Taxonomic position of holothurian Eupentacta fraudatrix (Echinodermata, Holothuroidea)
Authors/Creators
- 1. A.V. Zhirmunsky National Scientific Center of Marine Biology, Russian Academy of Sciences, Vladivostok, Russia|Far Eastern State Technical Fisheries University, Vladivostok, Russia
- 2. Zoological Institute of Russian Academy of Sciences, St. Petersburg, Russia
- 3. A.V. Zhirmunsky National Scientific Center of Marine Biology, Russian Academy of Sciences, Vladivostok, Russia
Description
Samples of the holothurian Eupentacta fraudatrix (Djakonov & Baranova in Djakonov, Baranova & Saveljeva, 1958) from the Sea of Japan were studied and the relationships of the genera Eupentacta and Sclerodactyla, as well as related taxa, were evaluated on the basis of phylogenetic analysis of the mitochondrial DNA COI and 16S rRNA genes. Using three methods, phylogenetic trees were constructed, and the degree of reliability of topological reconstructions was estimated by means of a nonparametric bootstrap test for the neighbor joining (NJ) and maximum likelihood (ML) techniques, as well as by a posteriori probability for Bayesian inference (BI) analysis. Genetic data confirm the validity of the assignment of Cucumaria fraudatrix to the genus Eupentacta Deichmann, 1938. The study of sequences obtained from the holothurian specimens collected in Russian waters, near the city of Vladivostok, and determined by morphological characters clearly indicate that these specimens belong to the genus Eupentacta and are assigned as E. fraudatrix . The specimens from China in GenBank named as Sclerodactyla multipes and used in the present study, were likely misidentified, and after re-examination they may be assigned to the genus Eupentacta, either as E. fraudatrix or another taxon. Analyses of morphological characters of S. multipes unequivocally affirm that this species must be excluded from Sclerodactyla Ayres, 1851 and is provisionally assigned to the genus Sclerothyone Thandar, 1989 based on the external morphological characters and the body wall ossicles.
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References
- Arndt A, Marquez C, Lambert P, Smith MJ (1996) Molecular phylogeny of eastern Pacific sea cucumbers (Echinodermata: Holothuroidea) based on mitochondrial DNA sequence. Molecular Phylogenetics and Evolution 6(3): 425–437. https://doi.org/10.1006/mpev.1996.0091
- Baranova ZI (1971) Echinoderms from the Possjet Bay of the Sea of Japan. Explorations of the fauna of the seas 8(16): 242–264. [In Russian]
- Baranova ZI (1979) Composition and distribution of holothurians (Echinodermata, Holothuroidea) on the shelf of the North-Western Pacific. In: Zhirmunsky AV (Ed.) XIV Pacific Science Congress. USSR, Khabarovsk, August 1979. Committee for marine sciences. Section F II. Marine biology. Section F II. a. Biology of shelf. Abstracts of papers. Pacific Sciences Association, Moscow, 76–77.
- Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Ostell J, Pruitt KD, Sayers EW (2018) GenBank. Nucleic Acids Research 46(D1): D41–D47. https://doi.org/10.1093/nar/gkx1094
- Chang F-Y (1948) Echinoderms of Tsingtao. Contributions from the Institute of Zoology National Academy of Peiping 4(2): 33–104. [pls 1–11]
- Clark HL (1901) Echinoderms from Puget Sound: observations made on the Echinoderms collected by the parties from Columbia University, in Puget Sound in 1896 and 1897. Proceedings Boston Society Natural History 29(15): 323–337. [pls 1–4]
- Clark HL (1902) The echinoderms of the Woods Hole Region. Bulletin of the United States Fish Commission 22: 547–576. [pls 1–14]
- Coe WR (1912) Echinoderms of Connecticut. State geological and natural History Survey, Bulletin 19: 1–152. [pls 1–32] https://doi.org/10.5962/bhl.title.56252
- Deichmann E (1930) The Holothurians of the western part of the Atlantic Ocean. Bulletin of the Museum of Comparative Zoology at Harvard College 71(3): 43–226. [pls 1–24]
- Deichmann E (1938) New holothurians from the western coast of North America and some remarks on the genus Caudina. Proceedings New England Zoological Club 16: 103–115.
