Molecular phylogeny reveals Cenonovaculina gen. nov. (Adapedonta: Pharidae), a new freshwater razor clam genus from Indochina
Ekgachai Jeratthitikul A * and Chirasak Sutcharit BA
B
Abstract
The razor clam genus Novaculina is a secondary marine-derived freshwater taxa within the otherwise exclusively marine family Pharidae. Novaculina currently comprises four valid species that are distributed allopatrically across several drainages in Asia. We employed an integrated approach, combining morphology and molecular phylogenetic analyses to elucidate the taxonomic placement of members within this genus. The multi-locus phylogenetic trees based on cytochrome c oxidase subunit I (COI), 16S rRNA and 28S rRNA gene sequences demonstrate that Novaculina is polyphyletic. Specimens identified as N. siamensis form a distinct clade that is not sister group to other currently recognised congeners. Furthermore, morphological examination reveals distinct characteristics in ‘N. siamensis’, namely a fused, fringed siphon, in contrast to the separated, smooth siphons observed in other species. Based on these findings, we propose the establishment of a new genus, Cenonovaculina gen. nov., to accommodate ‘N. siamensis’. The new genus is distinguished from other genera in having a short shell, deep pallial sinus, elongate, oval to bean-shaped anterior adductor scar and long fused siphons surrounded by conical tentacles.
ZooBank: urn:lsid:zoobank.org:pub:6E16FC43-5BBA-4791-A805-1C84859877A3
Keywords: freshwater razor clams, Indochina, marine-derived freshwater taxa, multi-locus phylogeny, new taxa, Pharidae, siphon anatomy, Thailand.
References
American Veterinary Medical Association (2020) AVMA guidelines for the euthanasia of animals. (AVMA) Available at https://www.avma.org/sites/default/files/2020-02/Guidelines-on-Euthanasia-2020.pdf
Baki MA, Hossain MM, Bhouiyan NA (2016) Checklist of freshwater mollusca (Gastropoda and Bivalvia) recorded from the Buriganga and Turag rivers, Dhaka, Bangladesh. The Festivus 48, 221-228.
| Crossref | Google Scholar |
Benson WH (1830) Description of Novaculina, a new genus of fresh-water bivalves, inhabiting the Ganges and its branches. Gleanings in Science 2, 63-65.
| Google Scholar |
Benson WH (1858) XXXVIII.—Characters of Tanysiphon, a new genus of fluviatile shells, allied to the Myacidæ. Annals and Magazine of Natural History 1, 407-410.
| Crossref | Google Scholar |
Bieler R, Mikkelsen PM, Collins TM, Glover EA, González VL, Graf DL, Harper EM, Healy J, Kawauchi GY, Sharma PP, Staubach S, Strong EE, Taylor JD, Tëmkin I, Zardus JD, Clark S, Guzmán A, McIntyre E, Sharp P, Giribet G (2014) Investigating the Bivalve Tree of Life – an exemplar-based approach combining molecular and novel morphological characters. Invertebrate Systematics 28, 32-115.
| Crossref | Google Scholar |
Bloomer HH (1905) Anatomy of certain species of Solenidae. Journal of Malacology 12, 78-85.
| Google Scholar |
Bloomer HH (1912) On the anatomy of species of Cultellus and Azor. Proceedings of the Malacological Society of London 10(1), 5-10.
| Google Scholar |
Bolotov IN, Aksenova OV, Bakken T, Glasby CJ, Gofarov MY, Kondakov AV, Konopleva ES, Lopes-Lima M, Lyubas AA, Wang Y, Bychkov AY, Sokolova AM, Tanmuangpak K, Tumpeesuwan S, Vikhrev IV, Shyu JBH, Win T, Pokrovsky OS (2018a) Discovery of a silicate rock-boring organism and macrobioerosion in fresh water. Nature Communications 9, 2882.
