Genetic variation of longtail tuna Thunnus tonggol landed in four fish markets in Indonesia based on mitochondrial DNA
##plugins.themes.bootstrap3.article.sidebar##
Issue
Section
Articles
##plugins.themes.bootstrap3.article.main##
IDA AYU ASTARINI
♥
https://orcid.org/0000-0002-0311-5183
ENEX YUNIARTI NINGSIH
DEVY SIMANUNGKALIT
SHELLA AYU ARDIANA
M. DANIE AL MALIK
NI LUH ASTRIA YUSMALINDA
ANDRIANUS SEMBIRING
NI PUTU DIAN PERTIWI
NI KADEK DITA CAHYANI
ALLEN COLLINS
Abstract
Abstract. Astarini IA, Ningsih EY, Simanungkalit D, Ardiana SA, Al Malik MD, Yusmalinda NLA, Sembiring A, Pertiwi NPD, Cahyani NKD, Collins A. 2021. Genetic variation of longtail tuna Thunnus tonggol landed in four fish markets in Indonesia based on mitochondrial DNA. Biodiversitas 22: 1644-1651. Longtail tuna (Thunnus tonggol, Family: Scombridae) is an economically valuable neritic species found in tropical and subtropical waters in the Indo-Pacific region. High catch numbers, which have been decreasing, could negatively impact this tuna’s population level. Little research has been conducted on the longtail tuna population in Indonesia. This study aims to determine the genetic diversity and potential population structure of longtail tuna landed in four fish markets in Indonesia (representing three sampling locations because two markets are relatively close to each other) based on sequences of a region of mitochondrial control region (d-loop). A total of 101 samples, out of 110, were identified and confirmed as T. tonggol species by amplifying and sequencing a fragment of d-loop (amplicons ranging from 482 - 523 bp). Neighbor-joining analysis resulted in a topology with all samples grouped into one clade with an average genetic distance of 0.020. Meanwhile, haplotype diversity (Hd) and nucleotide diversity (?) values of the longtail tuna samples were 0.9939 and 0.0192, respectively. The fixation index (Fst) value was -0.00507, with p> 0.05, which indicates that there is no significant population structure among the longtail tuna collected from four fish markets representing three sampling locations. The results of this analysis can be used as basic data in planning sustainable fisheries management efforts.
##plugins.themes.bootstrap3.article.details##
References
Abdussamad EM, Koya KP, Ghosh S, Rohit P, Joshi KK, Manojkumar B, Prakasa D, Kemparaju S, Elayath MNK, Dhokia HK, Sebastine M, Bineesh KK. 2012. Fishery, biology and population characteristics of longtail tuna, Thunnus tonggol (Bleeker, 1851) caught along the Indian coast. Indian J Fisheries 59 (2): 7-16.
Abdulhaleem SZ. 1989. Gill raker counts: a possible means of stock separation for longtail tuna (Thunnus tonggol) in the Indian Ocean. Indo-Pac. Tuna Dev. Mgt. Programme IPTP/89/GEN/, 16: 64–68.
Akbar N, Zamani NP, Madduppa HH. 2014. Keragaman genetik ikan tuna sirip kuning (Thunnus albacares) dari dua populasi di Laut Maluku, Indonesia. DEPIK Jurnal Ilmu-Ilmu Perairan, Pesisir dan Perikanan 3 (1): 65-73.
Alfajri SI. 2017. Kepentingan Indonesia Mengekspor Ikan Tuna Ke Amerika Serikat Tahun 2012-2015. Fakultas Ilmu Sosial dan Ilmu Politik. Universitas Riau.
Allen GR, Erdmann MV, Pertiwi PD. 2017. Description of four new species of damselfishes (Pomacentridae) in the Pomacentrus philippinus complex from the tropical western Pacific Ocean. J Ocean Sci Found 25: 47-76.
