Integrative Description of Cryptic Tigriopus Species From Korea Using MALDI-TOF MS and DNA Barcoding

Yeom, Jisu; Park, Nayeon; Jeong, Raehyuk; Lee, Wonchoel

doi:10.3389/fmars.2021.648197

Cited by 12 publications

(9 citation statements)

References 54 publications

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“…In line with previous studies on marine copepods (Riccardi et al, 2012, Laakmann et al, 2013, Bode et al, 2017, Kaiser et al, 2018, Rossel & Martinez Arbizu, 2018a, Renz et al, 2021, Yeom et al, 2021, our results clearly support the high discriminatory power of proteomic fingerprinting on species level in this taxonomic group. All specimens were correctly assigned to the different 27 species by a RF model for classification with only low sensitivity to data processing indicating high robustness of the method.…”

Section: Species Identification and Species-specific Markerssupporting

confidence: 92%

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Perspectives of species identification by MALDI-TOF MS in monitoring - stability of proteomic fingerprints in marine epipelagic copepods

Peters

Laakmann

Rossel

et al. 2022

Preprint

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We analyzed robustness of species identification based on proteomic composition to data processing and intraspecific variability, specificity and sensitivity of species-markers as well as discriminatory power of proteomic fingerprinting and its sensitivity to phylogenetic distance. Our analysis is based on MALDI-TOF MS data from 32 marine copepod species coming from 13 regions (North and Central Atlantic and adjacent seas). A random forest (RF) model correctly classified all specimens to species level with only small sensitivity to data processing, demonstrating the strong robustness of the method. Compounds with high specificity showed low sensitivity i.e., identification was rather based on complex pattern-differences than on presence of single markers. Proteomic distance was not consistently related to phylogenetic distance. A species-gap in proteome composition appeared at 0.8 Euclidean distance when using only specimens from the same sample. When other regions or seasons were included, intra-specific variability increased, resulting in overlaps of intra- and inter-specific distance. Highest intra-specific distances (> 0.8) were observed between specimens from brackish and marine habitats i.e., salinity likely affects proteomic patterns. When testing library sensitivity of the RF model to regionality, strong misidentification was only detected between two congener pairs. Still, choice of reference library may have an impact on identification of closely related species and should be tested before routine application. We envision high relevance of this time- and cost-efficient method for future zooplankton monitoring as it provides not only in-depth taxonomic resolution for counted specimens but also add-on information e.g., on developmental stage or environmental conditions.

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Section: Species Identification and Species-specific Markerssupporting

confidence: 92%

“…In the aquatic realm, research is mainly focused on groups which hold pivotal positions in marine and limnic food webs, i.e. copepods (Riccardi et al, 2012, Laakmann et al, 2013, Bode et al, 2017, Kaiser et al, 2018, Yeom et al, 2021, Renz et al, 2021, cladocerans (Hynek et al, 2018) and fish (Volta et al, 2012, Maasz et al, 2017.…”

Section: Introductionmentioning

confidence: 99%

Perspectives of species identification by MALDI-TOF MS in monitoring - stability of proteomic fingerprints in marine epipelagic copepods

Peters

Laakmann

Rossel

et al. 2022

Preprint

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“…Thus, we assumed that S . intermedia has high intra-population variability in this leg, although the details of P5 are important for separating harpacticoid species ( e.g ., Kim, Lee & Huys, 2021 ; Yeom et al, 2021 ).…”

Section: Resultsmentioning

confidence: 99%

Taxonomic review of the genus Stenocaris Sars (Copepoda, Harpacticoida, Cylindropsyllidae), with (re)descriptions of two Stenocaris species from the Far East

