Phylogenetic and Genetic Distance Analysis of the Mangrove Worm (Namalycastis) Based on the 18S rRNA Gene Using in Silico Methods
Abstract
Namalycastis is a polychaete worm that inhabits dynamic aquatic environments and exhibits high genetic and morphological variability. This study investigates the phylogeny of the genus Namalycastis through an in silico analysis using the 18S ribosomal RNA (rRNA) gene. This genetic marker is considered ideal as it combines conserved and variable regions, both essential for taxonomic and evolutionary analyses. The objective of this research was to examine the phylogenetic relationships and genetic distances among 12 species of the genus Namalycastis based on their 18S rRNA gene sequences. DNA sequences were obtained from the NCBI database and aligned using Clustal-W in MEGA XI software. Phylogenetic reconstruction was performed using the Neighbor-Joining method with 1000 bootstrap replications, applying the Kimura 2-Parameter (K2P) model. The results revealed that Namalycastis jaya shares a very close evolutionary relationship with Namalycastis abiuma, forming a monophyletic clade that is distinct from Namalycastis hawaiiensis. The genetic distances among N. jaya, N. abiuma, and N. abiuma group sp. indicate a close evolutionary affinity, whereas N. hawaiiensis displays greater genetic divergence from the other two species. Overall, this study demonstrates that the 18S rRNA gene is an effective molecular marker for identifying phylogenetic relationships among Namalycastis species. The findings also highlight the potential of in silico methods in elucidating evolutionary patterns within the genus Namalycastis.
References
Abe, H., Tanaka, M., & Ueno, Y. (2017). First report of the non-native freshwater nereidid polychaete namalycastis hawaiiensis (Johnson, 1903) from a private goldfish aquarium in eastern Japan. BioInvasions Records, 6(3), 217–223. https://doi.org/10.3391/bir.2017.6.3.06
Abushattal, S., Alnasarat, H., Alnaimat, S. M., & Eid, E. (2024). The use of 18S rRNA for identification of the first record of Tadpole Shrimp Lepidurus apus (Linnaeus, 1758) from Jordan. Biodiversitas, 25(3), 1223–1229. https://doi.org/10.13057/biodiv/d250338
Alves, P. R., Glasby, C. J., Paiva, P. C., & Santos, C. S. G. (2024). Is Namalycastis abiuma (Grube, 1871) (Annelida: Nereididae) restricted to its type-locality? Evidence from morphological and molecular data. Ocean and Coastal Research, 72(suppl 1). https://doi.org/10.1590/2675-2824072.23098
Aulia, A. (2022). Studi In Silico Potensi DNA Barcode Berbasis DNA Kloroplas (CpDNA) untuk Identifikasi Variasi Genetik Opuntia sp. Jurnal Syntax Admiration, 3(11), 1383–1394. https://doi.org/10.46799/jsa.v3i11.512
Birader, K. (2023). Journal of Biodiversity & Endangered Species Perspective Genetic Diversity and the Adaptation of Species to Changing Environments. Journal of Biodiversity & Endangered Species, 3(11), 1–2. https://doi.org/10.37421/2332-2543.2023.11.474
E. Gutiérrez, E., & S. T. Garbino, G. (2018). Species delimitation based on diagnosis and monophyly, and its importance for advancing mammalian taxonomy. Zoology Research, 39(5), 301–308. https://doi.org/10.24272/j.issn.2095-8137.2018.037
Hayden, J. E. (2020). Monophyletic classification and information content. Cladistics, 36(4), 424–436. https://doi.org/10.1111/cla.12410
Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16(2), 111–120. https://doi.org/10.1007/BF01731581
Magesh, M., Kvist, S., & Glasby, C. (2012). Description and phylogeny of Namalycastis jaya sp. n. (Polychaeta, Nereididae, Namanereidinae) from the southwest coast of India. ZooKeys, 238, 31–43. https://doi.org/10.3897/zookeys.238.4014
Mallet, J. (2007). Species, Concepts of. Encyclopedia of Biodiversity, 1–15. https://doi.org/10.1016/B0-12-226865-2/00254-6
Mulyani, L., Junardi, & Kurniatuhadi, R. (2023). The Composition of Arthropods in Nipah Fronds Decomposition at Sungai Kakap Mangrove Area in the West Kalimantan. Jurnal Biologi Tropis, 23(1), 208–213. https://doi.org/10.29303/jbt.v23i4b.5718
Panirman, J. V., Setyawati, T. R., & Junardi, J. (2023). Colonization of Nipa Worms (Namalycastis spp.) Based on Differences in Depth of Placement of Nipah Fronds in Kakap River of West Kalimantan. Jurnal Biologi Tropis, 23(2), 352–359. https://doi.org/10.29303/jbt.v23i2.6165
Romadhona, E. I., Megawati, N., Widantara, H., Sutanti, S., Rahman Ardiansyah, A., Mariya Dewi, K., Fitri Larassagita, A., Firman, A., Risky, M., Rahmat, R., & Ayub, A. (2024). Characterization of CO1 and 18S rDNA genes from Indonesian native ornamental shrimp Caridina boehmei cultured in Jakarta. Jurnal Akuakultur Indonesia, 23(2), 147–156. https://doi.org/10.19027/jai.23.2.147-156
Saitou, N., & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4(4), 406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
Saleky, D., Sianturi, R., Dailami, M., & Kusuma, A. B. (2021). Kajian Molekuler Ikan Oreochromis spp. dari Perairan Daratan Merauke-Papua, Berdasarkan DNA Mitokondria Fragmen Gen Sitokrom Oksidase Subunit I. Jurnal Perikanan Universitas Gadjah Mada, 23(1), 37. https://doi.org/10.22146/jfs.61026
Shofi, M. (2022). In silico test of toxicity and cytotoxic activity from trembesi seed bioactive compounds (samanea saman (jacq.) merr) as candidates for diabetes mellitus drug. Jurnal Pharma Bhakta, 1(2), 1–14.
Siregar, U. J., & Diputra, I. M. M. M. (2013). Keragaman Genetik Pinus merkusii Jungh. et de Vriese Strain Tapanuli Berdasarkan Penanda Mikrosatelit Diversity of Pinus merkusii Jungh. et de Vriese of Tapanuli Strain based on Microsatellite Markers. Jurnal Silvikultur Tropika, 4(2), 88–99.
Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Molecular Biology and Evolution, 38(7), 3022–3027. https://doi.org/10.1093/molbev/msab120
Ugbaja, S. C., Mushebenge, A. G.-A., Kumalo, H., Ngcobo, M., & Gqaleni, N. (2025). Potential Benefits of In Silico Methods: A Promising Alternative in Natural Compound’s Drug Discovery and Repurposing for HBV Therapy. Pharmaceuticals, 18(3), 419. https://doi.org/10.3390/ph18030419
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