- Djakonov AM, Baranova ZI, Saveljeva TS (1958) Note on holothurians (Holothuroidea) of the region of southern Sakhalin and the southern Kuril Islands. Research of the Far Eastern Seas of the USSR 5: 358–380. [In Russian]
- Edgar RC (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5): 1792–1797. https://doi.org/10.1093/nar/gkh340
- Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3(5): 294–299.
- Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Systematic Biology 59(3): 307–321. https://doi.org/10.1093/sysbio/syq010
- Hendler G, Miller JE, Pawson DL, Kier PM (1995) Sea Stars, Sea Urchins, and Allies Echinoderms of Florida and the Caribbean. Smithsonian Institution Press, Washington DC, [xii +] 390 pp.
- Kartavtsev YP (2011) Sequence divergence at Co‐1 and Cyt‐b mtDNA on different taxonomic levels and genetics of speciation in animals. Mitochondrial DNA 2: 55–65. https://doi.org/10.3109/19401736.2011.588215
- Kartavtsev YP (2013) Genetic divergence of species and other taxa. Geographical speciation and the genetic paradigm of Neo‐Darwinism in action. Uspekhi Sovremennoi Biologii 5: 419–451.
- Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A (2012) Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics (Oxford, England) 28(12): 1647–1649. https://doi.org/10.1093/bioinformatics/bts199
- Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33(7): 1870–1874. https://doi.org/10.1093/molbev/msw054
- Lambert P (1997) Sea cucumbers of British Columbia, Southeast Alaska and Puget Sound. Royal British Columbia Museum Handbook. UBC Press, Vancouver, 166 pp. [16 pls]
- Lanfear R, Calcott B, Ho SYW, Guindon S (2012) PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution 29(6): 1695–1701. https://doi.org/10.1093/molbev/mss020
- Lanfear R, Calcott B, Kainer D, Mayer C, Stamatakis A (2014) Selecting optimal partitioning schemes for phylogenomic datasets. BMC Evolutionary Biology 14(1): 82. https://doi.org/10.1186/1471-2148-14-82
- Leray M, Ho SL, Lin IJ, Machida RJ (2018) MIDORI server: A webserver for taxonomic assignment of unknown metazoan mitochondrial-encoded sequences using a curated database. Bioinformatics (Oxford, England) 34(21): 3753–3754. https://doi.org/10.1093/bioinformatics/bty454
- Levin VS, Bekova NV (2005) Dendrochirotida holothurians of the Far Eastern Seas by the collections of TINRO-center. Izvestiâ Tihookeanskogo naučno-issledovatel'skogo rybohozâjstvennogo centra 142: 310–322. [In Russian]
- Miller AK, Kerr AM, Paulay G, Reich M, Wilson NG, Carvajal JI, Rouse GW (2017) Molecular phylogeny of extant Holothuroidea (Echinodermata). Molecular Phylogenetics and Evolution 111: 110–131. https://doi.org/10.1016/j.ympev.2017.02.014
- Mitsukuri K (1912) Studies on Actinopodous Holothuroidea. Journal of the College of Science. Imperial University of Tokyo 29(2): 1–284. [pls 1–8] https://doi.org/10.5962/bhl.title.37880
- Nei M, Kumar S (2000) Molecular Evolution and Phylogenetics. Oxford University Press, Oxford and New York, [xiv +] 333 pp.
- Ohshima H (1918) Northwestern Pacific holothurians collected by the U.S. Fisheries Steamer "Albatross". Dobutsugaku zasshi [Zoological Magazine] 30: 177–182. [In Japanese]
- Palumbi S (1996) Nucleic acids II: The polymerase chain reaction. In: Hillis D, Moritz C, Mable B (Eds) Molecular Systematics. Sinauer & Associates, Sunderland, Massachusetts, 205–247.
