Morphological and molecular characterization of mole crab (Genus: Emerita) in the Cilacap coastlines of Indonesia, with particular focus on genetic diversity of Emerita sp. nov.




Abstract.Bhagawati D, Nuryanto A, Winarni ET, Pulungsari AE. 2022. Morphological and molecular characterization of mole crab (Genus: Emerita) in the Cilacap coastlines of Indonesia, with particular focus on genetic diversity of Emerita sp. nov. Biodiversitas 23: 2395-2404Previous studies reported Emerita emeritus is the only species of the Genus Emerita inhabiting the coastal ecosystem of the Cilacap District. A recent study reported the presence of suspected new Emerita species living on the Cilacap sandy beach but used a small number of specimens and no reports about genetic diversity. This study used more Emerita samples than the previous study. This study aimed to identify Emerita specimens based on the morphology and the cytochrome c oxidase 1 gene and analyzed the genetic diversity of Emerita sp. nov. Emerita samples were collected from three different beaches in Cilacap District, Central Java, Indonesia. Morphological identification placed the samples into two different morphotypes. Morphotype A was identified as Emerita emeritus. Morphotype B was determined as Emerita sp. nov. Molecular data support the placement of Emerita samples into Emerita emeritus, and Emeritasp. nov. Emeritasp. nov. has haplotype diversity of 0.857±0.057, indicating a high genetic diversity. Haplotype H2 was suggested as the most primitive one because other haplotypes radiated from it. This study concluded that two sympatric Emerita species inhabit Cilacap coastlines, and Emeritasp. nov. has high genetic diversity.


Abbas K, Xiaoyun Z, Weimin W. 2017. Microsatellite markers reveal genetic differentiation of Chinese dojo loach Misgurnus anguillicaudatus in the Yangtze River basin. Turkish Journal of Fisheries and Aquatic Sciences 17:1167-1177.
Achrem M, Skuza L, Kirczuk L, Domagala J, Pilecka-Rapacz M, Czerniawski R. 2017. Assessment of genetic variability in common whitefish from the catchment area of the Oder River using microsatellite markers. Acta Biologica 24: 5-13.
Adamson EAS, Hurwood DA, Mather PB. 2012. Insights into historical drainage evolution based on the phylogeography of the chevron snakehead fish (Channa striata) in the Mekong Basin. Freshwater Biology
Ahyong ST, Schnabel KE, Maas EW. 2009. Anomuran phylogeny: new insights from molecular data. DOI: 10.13140/2.1.2705.5684
Aquilino SVL, Tango JM, Fontanilla IKC, Pagulayan RC, Basiao ZU, Ong PS, Quilang JP. 2011. DNA barcoding of the ichthyofauna of Taal Lake, Philippines. Molecular Ecology Resources 11(4): 612–619.
Ariyaraphong N, Laopichienpong N, Singchat W, Panthum T, Ahmad SF, Jattawa D, Duengkae P, Muangmai N, Suwanasopee T, Koonawootrittriron S, Srikulnath K. 2021. High-Level gene flow restricts genetic differentiation in dairy cattle populations in Thailand: insights from large-scale Mt D-loop sequencing. Animals 11: 1680.
Baisvar VS, Kumar R, Singh M, Kushwaha B. 2019. Cytochrome c oxidase i gene-based genetic divergence and molecular phylogeny among the species of fish Genus Channa. Proceedings of the National Academy of Sciences India Section B - Biological Sciences 89(4): 1455–1463.
Baisvar VS, Singh M, Kumar R. 2018. Population structuring of Channa striata from Indian waters using control region of mtDNA. Mitochondrial DNA Part A 30(3): 414–423.
Balkhis ABS, Firdaus A, Jamsari J, Hwai TS, Yasin Z. 2011. Evidence of geographical structuring in the Malaysian Snakehead, Channa striata based on a partial segment of the CO1 gene. Genetics and Molecular Biology 34(3): 520-523.
Bandelt HJ, Foster P, Rohl A. 1999. Median-joining networks for inferring intraspeci?c phylogenies. Molecular Biology and Evolution 16(1): 37-48.
