Genetic variation and population structure of brachiopods, Lingula anatina Lamarck, 1801 in the Northern Aceh shore, Indonesia

##plugins.themes.bootstrap3.article.main##

CHITRA OCTAVINA
MUTIA RAMADHANIATY
RAHMA EFFENDIE DAULAY
IRMA DEWIYANTI
MARIA ULFAH

Abstract

Abstract. Octavina C, Ramadhaniaty M, Daulay RE, Dewiyanti I, Ulfah M. 2023. Genetic variation and population structure of brachiopods, Lingula anatina Lamarck, 1801 in the Northern Aceh shore. Biodiversitas 24: 3951-3959. Lingula anatina is one of the brachiopods recognized as one of the most primitive groups with a fossil record from the early Cambrian period. Although L. anatina has been targeted as an object of biological studies, the information about the genetic variation within species is still limited. The purpose of this research is to identify the genetic variation and population structure of the species L. anatina found in the Aceh northern shore based on the mtDNA Cytochrome Oxidase I (COI) gene sequence. In this study, L. anatina specimens collected from five populations on Aceh's northern shore, namely Krueng Raya, Syiah Kuala, Ulee Lheue, and Ujong Pancu, with complete mitochondrial genome sequences were analyzed and compared with genebank sequences. The total nucleotide base of L. anatina is 657 bp, with 18 haplotypes. Based on the results of a comparison of the distribution of L. anatina in Asia shows that the Japanese population has the highest population structure value compared to the other five populations. The Fst value obtained from this study is 0.7, so it is classified as high and structured. Phylogenetic analysis showed that the correlation between geographic location and geographic distance affects the genetic distance between populations.

