Reanalysis of Mitochondrial and Nuclear Markers (COI, 16S, 28S) in Coenobitidae, Diogenidae, and Paguridae for Species Delimitation
Article Sidebar
-
Genetic distance, Public data review, Paguroidea, Species delimination
Abstract
Public sequence repositories, such as GenBank, contain an extensive collection of molecular data that are widely used for phylogenetic inference and species identification. However, inconsistent annotation and potential misidentifications can obscure true genetic patterns, particularly in groups with complex morphology such as Paguroidea. This study reanalyzed 4,871 COI, 16S, and 28S sequences belonging to the families Coenobitidae, Diogenidae, and Paguridae retrieved from GenBank. Following rigorous quality filtering, 2,450 sequences were retained for downstream analyses to quantify intra and interspecific genetic distances for each family and each molecular marker. The results reveal substantial heterogeneity in genetic divergence across families, with COI and 16S exhibiting broad ranges and frequent overlap between intra and interspecific distances, whereas 28S displayed very low variation consistent with its slower evolutionary rate. Elevated intraspecific distances in several taxa suggest potential cryptic lineages, while unusually shallow interspecific values indicate possible synonymy or recent divergence. Rather than proposing taxonomic changes, this study provides a curated reference framework that establishes empirical distance thresholds for molecular species delimitation in Paguroidea. These findings offer a practical baseline for future research employing COI, 16S, and 28S markers in species identification, validation of public sequence data, and the refinement of hermit crab systematics.
Full text article
References
Altschul, S.F., Gish, W., Miller, W., Myers, E.W., & Lipman, D.J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403-410. https://doi.org/10.1016/S0022-2836(05)80360-2
Antu, D.R., Jahan, I., Islam, T.T., Mahjabin, M., Datta, S.K., Ahmed, S., & Ahmed, M.S. (2024). Morphology and DNA barcoding reveal four new species of hermit crab (Crustacea: Decapoda: Anomura) for the fauna of Bangladesh. Zoology and Ecology, 34(2), 144-153. https://doi.org/10.35513/21658005.2024.2.8
Asakura, A. (2001). A revision of the hermit crabs of the genera Catapagurus A. Milne-Edwards and Hemipagurus Smith from the Indo-West Pacific (Crustacea : Decapoda : Anomura : Paguridae). Invertebrate Systematics, 15(6), 823. https://doi.org/10.1071/IT00034
Bokulich, A. (2020). Understanding scientific types: holotypes, stratotypes, and measurement prototypes. Biology & Philosophy, 35(5), 54. https://doi.org/10.1007/s10539-020-09771-1
Bracken-Grissom, H.D., Cannon, M.E., Cabezas, P., Feldmann, R.M., Schweitzer, C.E., Ahyong, S.T., Felder, D.L., Lemaitre, R., & Crandall, K.A. (2013). A comprehensive and integrative reconstruction of evolutionary history for Anomura (Crustacea: Decapoda). BMC Evolutionary Biology, 13(128), 1-28. https://doi.org/10.1186/1471-2148-13-128
Collins, R.A., & Cruickshank, R.H. (2013). The seven deadly sins of DNA barcoding. Molecular Ecology Resources, 13(6), 969-975. https://doi.org/10.1111/1755-0998.12046
Daniels, S.R., Cumberlidge, N., Pérez-Losada, M., Marijnissen, S.A.E., & Crandall, K.A. (2006). Evolution of Afrotropical freshwater crab lineages obscured by morphological convergence. Molecular Phylogenetics and Evolution, 40(1), 227–235. https://doi.org/10.1016/j.ympev.2006.02.022
Daniels, S.R., Marais, H.J., Da Fonseca, M., & Peer, N. (2025). Mind the gap: DNA barcoding as a tool to delineate evolutionary units in Afrotropical freshwater crabs (Decapoda: Brachyura: Potamoidea: Deckeniidae and Potamonautidae). Journal of Crustacean Biology, 45(4), 1-11. https://doi.org/10.1093/jcbiol/ruaf061
Hadadi, N., Madduppa, H., Shita Azaraly, I., & Anggraini, N.P. (2023). DNA Barcoding, Identifikasi Morfologi dan Kepadatan Populasi Genus Tridacna di Perairan Maluku Utara. Jurnal Ilmu Dan Teknologi Kelautan Tropis, 15(3), 349-368. https://doi.org/10.29244/jitkt.v15i3.47110
Hamasaki, K., Iizuka, C., Sanda, T., Imai, H., & Kitada, S. (2017). Phylogeny and phylogeography of the land hermit crab Coenobita purpureus (Decapoda: Anomura: Coenobitidae) in the Northwestern Pacific Region. Marine Ecology, 38(1), 1-17. https://doi.org/10.1111/maec.12369
Hebert, P.D.N., Cywinska, A., Ball, S.L., & DeWaard, J.R. (2003). Biological identifications through DNA barcodes. Proceeding of Royal Society London, 270(1512), 313-321. https://doi.org/10.1098/rspb.2002.2218
ICZN. (1999). Article 72. General provisions. International Code of Zoological Nomenclature (4th Ed.). London, United Kingdom: The International Trust for Zoological Nomenclature.