Kim

Cho

Yoon

et al. 2023

PeerJ

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The taxonomic concept of the genus Stenocaris Sars, 1909 is uncertain because none of the synapomorphies for the species of Stenocaris are defined. Detailed comparison of previous records of Stenocaris minor (T. Scott, 1892) from different localities reveals that this species represents a species complex composed of two species, S. minor s. str. and S. minor sensu Cottarelli & Venanzetti, 1989. Because the latter species has fundamental differences in the nature of the fifth leg in females and the sexual dimorphism of the second leg in males, we propose a new species for S. minor sensu Cottarelli & Venanzetti, 1989, S. figaroloensis sp. nov. We also suggest that S. minor sensu Apostolov, 1971, S. minor sensu Marinov, 1971, and S. minor sensu Apostolov & Marinov, 1988 from the Black Sea and S. minor sensu Wilson, 1932 from North America should be relegated to species inquirenda in the genus. Taxonomic review of the morphology of all Stenocaris species indicated that the generic concept must be restricted to accommodate S. minor s. str., S. gracilis Sars, 1909, S. intermedia Itô, 1972, S. figaroloensis sp. nov., and the South Korean new species, S. marcida sp. nov., based on the synapomorphic condition of the confluent fifth leg in males. As a result of our analysis, two Stenocaris species, S. baltica Arlt, 1983 and S. pygmaea Noodt, 1955, are transferred to the genus Vermicaris Kornev & Chertoprud, 2008 as V. baltica (Arlt, 1983) comb. nov. and V. pygmaea (Noodt, 1955) comb. nov. based on the synapomorphic characters of a reduced condition of the second and fifth legs. Additionally, S. arenicola Wilson, 1932 and S. kliei (Kunz, 1938) are allocated to a new genus, Huysicaris gen. nov., mainly characterized by obvious caudal rami with a recurved dorsal spinous process and convex inner margins, as H. arenicola (Wilson, 1932) comb. nov. and H. kliei (Kunz, 1938) comb. nov. A marine interstitial harpacticoid collected from the subtidal substrate off Dok-do Island in the East Sea of South Korea is proposed as S. marcida sp. nov. and the distribution of S. intermedia, originally known from its type locality in Japanese waters only, is extended to the East Sea of Korea and Russia. We provide their detailed descriptions and illustrations and discuss the morphological characters supporting their identities.

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“…Thus, with good-quality measurement as a prerequisite, proteome-based data are generally capable of providing an accurate picture of species richness, which is also supported on community level by the Mantel test. Also, even though high overlap of species defined by proteome fingerprinting and by COI DNA barcoding was shown various times (Bode et al 2017;Renz et al 2021;Yeom et al 2021), none of the methods can claim to actually show natural species boundaries. Different methods can, even applied to the same data, return different species boundaries as is shown by the comparison of GMYC and ABGD.…”

Section: Discussionmentioning

confidence: 99%

Evaluating species richness using proteomic fingerprinting and DNA barcoding—a case study on meiobenthic copepods from the Clarion Clipperton Fracture Zone

et al. 2022

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The Clarion Clipperton Fracture Zone (CCZ) is a vast deep-sea region harboring a highly diverse benthic fauna, which will be affected by potential future deep-sea mining of metal-rich polymetallic nodules. Despite the need for conservation plans and monitoring strategies in this context, the majority of taxonomic groups remain scientifically undescribed. However, molecular rapid assessment methods such as DNA barcoding and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) provide the potential to accelerate specimen identification and biodiversity assessment significantly in the deep-sea areas. In this study, we successfully applied both methods to investigate the diversity of meiobenthic copepods in the eastern CCZ, including the first application of MALDI-TOF MS for the identification of these deep-sea organisms. Comparing several different species delimitation tools for both datasets, we found that biodiversity values were very similar, with Pielou’s evenness varying between 0.97 and 0.99 in all datasets. Still, direct comparisons of species clusters revealed differences between all techniques and methods, which are likely caused by the high number of rare species being represented by only one specimen, despite our extensive dataset of more than 2000 specimens. Hence, we regard our study as a first approach toward setting up a reference library for mass spectrometry data of the CCZ in combination with DNA barcodes. We conclude that proteome fingerprinting, as well as the more established DNA barcoding, can be seen as a valuable tool for rapid biodiversity assessments in the future, even when no reference information is available.

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Integrative Description of Cryptic Tigriopus Species From Korea Using MALDI-TOF MS and DNA Barcoding

Cited by 12 publications

References 54 publications

Perspectives of species identification by MALDI-TOF MS in monitoring - stability of proteomic fingerprints in marine epipelagic copepods

Perspectives of species identification by MALDI-TOF MS in monitoring - stability of proteomic fingerprints in marine epipelagic copepods

Taxonomic review of the genus Stenocaris Sars (Copepoda, Harpacticoida, Cylindropsyllidae), with (re)descriptions of two Stenocaris species from the Far East

Evaluating species richness using proteomic fingerprinting and DNA barcoding—a case study on meiobenthic copepods from the Clarion Clipperton Fracture Zone

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