| Crossref | Google Scholar |
Bolotov IN, Vikhrev IV, Lopes-Lima M, Lunn Z, Chan N, Win T, Aksenova OV, Gofarov MY, Kondakov AV, Konopleva ES, Tumpeesuwan S (2018b) Discovery of Novaculina myanmarensis sp. nov. (Bivalvia: Pharidae: Pharellinae) closes the freshwater razor clams range disjunction in Southeast Asia. Scientific Reports 8, 16325.
| Crossref | Google Scholar |
Brandt RAM (1974) The non-marine aquatic Mollusca of Thailand. Archiv für Molluskenkunde 105, 1-423.
| Google Scholar |
Distel DL, Amin M, Burgoyne A, Linton E, Mamangkey G, Morrill W, Nove J, Wood N, Yang J (2011) Molecular phylogeny of Pholadoidea Lamarck, 1809 supports a single origin for xylotrophy (wood feeding) and xylotrophic bacterial endosymbiosis in Bivalvia. Molecular Phylogenetics and Evolution 61(2), 245-254.
| Crossref | Google Scholar | PubMed |
Dreyer H, Steiner G (2006) The complete sequences and gene organisation of the mitochondrial genomes of the heterodont bivalves Acanthocardia tuberculata and Hiatella arctica – and the first record for a putative ATPase subunit 8 gene in marine bivalves. Frontiers in Zoology 3, 13.
| Crossref | Google Scholar | PubMed |
Ghosh R (1920) Taxonomic studies on the soft parts of the Solenidae. Records of the Indian Museum 19, 47-78.
| Google Scholar |
Graf DL (2013) Patterns of freshwater bivalve global diversity and the state of phylogenetic studies on the Unionoida, Sphaeriidae, and Cyrenidae. American Malacological Bulletin 31(1), 135-153.
| Crossref | Google Scholar |
Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS (2018) UFBoot2: improving the ultrafast bootstrap approximation. Molecular Biology and Evolution 35(2), 518-522.
| Crossref | Google Scholar | PubMed |
Khan AN, Kamal D, Mahmud MM, Rahman MA, Hossain MA (2007) Diversity, distribution and abundance of benthos in Mouri River, Khulna, Bangladesh. International Journal of Sustainable Crop Production 2, 19-23.
| Google Scholar |
Kon K, Kurokura H, Hayashizaki K (2007) Role of microhabitats in food webs of benthic communities in a mangrove forest. Marine Ecology Progress Series 340, 55-62.
| Crossref | Google Scholar |
Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B (2017) PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular Biology and Evolution 34(3), 772-773.
| Crossref | Google Scholar | PubMed |
Liu YY, Zhang WZ (1979) A new species of freshwater razor clam, Novaculina chinensis, from Jiangsu Province, China. Acta Zootaxonomica Sinica 7, 356-357.
| Google Scholar |
Miller MA, Pfeiffer W, Schwartz T (2010) Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In ‘Proceedings of the Gateway Computing Environments Workshop (GCE)’, 14 November 2010, New Orleans, LA, USA. INSPEC Accession Number 11705685. (IEEE) 10.1109/GCE.2010.5676129
Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R (2020) IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution 37(5), 1530-1534.
| Crossref | Google Scholar | PubMed |
Morlet L (1889) Catalogue des coquilles recueillies, par M. Pavie, dans le Cambodge et le Royaume de Siam, et description d’espèces nouvelles. Journal de Conchyliologie. 37(2), 121-199 [In French].
| Google Scholar |
Nasution S, Mardalisa M, Effendi I, Nedi S (2022) Species identification and molecular analysis of the mangrove Bivalvia (Pharella acutidens) from Rupat Strait waters, Indonesia based on COI mtDNA. AACL Bioflux 15(2), 1040-1049.
| Google Scholar |
Ng TH, Jeratthitikul E, Sutcharit C, Chhuoy S, Pin K, Pholyotha A, Siriwut W, Srisonchai R, Hogan ZS, Ngor PB (2020) Annotated checklist of freshwater molluscs from the largest freshwater lake in Southeast Asia. ZooKeys 958, 107-141.