Barasa JE, Abila R, Grobler JP, Dangasuk OG, Njahira MN. 2014. Genetic diversity and gene flow in Clarias gariepinus from Lakes Victoria and Kanyaboli, Kenya. African Journal of Aquatic Science 39(3): 287-293. DOI: 10.2989/16085914.2014.933734
Bekker EI, Karabanov DP, Galimov YR, Kotov AA. 2016. DNA barcoding reveals high cryptic diversity in the North Eurasian Moina species (Crustacea: Cladocera). PLoS One 11 (8): e0161737. DOI:10.1371/journal.pone.0161737.
Bhagawati D, Winarni ET, Nuryanto A. 2020. Molecular barcoding reveals the existence of mole crabs Emerita emeritus in North Coast of Central Java. Biosaintifika 12 (1): 104-110. DOI: 10.15294/biosaintifika.v12i1.20497.
Bhagawati D, Anggoro S, Zainuri M, Sya’rani L. 2016. Ethnotaxonomical study of mole crab (Crustacea:Hippoidea) on coastal community of Cilacap. Biosaintifika 8(2): 222-230.
Bilgin R, Utkan MA, Kalkan E, Karhan SU, Bekbolet M. 2015. DNA barcoding of twelve shrimp (Crustacea: Decapoda) from Turkish sea reveals cryptic diversity. Mediterr Mar Sci 16 (1): 36-45. DOI:10.12681/mms.548.
Boyko CB, Mclaughlin PA 2010 Annotated checklist of anomuran decapod crustaceans of the world (exclusive of the Kiwaoidea and families Chirostylidae and Galatheidae of the Galatheoidea) Part IV – Hippoidea. Raffles Bull. Biol 23 139–51
Boyko CB. 2002. A worldwide revision of the recent and fossil sand crabs of the Albuneidae Stimpson and Blepharipodidae, new family (Crustacea: Decapoda: Anomura: Hippoidea). Bulletin of the American Museum of Natural History: 1-396.
Boyko CB, Harvey AW. 1999. Crustacea Decapoda: Albuneidae and Hippidae of the tropical Indo-West Pacific region, in Crosnier A. (ed.), Résultats des Campagnes MUSORSTOM. Mémoires du Muséum national d’Histoire naturelle 20 (180): 379-406.
Butet NA, Dewi IABP, Zairion, Hakim AA. 2019. Species validation of mole crabs based on molecular marker of 16s rRNA from Bantul and Purworejo waters. Journal of Tropical Fisheries Management 3(2): 28-35. [Indonesia].
Candek K, Kuntner M. 2015. DNA barcoding gap: Reliable species identi?cation over morphological and geographical scales. Molecular Ecology Resources 15 (2): 268-277.
Chan BKK, Chen H-N, Dando PR, Southward AJ, Southward EC. 2016. Biodiversity and biogeography of Chthamalid barnacles from the North-Eastern Pacific (Crustacea Cirripedia). PLoS ONE 11(3): e0149556. doi:10.1371/journal. pone.0149556.
Cheng F, Zhao S, Schmidt BV, Ye L, Hallerman EM, Xie S. 2017. Morphological but no genetic differentiation among fragmented populations of Hemiculter leucisculus (Actinopterygii, Cyprinidae) from a lake complex in the middle Yangtze, China. Hydrobiology. DOI: 10.1007/s10750-017-3464-0.
Dahruddin H, Hutama A, Busson F, Sauri S, Hanner R, Keith P, Hadiaty R, Hubert N. 2016. Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identi?cation accuracy, cryptic diversity and identi?cation of exotic species. Molecular Ecology Resources DOI: 10.1111/1755-0998.12528
da Silva JM, Creer S, dos Santos A, Costa AC, Cunha MR, Costa FO, Carvalho GR. 2011. Systematic and evolutionary insights derived from mtDNA COI barcode diversity in the Decapoda (Crustacea: Malacostraca). PloS ONE 6 (5): e19449. DOI: 10.1371/journal.pone.0019449.