Astuti D, Kurniati H. 2010. Keragaman Genetik Amfibia Kodok (Rana nicobariensis) di Ecology Park, Cibinong Berdasarkan Sekuen DNA dari Mitokondria D-loop. Jurnal Biologi Indonesia 6(3): 405-414.
Barata RBY, Setyono H, Harsono G. 2014. Dinamika upwelling dan downwelling berdasarkan variabilitas suhu permukaan laut dan klorofil-a di perairan Selatan Jawa. Jurnal Oseanografi 3(1): 57-66.
Excoffier L, Lischer HE. 2010. Arlequin suite ver 3.5 a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10(3): 564-567.
Griffiths SP, Fry GC, Manson FJ,Lou DC. 2010. Age and growth of Longtail Tuna (Thunnus tonggol) in tropical and temperate waters of the central Indo-Pacific. ICES J Mar Sci 67(1): 125-134.
Griffiths SP, Leadbitter D, Willette D, Kaymaram F, Moazzam M. 2020. Longtail tuna, Thunnus tonggol (Bleeker, 1851): a global review of population dynamics, ecology, fisheries, and considerations for future conservation and management. Rev in Fish Biol and Fisheries 30(1): 25-66.
Grewe P, Hampton J. 1998. An assessment of bigeye tuna (Thunnus obesus) population structure in the Pasific Ocean, based on mitochondrial DNA and DNA microsatellite analysis. Marine Research. Commonwealth Scientific and Industrial Research Organisation, Australia.
Habibi A, Sugiyanta DA. Perikanan Tuna-Panduan Penangkapan dan Penanganan. 2011. Seri Panduan Perikanan Skala Kecil. Best Management Practices. WWF-Indonesia. 27 hal.
Hany Y, Hidayat T. 2018. Analisis pertumbuhan dan laju eksploitasi ikan tongkol abu – abu, Thunnus tonggol (Bleeker, 1851) Di Perairan Lautan Jawa. Balai Riset Perikanan Laut. Bogor. Volume 10 No. 2.
Hughes AR, Inouye BD, Johnson MTJ, Underwood N, Vellend M. 2008. Ecological consequences of genetic diversity. Ecol letters 11: 609 – 623.
Joka SG. 2013. Stuktur genetik dan filogenetik ikan tuna (Thunnus sp.) di TPI Tanjung Luar, Lombok berdasarkan DNA Mitokondria. Skripsi. Institut Pertanian Bogor.
Kunal SP, Kumar G, Menezes MR, Meena RM. 2014. Genetic homogeneity in longtail tuna Thunnus tonggol (Bleeker, 1851) from the northwest coast of India inferred from direct sequencing analysis of the mitochondrial DNA D-loop region. Marine Biol Res 10(7): 738-743.
Kumar G, Kocour M. 2015. Population genetic structure of tunas inferred from molecular markers: a review. Rev in Fisheries Sci & Aquaculture 23(1): 72-89.
Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: Molecular Evolutionary Genetic Analysis across Computing Platform. Mol Biol Evol 35(6): 1547–1549.
Lee WJ, Conroy J, Howell WH, Kocher TD. 1995. Structure and evolution of teleost mitochondrial control regions. J Mol Evol 41(1): 54–66.
Lee T, Fukumori I, Menemenlis D, Xing Z, Fu LL. 2002. Effects of the Indonesian throughflow on the Pacific and Indian Oceans. J Physic Oceanography 32(5): 1404-1429.
Malik MDA, Pertiwi NPD., Sembiring A, Yusmalinda NLA, Ningsih EY, Astarini IA. 2020. Genetic structure of Longtail Tuna Thunnus tonggol (Bleeker, 1851) in Java Sea, Indonesia. Biodiversitas 21(8): 3637-3643.
Nugraha B. 2009. Studi tentang genetika populasi ikan tuna mata besar (Thunus obesus) hasil tangkapan tuna longline yang didaratkan di Benoa. Tesis. Bogor (ID): Institut Pertanian Bogor. 62 hal.