| Crossref | Google Scholar | PubMed |
Ngo QX, Sayenko EM, Lutaenko KA (2018) Bivalves composition and ecological aspects of the Ba Lai River, an estuary of the Mekong Delta, Vietnam. The Korean Journal of Malacology 34(3), 169-178.
| Crossref | Google Scholar |
Park J-K, Foighil DÓ (2000) Sphaeriid and corbiculid clams represent separate heterodont bivalve radiations into freshwater environments. Molecular Phylogenetics and Evolution 14(1), 75-88.
| Crossref | Google Scholar | PubMed |
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.
| Crossref | Google Scholar | PubMed |
Sharma PP, Zardus JD, Boyle EE, González VL, Jennings RM, McIntyre E, Wheeler WC, Etter RJ, Giribet G (2013) Into the deep: a phylogenetic approach to the bivalve subclass Protobranchia. Molecular Phylogenetics and Evolution 69(1), 188-204.
| Crossref | Google Scholar | PubMed |
Shu F, Zhu Q, Zhang N, Zhang X, Xie S (2013) Novaculina chinensis found in Lake Weishan, Shandong Province. Chinese Journal of Zoology 48, 278-280.
| Google Scholar |
Tamura K, Stecher G, Kumar S (2021) MEGA11: Molecular Evolutionary Genetics Analysis version 11. Molecular Biology and Evolution 38(7), 3022-3027.
| Crossref | Google Scholar | PubMed |
Taylor JD, Williams ST, Glover EA, Dyal P (2007) A molecular phylogeny of heterodont bivalves (Mollusca: Bivalvia: Heterodonta): New analyses of 18S and 28S rRNA genes. Zoologica Scripta 36(6), 587-606.
| Crossref | Google Scholar |
Vierna J, Cuperus J, Martínez‐Lage A, Jansen JM, Perina A, Van Pelt H, González‐Tizón AM (2014) Species delimitation and DNA barcoding of Atlantic Ensis (Bivalvia, Pharidae). Zoologica Scripta 43(2), 161-171.
| Crossref | Google Scholar |
von Cosel R (1990) An introduction to the razor shells (Bivalvia: Solenacea). In ‘The Bivalvia: Proceedings of a Memorial Symposium in Honour of Sir Charles Maurice Yonge (1899–1986) at the 9th International Malacological Congress’, 1986, Edinburgh, UK. (Ed. B Morton) pp. 283–311. (Hong Kong University Press: Hong Kong)
von Cosel R (1993) The razor shells of the eastern Atlantic. Part 1: Solenidae and Pharidae I (Bivalvia: Solenacea). Archiv für Molluskenkunde 122, 207-321.
| Crossref | Google Scholar |
Win T, Bolotov IN, Vikhrev IV, Lunn Z, Chan N, Konopleva ES, Gofarov MY, Tomilova AA, Kondakov AV (2021) Phylogeography and distribution of the freshwater razor clams Novaculina myanmarensis and N. gangetica in Myanmar, with notes on two doubtful nominal taxa described as Novaculina members (Bivalvia: Pharidae). Ecologica Montenegrina 40, 59-67.
| Crossref | Google Scholar |
Yu Z, Li Q, Kong L, Yu H (2015) Utility of DNA barcoding for Tellinoidea: a comparison of distance, coalescent and character-based methods on multiple genes. Marine Biotechnology 17(1), 55-65.
| Crossref | Google Scholar | PubMed |
Zhou Z, Song Y, Zheng Z, Liu Y, Yao H, Rao X, Lin G (2024) The complete mitochondrial genome and phylogenetic analysis of the freshwater shellfish Novaculina chinensis (Bivalvia: Pharidae). International Journal of Molecular Sciences 25, 67.
| Crossref | Google Scholar | PubMed |