Desi T, Suryanti, Widyorini N. 2020. Habitat preference and abundance of mole crab based on sea tides in coastal area of Kebumen Regency, Aquasains 9(1): 893-901. [Indonesia]
Dewi WK, Suaryanti S, Purnomo PW. 2019. Habitat preferences and abundance of mole crab at spring and neap tide in coastal area of Purworejo Central Java, Indonesia. International Journal of Applied Environmental Sciences 14(4): 383-394.
Dorn A, Ng'oma E, Janko K, Reichwald K, Polacik M, Platzer M, Cellerino A, Reichard M. 2011. Phylogeny, genetic variability and colour polymorphism of an emerging animal model: the short-lived annual Nothobranchius fishes from southern Mozambique. Mol Phylogenet Evol 61: 739-749
Dung DT, Hop, NT, Thaenkham U, Waikagul J. 2013. Genetic differences among Vietnamese Haplorchis taichui populations using the COI genetic marker. J Helimthol 87: 66-70
Elvyra R, Solihin DD, Affandi R, Junior MZ, Suhendra M. 2020. Molecular characteristics and phylogenetic relationships of silurid catfishes (Kryptopterus, Ompok and Phalacronotus) from the Kampar River, Indonesia, based on the cytochrome b gene. Biodiversitas 21(8): 3539-3546. DOI: 10.13057/biodiv/d210816.
Erlank E, Koekemoer LL, Coetzee M. 2018. The importance of morphological identification of African anopheline mosquitoes (Diptera: Culicidae) for malaria control programmes. Malaria Journal 17:43.
Esa Y, Rahim KAA. 2013. Genetic structure and preliminary findings of cryptic diversity of the Malaysian mahseer (Tor tambroides Valenciennes: Cyprinidae) inferred from mitochondrial DNA and microsatellite analyses. BioMed Res Intl 2013: 170980. DOI: 10.1155/2013/170980
Excoffier L, Lischer HEL. 2010. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10(3): 564–567.
Gouskov A, Reyes M, Wirthner-Bitterlin L, Vorburger C. 2016. Fish population genetic structure shaped by hydroelectric power plants in the upper Rhine catchment. Evol Appl 9: 394-408
Hall T. 2011. BioEdit: An important software for molecular biology. GERF Bulletin of Biosciences 2(1): 60–61.
Haig J. 1974. A review of the Australian crabs of Family Hippidae (Crustacea, Decapoda, Anomura). Memoirs of The Queensland Museum, 17(1), 175-189.
Hanim N, Farajallah A, Putri V, Wardiatno Y, Perwitasari F, Suman A. 2017. Emerita pangandaranensis sp. nov., a new sand crab (Anomura, Hippidae) from the South Coast of Java, Indonesia. Arpha Preprints. DOI:
Hartoko A, Muskananfola MR, Latifah N, Sulardiono B, Suprapto D, Rudiyanto S. 2019. Coastal sediment and benthic crustacean Emerita emeritus, Albunea symmysta, Hippa adactyla of South Coast Central Java Indonesia. International Journal of Applied Environmental Sciences 14(5): 523-539.
Haq M, Irmansyah, Maddu A, Riyanto B, Wardiatno Y, Zakiah AFN. 2018. Exploration of composition, elements, and microstructure of body and shell on tropical mole crab (Emerita emeritus). IOP Conf. Series: Earth and Environmental Science 187: 012021. doi :10.1088/1755-1315/187/1/012021
Higashi R, Tsukagoshi A, Kimura H, Kato K. 2011. Male dimorphism in a new interstitial species of the genus Microloxoconcha (Podocopida: Ostracoda). Journal of Crustacean Biology 31(1): 142-152.
Hubert N, Delieu-Trottin E, Irisson JO, Meyer C, Planes S. 2010. Identifying coral reef ?sh larvae through DNA barcoding: A test case with the families Acanthuridae and Holocentridae. Molecular Phylogenetics and Evolution 55: 1195-1203.
Irmawati I, Tresnati J, Nadiarti, Fachruddin L, Arma NR. 2017. Identification of wild stock and the first generation (F1) of domesticated snakehead fish, Channa spp using partial Cytochrome C Oxidase Subunit I (COI) gene. Jurnal Iktiologi Indonesia 17(2): 165–173. [Indonesia]
Jeffery NW, Elias-Guttierrez M, Adamowicz SJ. 2011. Species diversity and phylogeographical affinities of the Branchiopoda (Crustacea) of Churchill, Manitoba, Canada. PLoS ONE 6 (5): e18364.