Nishida T, Chow S, Grewe P. 1998. Review and research plan on the stock structure of yellowfin tuna (T. albacares) and bigeye tuna (Thunnus obesus) in the Indian Ocean. Indian Ocean Tuna Commission, Victoria, Seychelles, 9 – 14 November, pp 230 – 236.
Padmaningrat KB, Karang IWGA, Rahman Assyakur AR. 2017. Aplikasi Sistem Informasi Geografis (SIG) dan Penginderaan Jauh untuk Pemetaan Daerah Penangkapan Ikan Tuna Mata Besar di Selatan Jawa dan Bali. J Marine Aquatic Sci 3(1): 70-83.
Pertiwi NPD, Nugraha, B, Sulistyaningsih, R.K., Jatmiko, I, Sembiring, A., Mahardani A, Cahyani, N.K.D., Anggoro, A. W., Madduppa, H.H, Sutikno, A., Barber, P. H., Mahardika, G.G. 2017. Lack of differentiation within the bigeye tuna population of Indonesia. Biodiversitas 18(4): 1406-1413.
Rahayu DA, Nugroho D. 2015. Biologi molekuler dalam prospektif konservasi. Plantaxia. ISBN: 978 – 602 – 72959 – 2 – 6. Yogyakarta.
Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A. 2017. DnaSP 6: DNA Sequence Polymorphism Analysis of Large Datasets. Mol. Biol. Evol. 34: 3299-3302. DOI: 10.1093/molbev/msx248
Savira M. 2012. Analisis Variasi D-loop DNA Mitokondria pada populasi Gajah Sumatera (Elephas Maximus Sumatranus) di Taman Nasional Way Kambas [skripsi]. Depok :Fakultas Matematika dan Ilmu Pengetahuan Alam.h al 76.
Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4): 406–425.
Verawati I. 2015. Identifikasi Molekuler, Keragaman Genetik Dan Karakteristik Habitat Siput Laut (Nudibranchia) Dari Beberapa Populasi Di Indonesia [Skripsi]. Departemen Ilmu dan Teknologi Kelautan. Fakultas Perikanan dan Ilmu Kelautan. Institut Pertanian Bogor. Bogor.
Wijana IMS, Mahardika IGN. 2010. Struktur genetik dan filogeni yellowfin tuna (Thunnus albacares) berdasarkan sekuesn DNA mitokondria control region sitokrom oksidase I pada diversitas zone biogeografi. Jurnal Bumi Lestari. 10(2): 270 – 274.
Walsh PS, Metzger DA, Higushi R. 1991. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. BioTechniques 10 (4): 506–513.
White WT, Last PR, Dharmadi, Faizah R, Chodrijah U, Prisantoso BI, Pogonoski JJ, Puckridge M, Blaber SJM. 2013. Market fishes of Indonesia (jenis – jenis ikan di Indonesia. ACIAR Monograph No. 155. Autralian Center for internasional Agriculture Research : Canberra. 438 pp.
Willette DA, Santos MD, Leadbitter D. (2016). Lontail tuna Thunnus tonggol (Bleeker, 2851) shows genetic partitioning across, nut not within, basins of the Indo-Pasific based on mitochondrial DNA. J Appl Ichthyol 32(2): 312-323.
Abdulhaleem SZ. 1989. Gill raker counts: a possible means of stock separation for longtail tuna (Thunnus tonggol) in the Indian Ocean. Indo-Pac. Tuna Dev. Mgt. Programme IPTP/89/GEN/, 16: 64–68.
Akbar N, Zamani NP, Madduppa HH. 2014. Keragaman genetik ikan tuna sirip kuning (Thunnus albacares) dari dua populasi di Laut Maluku, Indonesia. DEPIK Jurnal Ilmu-Ilmu Perairan, Pesisir dan Perikanan 3 (1): 65-73.