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
Komai, T., & Rahayu, D.L. (2013). Six new species of the hermit crab genus Decaphyllus de Saint Laurent, 1968 (Crustacea: Decapoda: Anomura: Paguridae) from the Boholo Sea, The Philippines, and the Ryukyu Islands, Japan. Raffles Bulletin of Zoology, 61(2), 589-620.
Komai, T., & Rahayu, D.L. (2014). New records and new species of the hermit crab genus Pagurus Fabricius, 1775 (Crustacea: Decapoda: Anomura: Paguridae) from the Philippines. Raffles Bulletin of Zoology, 62, 620-646.
Komai, T., Rahayu, D.L., & Fujita, Y. (2021). Hermit crabs of the family paguridae (Crustacea: Decapoda: Anomura) from christmas and cocos (keeling) islands, indian ocean territory of australia, with descriptions of three new species and reappraisal of the genus kumepagurus komai & osawa, 2012. Raffles Bulletin of Zoology, 69(1), 378-402. https://doi.org/10.26107/RBZ-2021-0059
Lemaitre, R., & Felder, D.L. (2023). A new genus and species of micro-pagurid hermit crab (Crustacea, Decapoda, Paguridae) from the rariphotic reef zone in Curaçao, Lesser Antilles, Caribbean Sea. Zootaxa, 5277(2), 374-380. https://doi.org/10.11646/ZOOTAXA.5277.2.7
Lemaitre, R., Rahayu, D.L., & Komai, T. (2018). A revision of “blanket-hermit crabs” of the genus paguropsis henderson, 1888, with the description of a new genus and five new species (Crustacea, anomura, diogenidae). ZooKeys, 2018(752), 17-97. https://doi.org/10.3897/zookeys.752.23712
Malay, M.C.M.D., & Paulay, G. (2010). Peripatric speciation drives diversification and distributional pattern of reef hermit crabs (Decapoda: Diogenidae: Calcinus). Evolution, 64(3), 634-662. https://doi.org/10.1111/j.1558-5646.2009.00848.x
Mclaughlin, P.A., Komai, T., Lemaitre, R., & Rahayu, D.L. (2010). Annotated Checklist of Anomuran Decapod Crustaceans of the World (Exclusive of the Kiwaoidea and Families Chirostylidae and Galatheidae of the Galatheoidea) Part I – Lithodoidea, Lomisoidea and Paguroidea. Raffles Bulletin of Zoology, 23, 5-107.
McLaughlin, P.A., Lemaitre, R., & Sorhannus, U. (2007). Hermit crab phylogeny: A reappraisal and its “fall-out.” Journal of Crustacean Biology, 27(1), 97-115. https://doi.org/10.1651/S-2675.1
McLaughlin, P.A., & Rahayu, D.L. (2008). A new genus and species of hermit crab of the family Paguridae (Crustacea: Anomura: Paguroidea) from the Vanuatu Archipelago. Proceedings of the Biological Society of Washington, 121(3), 365-373. https://doi.org/10.2988/08-07.1
Rahayu, D.L., & Komai, T. (2000). Shallow-Water Hermit Crabs (Crustacea: Decapoda: Anomura: Diogenidae and Paguridae) of Phuket, Thailand. Phuket Mar. Biol. Cent. Res. Bull., 63, 21-44.