Jong MA, de Wahlberg N, van Eijk M, Brakefield PM, Zwaan BJ. 2011. Mitochondrial DNA signature for range-wide populations of Bicyclus anynana suggests a rapid expansion from recent refugia. PLoS ONE 6(6): e21385. doi:10.1371/journal.pone.0021385
Karanovic I. 2015. Barcoding of ancient lake Ostracods (Crustacea) reveals cryptic speciation with extremely low distances. PLoS ONE 10 (3): e0121133. DOI: 10.1371/journal.pone.0121133.
Kazmi QB, Siddiqui FA. 2006. An illustrated key to the Malacostraca (Crustacea) of northern Arabian Sea Part VI: Decapoda Anomura. Pakistan Journal of Marine Sciences, 15(1), 11-79.
Ko H-L, Wang Y-T, Chiu T-S, Lee M-A, Leu M-Y, Chang K-Z, Chen W-Y, Shao K-T. 2013. Evaluating the accuracy of morphological identification of larval fishes by applying DNA barcoding. PLoS ONE 8(1): 3–9.
Korovchinsky NM. 2019. Morphological assessment of the North Eurasian interspecific hybrid forms of the genus Bythotrephes Leydig, 1860 (Crustacea: Cladocera: Cercopagididae). Zootaxa 4550 (3): 340-356.
Krisanti M, Ramadhan BF, Mashar A, Butet NA, Hakim AA, Wardiyatno Y. 2020. Mole crab phylogenetics relationship analysis in Parangkusumo and Ketawang Beach Waters. IOP Conf. Series: Earth and Environmental Science 420: 012018. doi:10.1088/1755-1315/420/1/012018
Kusbiyanto, Bhagawati D, Nuryanto A. 2020. DNA barcoding of crustacean larvae in Segara Anakan, Cilacap, Central Java, Indonesia using cytochrome c oxidase gene. Biodiversitas 21(10): 4878-4887.
Lau J-S, Ransangan J, Rodrigues KF. 2018. Genetic diversity and population structure of the Asian green mussel (Perna viridis) in the waters of Sabah, Malaysia based on mitochondrial DNA D-Loop sequences. Turkish Journal of Fisheries and Aquatic Sciences 18: 109-117. DOI: 10.4194/1303-2712-v18_1_12
Liu J, Ding X, Zeng Y, Yue Y, Guo X, Guo T, Chu M, Wang F, Han J, Feng R, Sun X, Niu C, Yang B, Guo J, Yuan C. 2016. Genetic diversity and phylogenetic evolution of Tibetan sheep based on mtDNA D-Loop sequences. PLoS ONE 11(17): e0159308. doi:10.1371/journal.pone.0159308
Mahapatro D, Karna SK, Mohanty SK, Mohanty B, Muduli PR, Pattnaik AK, Nanda S. 2018. First record of a burrowing mole crab Emerita emeritus (Decapoda: Anomura: Hippidae) from Chilika Lake, East coast of India. Indian Journal of Geo-Marine Sciences, 47(01), 109-113.
Mauroka N, Ohtsuki H, Makino W, Urabe J. 2018. Rediscovery after almost 120 years: morphological and genetic evidence supporting the validity of Daphnia mitsukuri (Crustacea: Cladocera). Zoological Scrince 35(5): 468-475.
Mohammed MA, Nuryanto A, Kusmintarsih ES. 2021. Genetic differentiation of dengue vector Aedes aegypti in the small geographical scale of Banyumas District, Indonesia based on Cytochrome Oxidase I. Biodiversitas 22(2): 675-683
Muchlisin ZA, Thomy Z, Fadli N, Sarong MA, Siti-Azizah MN. 2013. DNA barcoding of freshwater fishes from Lake Laut Tawar, Aceh Province, Indonesia. Acta Ichthyologica et Piscatoria 43(1): 21–29.