Alfajri SI. 2017. Kepentingan Indonesia Mengekspor Ikan Tuna Ke Amerika Serikat Tahun 2012-2015. Fakultas Ilmu Sosial dan Ilmu Politik. Universitas Riau.
Allen GR, Erdmann MV, Pertiwi PD. 2017. Description of four new species of damselfishes (Pomacentridae) in the Pomacentrus philippinus complex from the tropical western Pacific Ocean. J Ocean Sci Found 25: 47-76.
Astuti D, Kurniati H. 2010. Keragaman Genetik Amfibia Kodok (Rana nicobariensis) di Ecology Park, Cibinong Berdasarkan Sekuen DNA dari Mitokondria D-loop. Jurnal Biologi Indonesia 6(3): 405-414.
Barata RBY, Setyono H, Harsono G. 2014. Dinamika upwelling dan downwelling berdasarkan variabilitas suhu permukaan laut dan klorofil-a di perairan Selatan Jawa. Jurnal Oseanografi 3(1): 57-66.
Excoffier L, Lischer HE. 2010. Arlequin suite ver 3.5 a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10(3): 564-567.
Griffiths SP, Fry GC, Manson FJ,Lou DC. 2010. Age and growth of Longtail Tuna (Thunnus tonggol) in tropical and temperate waters of the central Indo-Pacific. ICES J Mar Sci 67(1): 125-134.
Griffiths SP, Leadbitter D, Willette D, Kaymaram F, Moazzam M. 2020. Longtail tuna, Thunnus tonggol (Bleeker, 1851): a global review of population dynamics, ecology, fisheries, and considerations for future conservation and management. Rev in Fish Biol and Fisheries 30(1): 25-66.
Grewe P, Hampton J. 1998. An assessment of bigeye tuna (Thunnus obesus) population structure in the Pasific Ocean, based on mitochondrial DNA and DNA microsatellite analysis. Marine Research. Commonwealth Scientific and Industrial Research Organisation, Australia.
Habibi A, Sugiyanta DA. Perikanan Tuna-Panduan Penangkapan dan Penanganan. 2011. Seri Panduan Perikanan Skala Kecil. Best Management Practices. WWF-Indonesia. 27 hal.
Hany Y, Hidayat T. 2018. Analisis pertumbuhan dan laju eksploitasi ikan tongkol abu – abu, Thunnus tonggol (Bleeker, 1851) Di Perairan Lautan Jawa. Balai Riset Perikanan Laut. Bogor. Volume 10 No. 2.
Hughes AR, Inouye BD, Johnson MTJ, Underwood N, Vellend M. 2008. Ecological consequences of genetic diversity. Ecol letters 11: 609 – 623.
Joka SG. 2013. Stuktur genetik dan filogenetik ikan tuna (Thunnus sp.) di TPI Tanjung Luar, Lombok berdasarkan DNA Mitokondria. Skripsi. Institut Pertanian Bogor.
Kunal SP, Kumar G, Menezes MR, Meena RM. 2014. Genetic homogeneity in longtail tuna Thunnus tonggol (Bleeker, 1851) from the northwest coast of India inferred from direct sequencing analysis of the mitochondrial DNA D-loop region. Marine Biol Res 10(7): 738-743.
Kumar G, Kocour M. 2015. Population genetic structure of tunas inferred from molecular markers: a review. Rev in Fisheries Sci & Aquaculture 23(1): 72-89.
Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: Molecular Evolutionary Genetic Analysis across Computing Platform. Mol Biol Evol 35(6): 1547–1549.
Lee WJ, Conroy J, Howell WH, Kocher TD. 1995. Structure and evolution of teleost mitochondrial control regions. J Mol Evol 41(1): 54–66.
Lee T, Fukumori I, Menemenlis D, Xing Z, Fu LL. 2002. Effects of the Indonesian throughflow on the Pacific and Indian Oceans. J Physic Oceanography 32(5): 1404-1429.