##plugins.themes.bootstrap3.article.details##

References
Agustina S, Octavina C, Sarong A, Nurhaliza A, Dewiyanti I, Iqbal T. 2019. The density and distribution of Lingula sp. in Aceh Northern Shore. In: Proceedings of 2nd ICFAES 2019 International Conference on Fisheries, Aquatic and Environmental Sciences 2019 In Conjunctions with The 6th ASI 2019 Annual Conference of The Asian Society of Ichthyologist 2019. 19-20 Juni 2019 [Indonesia]
Ambarwati R, Rahayu DA, Rachmadiarti F, Khaleyla F. 2021. DNA barcoding of lamp shells (Brachiopoda: Lingula anatina) from Probolinggo, East Java, Indonesia. Biodiversitas Journal of Biological Diversity, 22: 1764-1774.
Blair C. Murphy RW. 2011. Recent trends in molecular phylogenetic analysis: where to next? Journal of Heredity, 102: 130-138.
Christian B. Skovsted BP, Topper TP, Marissa JB, Guoxiang L, Glenn AB. 2016. The operculum and mode of life of the lower Cambrian hyolith Cupitheca from South Australia and North China. Palaeogeography, Palaeoclimatology, Palaeoecology, 443.
Darmarini AS, Wardiatno Y, Prartono T, Soewardi K. 2017. New record of a primitive brachiopod, Lingula sp. in Lubuk Damar, Indonesia. Biodiversitas Journal of Biological Diversity, 18: 1438-1444.
Endo K, Ozawa T, Kojima S. 2001. Nuclear and mitochondrial gene sequences reveal unexpected genetic heterogeneity among northern Pacific populations of the brachiopod Lingula anatina. Marine Biology, 139: 105-112.
Excoffierd L, Lischer HE. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetic analysis under Linux and Windows. Mol.Ecol.Resour., 10.
Hasanudin M, Kusmanto E, Budisetyawan W. 2016. Amplifikasi pasang surut dan dampaknya terhadap perairan pesisir Probolinggo. OLDI (Oseanologi dan Limnologi di Indonesia), 1: 69-80.
Hatje K, Kollmar M. 2012. A phylogenetic analysis of the brassicales clade based on an alignment-free sequence comparison method. Frontiers in plant science, 3: 192.
Kim SG, Karagozlu MZ, Kim CB. 2017. Phylogenetic investigations of Lingula anatina among some northwestern Pacific populations, based on mitochondrial DNA cytochrome c oxidase subunit I gene. Journal of Asia-Pacific Biodiversity, 10: 162-166.
Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25.
Lumaret R, Michaud H, Ripoll JP, Toumi J. 1998. Chloroplast DNA extraction procedure for species high in phenolics and polysaccharides. In Molecular Tools for Screening Biodiversity (pp. 15-17): Springer.
Luo YJ, Satoh N, Endo K. 2015. Mitochondrial gene order variation in the brachiopod Lingula anatina and its implications for mitochondrial evolution in lophotrochozoans. Marine Genomics, 24: 31-40.
Madduppa HH, Timm J, Kochzius M. 2014. Interspecific, spatial and temporal variability of self-recruitment in anemonefishes. PloS one, 9: e90648.
Meinilä M, Kuusela J, Zi?tara MS, Lumme J. 2004. Initial steps of speciation by geographic isolation and host switch in salmonid pathogen Gyrodactylus salaris (Monogenea: Gyrodactylidae). International Journal for Parasitology, 3: 515-526.
Minoura K, Osaka Y. 1992. Sediments and sedimentary processes in Mutsu Bay, Japan: Pelletization as the most important mode in depositing argillaceous sediments. Marine geology, 103: 487-502.
Mondini L, Noorani A, Pagnotta MA. 2009. Assessing plant genetic diversity by molecular tools. Diversity, 1(1): 19-35.
Nurhayati. 2011. Struktur Pola Pergerakan Arus Dan Pengaruhnya Pada Orientasi Kelimpahan Ikan Di Perairan Selat Benggala Banda Aceh. Lingkungan Tropis, 5: 45-52.
Octavina C, Agustina S, Sarong M, Sari P, Sahidin A, Razi NM, Agustiar M, Sakinah R, Fazillah M. 2021. Length-weight relationship of Lingula sp. in Aceh Southern Shore. In: IOP Conference Series: Earth and Environmental Science 674, 24 September 2020 [Indonesia]
Rakmawati dan Ambarwati. 2020. Komunitas bivalvia yang berasosiasi dengan Kerang Lentera (Brachiopoda: Lingulata) di zona intertidal Selat Madura. Jurnal Riset Biologi dan Aplikasinya, 2: 36-41.
Saito M, Kojima S, Endo K. 2000. Mitochondrial COI sequences of brachiopods: genetic code shared with protostomes and limits of utility for phylogenetic reconstruction. Molecular Phylogenetics and Evolution, 15: 331-344.
Samanta SCA. 2014. New record of a primitive brachiopod benthic fauna from the North-East coast of India. Int J Curr Res Aca Rev, 2: 70-73.
Samanta SCA. 2015. Eco-biology of a precambrian intertidal benthic brachiopod, Lingula anatina from the confluence of Subarnarekha estuary with Bay of Bengal, India. J Mar Biol Ass India, 57: 41-46.
Surzycki S. 2000. General aspects of DNA isolation and purification. In Basic Techniques in Molecular Biology: Springer.
Tamura K, Stecher D, Peterson A, Filipski, Kumar S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular biology and evolution. 30: 2725-2729.
Tarwinangsih W, Farajallah A, Sumantri C, Andreas E. 2011. Analisis keragaman genetik kerbau lokal (Bubalus bubalis) berdasarkan haplotipe DNA mitokondria. In: Seminar Nasional Teknologi Peternakan dan Veteriner: 59-67.
Taylor DR, Aarssen LW. 1988. An interpretation of phenotypic plasticity in Agropyron repens (Graminae). American journal of botany, 75: 401-413.
Templeton AR, Routman E, Phillips CA. 1995. Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum. Genetics, 140: 767-782.
Williams A, Carlson S, Brunton CHC, Holmer LE, Popov LE. 1996. A supra-ordinal classification of the Brachiopoda. Philosophical Transactions of the Royal Society, Biological Sciences, 351: 1117-1193.
Wu LS, Guilian, Lai, Xulong, Hou, Xindong, Yuan, Junxia. 2010. Geographical pattern analysis of the Brachipod Lingula anatina based on mitochondrial COI gene sequences. Geological Science and Technology Information, 29: 17-22.
Zein MS. 2007. Keragaman Daerah Kontrol DNA Mitokondria Rusa Timor (Cervus timorensis timorensis) di Pulau Timor, Alor, dan Pantar. Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati: 138-144.