- Panina EG (2015) List of species of the sea cucumbers (Holothuroidea) in the Far-Eastern seas of Russia, IV. Families Sclerodactylidae, Thyonidae, Ypsilorthuriidae and Thyonidiidae (Echinodermata: Holothuroidea: Dendrochirotida). Bulletin of Kamchatka State Technical University 33: 37–53. [In Russian] https://doi.org/10.17217/2079-0333-2015-33-37-53
- Panning A (1949) Versuch einer Neuordnung der Familie Cucumariidae (Holothuroidea, Dendrochirota). Zoologische Jarbücher. Abteilung für Systematik, Ökologie und Geographie der Tiere 78(4): 403–470.
- Paradis E, Claude J, Strimmer K (2004) APE: Analyses of phylogenetics and evolution in R language. Bioinformatics (Oxford, England) 20(2): 289–290. https://doi.org/10.1093/bioinformatics/btg412
- R Core Team (2021) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/
- Revell LJ (2023) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). BioRxiv 2023-03. https://doi.org/10.1101/2023.03.08.531791
- Rho BG, Shin S (1984) A systematic study on the Holothuroidea in Korea. 1 Dendrochirotida. Bulletin of Institute of Littoral Biota Mokpo National College 1(1): 43–55.
- Ronquist F, Teslenko M, Van Der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (2012) Mrbayes 3.2: Efficient bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61(3): 539–542. https://doi.org/10.1093/sysbio/sys029
- Schliep KP (2011) phangorn: Phylogenetic analysis in R. Bioinformatics (Oxford, England) 27(4): 592–593. https://doi.org/10.1093/bioinformatics/btq706
- Selenka E (1867) Beiträge zur Anatomie und Systematik der Holothurien. Zeitschrift für wissenschaftliche. Zoologie 17: 291–374. [pls 18–20]
- Shin S, Rho BG (1996) Illustrated Encyclopedia of Fauna and Flora of Korea. Vol. 36. Echinodermata. Ministry of Education, Seoul, 780 pp. [in Korean]
- Stukova TV, Levin VS (1990) Age-related changes in the spicules of holothurian Eupentacta fraudatrix. Vladivostok. Manuscript deposited in VINITI on 09/20/1990, No. 5109 B90, 17 pp. [In Russian]
- Thandar A (2021) Nomenclatural changes in some sea cucumbers with the erection of a new genus and description of a Thyone? juvenile (?n. sp.) from the Gulf of California (Echinodermata: Holothuroidea: Dendrochirotida). Zootaxa 5026(4): 507–526. https://doi.org/10.11646/zootaxa.5026.4.3
- Théel H (1886) Report on the Holothuroidea dredged by HMS Challenger, during the years 1873–1876. Part II. Scientific Results of the HMS Challenger during the years 1873–1876. Zoology 14(39): 1–290. [pls 1–16]
- Turanov SV, Kartavtsev YP (2014) Taxonomic Composition and Distribution of Sand Lances from the Genus Ammodytes (Perciformes: Ammodytidae) in the North Pacific. Russian Journal of Marine Biology 40(6): 447–454. https://doi.org/10.1134/S1063074014060212
- Ward RD (2009) DNA barcode divergence among species and genera of birds and fishes. Molecular Ecology Resources 4(4): 1077–1085. https://doi.org/10.1111/j.1755-0998.2009.02541.x
- WoRMS (2024a) Eupentacta Deichmann, 1938. https://www.marinespecies.org/aphia.php?p=taxdetails&id=528610 [Accessed on 2023-10-10]
- WoRMS (2024b) Eupentacta fraudatrix (D'yakonov & Baranova in D'yakonov, Baranova & Savel'eva, 1958). https://www.marinespecies.org/aphia.php?p=taxdetails&id=529482 [Accessed on 2024-03-29]
- WoRMS (2024c) Sclerodactyla Ayres, 1851. https://marinespecies.org/aphia.php?p=taxdetails&id=158531 [Accessed on 2024-03-29]