Rahayu, D.L., & Komai, T. (2013). Two new species of Pylopaguropsis alcock Crustacea: Decapoda: Anomura: Paguridae) from the Philippines. Raffles Bulletin of Zoology, 61(2), 621-631.
Rahayu, D.L., Shih, H.Te, & Ng, P.K.L. (2016). A new species of land hermit crab in the genus Coenobita Latreille, 1829 from Singapore, Malaysia and Indonesia, previously confused with C. cavipes Stimpson, 1858 (Crustacea: Decapoda: Anomura: Coenobitidae). Raffles Bulletin of Zoology, 34, 470-488.
Ratnasingham, S., & Hebert, P.D.N. (2007). BOLD: The Barcode of Life Data System: Barcoding. Molecular Ecology Notes, 7(3), 355-364. https://doi.org/10.1111/j.1471-8286.2007.01678.x
Schlick-Steiner, B.C., Steiner, F.M., Seifert, B., Stauffer, C., Christian, E., & Crozier, R.H. (2010). Integrative taxonomy: A multisource approach to exploring biodiversity. In Annual Review of Entomology (Vol. 55, pp. 421-438). https://doi.org/10.1146/annurev-ento-112408-085432
Schubart, C.D. (2009). Mitochondrial DNA and Decapod Phylogenies. In Decapod Crustacean Phylogenetics (pp. 47-65). CRC Press. https://doi.org/10.1201/9781420092592-c4
Sultana, Z., Babarinde, I.A., & Asakura, A. (2022). Diversity and Molecular Phylogeny of Pagurid Hermit Crabs (Anomura: Paguridae: Pagurus). Diversity, 14(2). https://doi.org/10.3390/d14020141
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
Thompson, J.D., Higgins, D.G., & Gibson, T.J. (1994). CLUSTAL W : improving the sensitivity of progressive multiple sequence alignment through sequence weighting , position-specific gap penalties and weight matrix choice. 22(22), 4673-4680. https://doi.org/10.1093/nar/22.22.4673
Tsang, L. M., Chan, T.Y., Ahyong, S.T., & Chu, K.H. (2011). Hermit to king, or hermit to all: Multiple transitions to crab-like forms from hermit crab ancestors. Systematic Biology, 60(5), 616-629. https://doi.org/10.1093/sysbio/syr063
Vivien, R., & Martin, P. (2025). Maintaining taxonomic accuracy in genetic databases: A duty for taxonomists—Reanalysis of the DNA sequences from Mercan et al. (2024) on the genus Potamothrix (Annelida, Clitellata) in Turkish lakes. Zootaxa, 5575(4), 555-562. https://doi.org/10.11646/zootaxa.5575.4.5
Wong, T., Ly-Trong, N., Ren, H., Baños, H., Roger, A., Susko, E., Bielow, C., De Maio, N., Goldman, N., Hahn, M., Huttley, G., Lanfear, R., & Minh, B. Q. (2025). IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models. https://doi.org/10.32942/X2P62N
Authors
Copyright (c) 2026 Tazkiah Auliaputri, Tyani Fitrian, Achmad Alfiyan, Intan Ratu Pratiwi, Vendi Eko Susilo, Ali Mashar, Dr. Ir. Achmad Farajallah, M.Si.
This work is licensed under a Creative Commons Attribution 4.0 International License.
This work is licensed under a Creative Commons Attribution 4.0 International License.
Jurnal Ilmu dan Teknologi Kelautan Tropis i is an open-access journal, meaning that all content is freely available without charge to the user or their institution. Users are allowed to read, download, copy, distribute, print, search, or link to the full texts of the articles in this journal without needing to request prior permission from the publisher or the author.
All articles published by Jurnal Ilmu dan Teknologi Kelautan Tropis are licensed under the Creative Commons Attribution 4.0 International License. This allows for unrestricted use, distribution, and reproduction in any medium, provided proper credit is given to the original authors.
Authors submitting manuscripts should understand and agree that the copyright of published manuscripts is retained by the authors. Copyright encompasses the exclusive rights of authors to reproduce, distribute, and sell any part of the journal articles in all forms and media. Reproduction of any part of this journal, its storage in databases, and its transmission by any form or media is allowed without written permission from Jurnal Ilmu dan Teknologi Kelautan Tropis.