Malik MDA, Pertiwi NPD., Sembiring A, Yusmalinda NLA, Ningsih EY, Astarini IA. 2020. Genetic structure of Longtail Tuna Thunnus tonggol (Bleeker, 1851) in Java Sea, Indonesia. Biodiversitas 21(8): 3637-3643.
Nugraha B. 2009. Studi tentang genetika populasi ikan tuna mata besar (Thunus obesus) hasil tangkapan tuna longline yang didaratkan di Benoa. Tesis. Bogor (ID): Institut Pertanian Bogor. 62 hal.
Nishida T, Chow S, Grewe P. 1998. Review and research plan on the stock structure of yellowfin tuna (T. albacares) and bigeye tuna (Thunnus obesus) in the Indian Ocean. Indian Ocean Tuna Commission, Victoria, Seychelles, 9 – 14 November, pp 230 – 236.
Padmaningrat KB, Karang IWGA, Rahman Assyakur AR. 2017. Aplikasi Sistem Informasi Geografis (SIG) dan Penginderaan Jauh untuk Pemetaan Daerah Penangkapan Ikan Tuna Mata Besar di Selatan Jawa dan Bali. J Marine Aquatic Sci 3(1): 70-83.
Pertiwi NPD, Nugraha, B, Sulistyaningsih, R.K., Jatmiko, I, Sembiring, A., Mahardani A, Cahyani, N.K.D., Anggoro, A. W., Madduppa, H.H, Sutikno, A., Barber, P. H., Mahardika, G.G. 2017. Lack of differentiation within the bigeye tuna population of Indonesia. Biodiversitas 18(4): 1406-1413.
Rahayu DA, Nugroho D. 2015. Biologi molekuler dalam prospektif konservasi. Plantaxia. ISBN: 978 – 602 – 72959 – 2 – 6. Yogyakarta.
Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A. 2017. DnaSP 6: DNA Sequence Polymorphism Analysis of Large Datasets. Mol. Biol. Evol. 34: 3299-3302. DOI: 10.1093/molbev/msx248
Savira M. 2012. Analisis Variasi D-loop DNA Mitokondria pada populasi Gajah Sumatera (Elephas Maximus Sumatranus) di Taman Nasional Way Kambas [skripsi]. Depok :Fakultas Matematika dan Ilmu Pengetahuan Alam.h al 76.
Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4): 406–425.
Verawati I. 2015. Identifikasi Molekuler, Keragaman Genetik Dan Karakteristik Habitat Siput Laut (Nudibranchia) Dari Beberapa Populasi Di Indonesia [Skripsi]. Departemen Ilmu dan Teknologi Kelautan. Fakultas Perikanan dan Ilmu Kelautan. Institut Pertanian Bogor. Bogor.
Wijana IMS, Mahardika IGN. 2010. Struktur genetik dan filogeni yellowfin tuna (Thunnus albacares) berdasarkan sekuesn DNA mitokondria control region sitokrom oksidase I pada diversitas zone biogeografi. Jurnal Bumi Lestari. 10(2): 270 – 274.
Walsh PS, Metzger DA, Higushi R. 1991. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. BioTechniques 10 (4): 506–513.
White WT, Last PR, Dharmadi, Faizah R, Chodrijah U, Prisantoso BI, Pogonoski JJ, Puckridge M, Blaber SJM. 2013. Market fishes of Indonesia (jenis – jenis ikan di Indonesia. ACIAR Monograph No. 155. Autralian Center for internasional Agriculture Research : Canberra. 438 pp.
Willette DA, Santos MD, Leadbitter D. (2016). Lontail tuna Thunnus tonggol (Bleeker, 2851) shows genetic partitioning across, nut not within, basins of the Indo-Pasific based on mitochondrial DNA. J Appl Ichthyol 32(2): 312-323.