Ng PKL. 1998 Crabs. p. 1045-1155. In Carpenter KE, Niem VH (eds) FAO species identification guide for fishery purposes. The living marine resources of the Western Central Pacific. Volume 2. Cephalopods, crustaceans, holothurians and sharks. Rome, FAO. 1998. pp. 687-1396.
Nugroho S, Suryanti S, Rudiyanti S. 2018. Distribution pattern of mole crab (Hippidae) based on the substrat’s salinity in Pagak Beach, Ngombol District, Purworejo Regency, Central Java. Indonesian Journal of Fisheries Science and Technology 14(1): 16-22. [Indonesia]
Nuryanto A, Bhagawati A, Rukayah S, Rahayu DRUS, Wibowo DN. 2020. Molecular barcoding reveals possible existence of sympatric species of Emerita emeritus in south coast of Cilacap Central Java. IOP Conf. Series: Earth and Environmental Science 593: 012014. doi:10.1088/1755-1315/593/1/012014
Nuryanto A, Komalawati N, Sugiharto. 2019. Genetic diversity assessment of Hemibagrus nemurus from rivers in Java Island, Indonesia using COI gene. Biodiversitas 20(9): 2707–2717.
Nuryanto A, Pramono H, Sastranegara MH. 2017. Molecular identification of fish larvae from East Plawangan of Segara Anakan, Cilacap, Central Java, Indonesia. Biosaintifika 9(1): 33-40.
Osawa M, Boyko C B and Chan T Y. 2010. Part I Hiipoidea (mole crabs). In Chan TY (ed.). Crustacean fauna of Taiwan: Crab-like Anomurans (Hippoidea, Lithodoidea and Porcellanidae). Keelung, Taiwan: National Taiwan University, 1–40..
Palecanda S, Feller KD, Porter ML. 2020. Using larval barcoding to estimate stomatopod species richness at Lizard Island, Australia for conservation monitoring. Sci Rep 10: 10990. DOI: 10.1038/s41598020-67696-x.
Palero F, Genis-Armero R, Hall MR, Clark PF. 2016. DNA barcoding the phyllosoma of Scyllarides squammosus (H. Milne Edwards, 1837) (Decapoda: Achelata: Scyllaridae). Zootaxa 4139 (4): 481- 498. DOI: 10.11646/zootaxa.4139.4.2.
Parmaksiz, A. (2019). Population genetic diversity of yellow barbell (Carasobarbus luteus) from Kueik, Euphrates and Tigris Rivers based on mitochondrial DNA D-loop sequences. Turkish Journal of Fisheries and Aquatic Sciences 20(1): 79-86.
Parmaksiz, A. & Eksi, E. (2017). Genetic diversity of the cyprinid fish Capoeta trutta (Heckel, 1843) populations from Euphrates and Tigris rivers in Turkey based on mtDNA COI sequences. Indian Journal of Fisheries 64(1): 18-22.
Pavesi L., De Matthaeis, E., Tiedemann, R., & Ket maier, V. (2011). Temporal population genetics and COI phylogeography of thesandhopper Macarorchestia remyi (Amphipoda: Talitridae). Zoological Studies 50(2): 220-229.
Poore G. (Ed.). 2004. Marine decapod Crustacea of southern Australia: A guide to identification. Australia: CSIRO Publishing.
Pramithasari FA, Butet NA, Wardiatno Y. 2017. Variation in morphometric characters in four sand crab (Albunea symmysta) populations collected from Sumatra and Java Island, Indonesia. Tropical Life Sciences Research 28(1): 103-115.
Pramono TB, Arfiati D, Widodo MS, Yanuhar U. 2017. Identifikasi ikan Genus Mystus dengan pendekatan genetik. Jurnal Sumberdaya Akuatik Indopasifik 1(2): 123–132. [Indonesia].
Riani S, Prabowo RE, Nuryanto A. 2021. Molecular characteristics and taxonomic status of morphologically similar barnacles (Amphibalanus) assessed using the cytochrome c oxidase 1 gene. Biodiversitas 22 (3): 1456-1466.
Rozas J, Ferrer-Mata A, Sanchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Osins SE, Sanchez-Gracia A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol 34 (12): 3299-3302. DOI: 10.1093/molbev/msx248.
