolus mussel in the East Pacific Rise

Scientific Reports (2022)

Ajit Kumar Patra Maëva Perez Sook‐Jin Jang Yong‐Jin Won

Abstract 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 observed that some mussel symbionts either possess or lack genes for hydrogen metabolism within the single-ribotype population and host mussel species level. Here, we found a hydrogenase cluster consisting of additional H 2 -sensing hydrogenase subunits in a complete genome of B. thermophilus symbiont sampled from an individual mussel from the East Pacific Rise (EPR9N). Also, we found methylated regions sparsely distributed throughout the EPR9N genome, mainly in the transposase regions and densely present in the rRNA gene regions. CRISPR diversity analysis confirmed that this genome originated from a single symbiont strain. Furthermore, from the comparative analysis, we observed variation in genome size, gene content, and genome re-arrangements across individual hosts suggesting multiple symbiont strains can associate with B. thermophilus . The ability to acquire locally adaptive various symbiotic strains may serve as an effective mechanism for successfully colonizing different chemosynthetic environments across the global oceans by host mussels.

Symbiotic bacteria

Hydrogenase

Mytilidae

10.1038/s41598-022-26669-y

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Citations (2)

Environmental Acquisition of Thiotrophic Endosymbionts by Deep-Sea Mussels of the Genus Bathymodiolus

Applied and Environmental Microbiology (2003)

Yong‐Jin Won Steven Hallam G. D. O’Mullan Irvin L. Pan Kurt R. Buck

ABSTRACT Deep-sea Bathymodiolus mussels, depending on species and location, have the capacity to host sulfur-oxidizing (thiotrophic) and methanotrophic eubacteria in gill bacteriocytes, although little is known about the mussels' mode of symbiont acquisition. Previous studies of Bathymodiolus host and symbiont relationships have been based on collections of nonoverlapping species across wide-ranging geographic settings, creating an apparent model for vertical transmission. We present genetic and cytological evidence for the environmental acquisition of thiotrophic endosymbionts by vent mussels from the Mid-Atlantic Ridge. Open pit structures in cell membranes of the gill surface revealed likely sites for endocytosis of free-living bacteria. A population genetic analysis of the thiotrophic symbionts exploited a hybrid zone where two Bathymodiolus species intergrade. Northern Bathymodiolus azoricus and southern Bathymodiolus puteoserpentis possess species-specific DNA sequences that identify both their symbiont strains (internal transcribed spacer regions) and their mitochondria (ND4). However, the northern and southern symbiont-mitochondrial pairs were decoupled in the hybrid zone. Such decoupling of symbiont-mitochondrial pairs would not occur if the two elements were transmitted strictly vertically through the germ line. Taken together, these findings are consistent with an environmental source of thiotrophic symbionts in Bathymodiolus mussels, although an environmentally “leaky” system of vertical transmission could not be excluded.

Endosymbiosis

Scleractinia

10.1128/aem.69.11.6785-6792.2003

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Citations (154)

Complete mitochondrial genome of the moon jellyfish,Aureliasp. nov. (Cnidaria, Scyphozoa)

Mitochondrial DNA (2013)

Dae‐Sik Hwang Eunji Park Yong‐Jin Won Jae‐Seong Lee

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. After comparison of Aurelia sp. nov. with Aurelia aurita, we found low-protein similarity of orf969 (59%) and orf324 (75%), respectively, while the other 13 PCGs showed 80% to 98% protein similarities.

Scyphozoa

Aurelia aurita

10.3109/19401736.2013.775273

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Citations (8)

Complete mitochondrial genome of the jellyfish,Chrysaora quinquecirrha(Cnidaria, Scyphozoa)

Mitochondrial DNA (2013)

Dae-Sik Hwang Eunji Park Yong‐Jin Won Woojin Lee Kyoungsoon Shin

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 telomeres at both ends. The PCGs of C. quinquecirrha shows anti-G bias on 2nd and 3rd positions of PCGs as well as anti-C bias on 1st and 3rd positions of PCGs.

Scyphozoa

10.3109/19401736.2013.775272

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Citations (7)

Additional file 4: Table S3. of Geographical structure of endosymbiotic bacteria hosted by Bathymodiolus mussels at eastern Pacific hydrothermal vents

Figshare (2017)

Phuong‐Thao Ho Eunji Park Soon Hyung Hong Eunhye Kim Kangchon Kim

Bacterial symbiont community in the gill tissues of host mussels, B. thermophilus and B. antarcticus, based on NGS data of 16S ribosomal RNA gene from 45 individual host mussels. (XLSX 16Â kb)

Table (database)

10.6084/m9.figshare.c.3791164_d4

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Citations (0)