Most read articles by the same author(s)
- NI PUTU DIAN PERTIWI, MAULID DIO SUHENDRO, NI LUH ASTRIA YUSMALINDA, I NYOMAN GIRI PUTRA, I GUSTI RICCA MAHATMA PUTRI, ENEX YUNI ARTININGSIH, M. DANIE AL-MALIK, NI KADEK DITA CAHYANI, ANDRIANUS SEMBIRING, Forensic genetic case study: Species identification and traceability of sea turtle caught in illegal trade in Bali, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 21 No. 9 (2020)
- IDA AYU PUTRI DARMAWATI, IDA AYU ASTARINI, HESTIN YUSWANTI, YUYUN FITRIANI, Pollination compatibility of Dendrobium spp. orchids from Bali, Indonesia, and the effects of adding organic matters on seed germination under in vitro culture , Biodiversitas Journal of Biological Diversity: Vol. 22 No. 5 (2021)
- AJIE IMAMSYAH, I WAYAN ARTHANA, IDA AYU ASTARINI, The influence of physicochemical environment on the distribution and abundance of mangrove gastropods in Ngurah Rai Forest Park Bali, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 21 No. 7 (2020)
- M. DANIE AL MALIK, NI PUTU DIAN PERTIWI, ANDRIANUS SEMBIRING, NI LUH ASTRIA YUSMALINDA, ENEX YUNIARTI NINGSIH, IDA AYU ASTARINI, Short Communication: Genetic structure of Longtail Tuna Thunnus tonggol (Bleeker, 1851) in Java Sea, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 21 No. 8 (2020)
- IDA AYU ASTARINI, MADE RIA DEFIANI, NI LUH SURIANI, PHILLIP D. GRIFFITHS, KATIA STEFANOVA, KADAMBOT H.M. SIDDIQUE, Adaptation of broccoli (Brassica oleracea var. italica L.) to high and low altitudes in Bali, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 21 No. 11 (2020)
- IDA AYU PUTRI DARMAWATI, I NYOMAN RAI, RINDANG DWIYANI, IDA AYU ASTARINI, Short Communication: The diversity of wild Dendrobium (Orchidaceae) in Central Bali, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 19 No. 3 (2018)
- GESTEN HAZERI, DWI LISTYO RAHAYU, BEGINER SUBHAN, ANDRIANUS SEMBIRING, AJI WAHYU ANGGORO, AHMAD TAUFIK GHOZALI, HAWIS H MADDUPPA, Latitudinal species diversity and density of cryptic crustacean (Brachyura and Anomura) in micro-habitat Autonomous Reef Monitoring Structures across Kepulauan Seribu, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 20 No. 5 (2019)
- PREHADI PREHADI, ANDRIANUS SEMBIRING, EKA MAYA KURNIASIH, RAHMAD RAHMAD, DONDY ARAFAT, BEGINER SUBHAN, HAWIS H. MADDUPPA, DNA barcoding and phylogenetic reconstruction of shark species landed in Muncar fisheries landing site in comparison with Southern Java fishing port , Biodiversitas Journal of Biological Diversity: Vol. 16 No. 1 (2015)
- MUHAMMAD DANIE AL MALIK, MOCHAMAD IQBAL HERWATA PUTRA, EDY TOPAN, NI PUTU DIAN PERTIWI, ENEX YUNI ARTININGSIH, SILA KARTIKA SARI, SARAH LEWIS, DERTA PRABUNING, ANDRIANUS SEMBIRING, Short Communication: Genetic variation of oceanic manta ray (Mobula birostris) based on mtDNA data in the Savu Sea, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 23 No. 3 (2022)
- NI PUTU DIAN PERTIWI, BUDI NUGRAHA, RIRIK KARTIKA SULISTYANINGSIH, IRWAN JATMIKO, ANDRIANUS SEMBIRING, ANGKA MAHARDINI, NI KADEK DITA CAHYANI, AJI WAHYU ANGGORO, HAWIS H. MADDUPPA, PAUL H. BARBER, GUSTI NGURAH MAHARDIKA, Short Communication: Lack of differentiation within the bigeye tuna population of Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 18 No. 4 (2017)