Sachithanandam V, Mohan PM, Muruganandam N, Chaaithanya IK, Dhivya P, Baskaaran R. 2012. DNA barcoding, phylogenetic study of Epinephelus spp. from Andaman coastal region, India. Indian Journal of Geo-Marine Sciences 41(4): 203-211.
Sankolli KN. 1965. On a new species of Emerita (Decapoda, Anomura) from India, with a note on Emerita Emeritus (L.). Crustaceana 8: 48-54.
Schnabel KE, Ahyong ST. 2010. A new classification of the Chirostyloidea (Crustacea: Decapoda: Anomura). Zootaxa 2687: 56-64.
Setyaningrum N, Lestari W, Krismono, Nuryanto A. 2022. Genetically continuous populations of Striped Snakehead (Channa striata) in the Cingcingguling River fragmented by Sempor Reservoir, Central Java, Indonesia. Biodiversitas 23(1): 222-230. DOI: 10.13057/biodiv/d230128.
Shu Q-H, Li S-D, Tian M, Meng Y, He S-M-Q, Zhu M, Wang M-M, Wang W-L. 2022. Morphological and molecular characterization of Paragonimus skrjabini complex from Yunnan, China: A brief report. Acta Parasitologica 67:316-321.
Song LM, Munian K, Rashid ZA, Bhassu S. 2013. Characterisation of Asian snakehead murrel Channa striata (Channidae) in Malaysia: An insight into molecular data and morphological approach. The Scientific World Journal: 917506.
Syaifudin M, Wijayanti M, Dwinanti SH, Muslim, Mahendra M, Marliana S. 2020. DNA barcodes and phylogenetic of striped snakehead and ocellated snakehead fish from South Sumatra, Indonesia. Biodiversitas 21(3): 1227-1235.
Tajima F. 1989. Statistical method for testing then mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
Triantafyllidis A, Bobori D, Koliamitra C, Gbandi E, Mpanti M, Petriki O, Karaiskou N. 2011. DNA barcoding analysis of fish species diversity in four north Greek lakes. Mitochondrial DNA 22(SUPPL. 1): 37–42.
Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. 2005. DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society B: Biological Sciences 360(1462): 1847–1857.
Wardiatno, Y., Ardika, P.U., Farajallah, A., Butet, N.A., Mashar, A., Kamal, M.M., Renjaan, E.A. (2015). Biodiversity of Indonesian sand crabs (Crustacea, Anomura, Hippidae) and assessment of their phylogenetic relationships. AACL Bioflux,8(2), 224–235.
Weis M, Macher JN, Seefeldt MA, Leese F. 2014. Molecular evidence for further overlooked species within the Gammarus fossarum complex (Crustacea: Amphipoda). Hydrobiol 721 (1): 165-184. DOI: 10.1007/s10750-013-1658-7.
Winarni ET, Kusbiyanto, Nuryanto A. 2021. Estimating crustacean species utilize Segara Anakan Estuary Cilacap, Indonesia as nursery ground through DNA barcoding. Journal of Hunan University (Natural Sciences) 48(10): 275-282.
Zhang W, Jiang S, Salumy KR, Xuan Z, Xiong Y, Jin S, Gong Y, Wu Y, Qiao H, Fu H. 2022. Comparison of genetic diversity and population structure of eight Macrobrachium nipponense populations in China based on D-loop sequences. Aquaculture Reports 23: 101086.
Zhang, G-H., Yuan, Z-J., Zhang, C-X., Yin, K-S., Tang, M-J., Guo, H-W., Fu, J-Y., & Xiao, Q. (2014). Detecting deep divergence in seventeen populations of tea geometrid (Ectropis obliqua Prout) in China by COI mtDNA and Cross-Breeding. PLoS ONE 9(6): e99373.
Zhong L, Song C, Wang M, Chen Y, Qin Q, Pan J, Chen X. 2013. Genetic diversity and population structure of yellow cat?sh Pelteobagrus fulvidraco from ?ve lakes in the middle and lower reaches of the Yangtze River, China, based on mitochondrial DNA control region. Mitochondrial DNA 24 (5): 552-558

Most read articles by the same author(s)

1 2 > >>