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Diversity of Scombridae in Cenderawasih Bay, Papua, as Revealed by DNA Barcoding

ILMU KELAUTAN: Indonesian Journal of Marine Sciences · Vol. 31 No. 3 (2026) · hlm. 323–332

DOI
10.14710/ik.ijms.31.3.323-332
ISSN
2406-7598, 0853-7291
Terbit
2026-09-10
Penerbit
Marine Science Department Diponegoro University
Bahasa
eng
Lisensi
creativecommons.org/licenses/by-sa/4.0

Abstrak

The family Scombridae comprises economically important pelagic fishes traded across. However, taxonomic knowledge of Scombridae in Cenderawasih Bay remains remarkably limited. This study applied DNA barcoding of the mitochondrial cytochrome c oxidase subunit I (COI) gene for species taxonomy resolution. A total of 57 specimens were successfully sequenced and identified through BLAST against the NCBI database. We detected 12 species from 9 genera, namely Auxis thazard, Katsuwonus pelamis, Euthynnus affinis, Thunnus albacares, Acanthocybium solandri, Scomberomorus commerson, Gymnosarda unicolor, Grammatorcynus bilineatus, Thunnus obesus, Rastrelliger kanagurta, Rastrelliger faughni, and Rastrelliger brachysoma. Genetic diversity varied among the five focal species analyzed; Thunnus albacares and Auxis thazard exhibited the lowest haplotype diversity, indicating potential population vulnerability. Intraspecific genetic distances were below 2%, while interspecific distances exceeded 2%, confirming the effectiveness of the COI gene for species discrimination. Phylogenetic reconstruction produced well-supported clades consistent with established taxonomic relationships. The observed species composition in Cenderawasih Bay was dominated by widespread Indo-Pacific taxa. Notably, among the five tuna species (Thunnus spp.) known to occur in Indonesian waters, only Thunnus albacares and Thunnus obesus was detected in Cenderawasih Bay, raising the question of what ecological and oceanographic factors limit the presence of other tuna species. The ecological characteristics of Cenderawasih Bay are suggested to contribute to shaping the local Scombridae diversity patterns. These findings provide a fundamental genetic reference for Scombridae fisheries management and highlight the need for further oceanographic and ecological studies to understand the mechanisms driving species composition in the unique marine environment of Cenderawasih Bay.

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  • Universitas Papua
  • University of Brawijaya
  • University of Bengkulu
  • IPB University
  • National Research and Innovation Agency
  • National Sun Yat-sen University
  • Diponegoro University
  • Organisasi lain
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Rekan penulisOrganisasiArtikel bersama
Risky Hadi WibowoAfiliasi tidak diketahui6
Ridwan SalaUniversitas Papua6
Debora Christin PurbaniNational Research and Innovation Agency6
Daniel F. MokodonganNational Research and Innovation Agency6
Destia Fitri AriyaniUniversity of Brawijaya4
Dian Fita LestariUniversity of Bengkulu2
Nisa Rachmania MubarikIPB University2
İman RusmanaIPB University2
Welly DarwisUniversity of Bengkulu2
Lalu Panji Imam AgamawanCenderawasih University2
Dandi SalekyMusamus Merauke University2
Corazon Ell Merilia Papuani MayorUniversitas Papua2
Alberth W. RenyaanUniversitas Papua2
Ambariyanto AmbariyantoDiponegoro University2
Emmanuel ManangkulangiAfiliasi tidak diketahui1
Fanny F. C. SimatauwAfiliasi tidak diketahui1
Tutik HandayaniUniversitas Papua1
Yohanes AibesaUniversitas Papua1
Mudjirahayu MudjirahayuUniversitas Papua1
Fitriyah Irmawati Elyas SalehUniversitas Papua1
Tasya M.R. SihabudinUniversitas Papua1
Vera SabariahUniversitas Papua1
Yuli E. DemanaInstitut Agama Islam Al-Yasini Pasuruan1
Febriyana Novita DamayantiUniversity of Brawijaya1
Agoes SoeprijantoUniversity of Brawijaya1
Surya Dewa RamadhanUniversity of Brawijaya1
Maheno Sri WidodoUniversity of Brawijaya1
Rakhmad Ndaru PratamaUniversity of Brawijaya1
Dedi ParendenUniversitas Papua1
Novelina TampubolonUniversitas Papua1
Jesihando Rafael TulungUniversitas Papua1

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Sumber metadata: OAI-PMH (metadata jurnal) http://ejournal.undip.ac.id/index.php/ijms/oai, pertama di-harvest 8 Nov 2026, terakhir terlihat 8 Nov 2026.
Metadata asli (oai_dc) 
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	<dc:title xml:lang="en-US">Diversity of Scombridae in Cenderawasih Bay, Papua, as Revealed by DNA Barcoding</dc:title>
	<dc:creator>Pranata, Bayu</dc:creator>
	<dc:creator>Toha, Abdul H.A.</dc:creator>
	<dc:creator>Maulana, Dwi Muhammad</dc:creator>
	<dc:creator>Binur, Robi</dc:creator>
	<dc:creator>Dailami, Muhammad</dc:creator>
	<dc:creator>Wangi, Esie Mega</dc:creator>
	<dc:creator>Mundoni, Yerri D</dc:creator>
	<dc:creator>Sipriyadi, Sipriyadi</dc:creator>
	<dc:creator>Kusuma, Aradea Bujana</dc:creator>
	<dc:subject xml:lang="en-US">COI gene; mtDNA; Thunnus; Diversity; Phylogenetic</dc:subject>
	<dc:description xml:lang="en-US">The family Scombridae comprises economically important pelagic fishes traded across. However, taxonomic knowledge of Scombridae in Cenderawasih Bay remains remarkably limited. This study applied DNA barcoding of the mitochondrial cytochrome c oxidase subunit I (COI) gene for species taxonomy resolution. A total of 57 specimens were successfully sequenced and identified through BLAST against the NCBI database. We detected 12 species from 9 genera, namely Auxis thazard, Katsuwonus pelamis, Euthynnus affinis, Thunnus albacares, Acanthocybium solandri, Scomberomorus commerson, Gymnosarda unicolor, Grammatorcynus bilineatus, Thunnus obesus, Rastrelliger kanagurta, Rastrelliger faughni, and Rastrelliger  brachysoma. Genetic diversity varied among the five focal species analyzed; Thunnus albacares and Auxis thazard exhibited the lowest haplotype diversity, indicating potential population vulnerability. Intraspecific genetic distances were below 2%, while interspecific distances exceeded 2%, confirming the effectiveness of the COI gene for species discrimination. Phylogenetic reconstruction produced well-supported clades consistent with established taxonomic relationships. The observed species composition in Cenderawasih Bay was dominated by widespread Indo-Pacific taxa. Notably, among the five tuna species (Thunnus spp.) known to occur in Indonesian waters, only Thunnus albacares and Thunnus obesus was detected in Cenderawasih Bay, raising the question of what ecological and oceanographic factors limit the presence of other tuna species. The ecological characteristics of Cenderawasih Bay are suggested to contribute to shaping the local Scombridae diversity patterns. These findings provide a fundamental genetic reference for Scombridae fisheries management and highlight the need for further oceanographic and ecological studies to understand the mechanisms driving species composition in the unique marine environment of Cenderawasih Bay.</dc:description>
	<dc:publisher xml:lang="en-US">Marine Science Department Diponegoro University</dc:publisher>
	<dc:date>2026-09-10</dc:date>
	<dc:type>info:eu-repo/semantics/article</dc:type>
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	<dc:identifier>https://ejournal.undip.ac.id/index.php/ijms/article/view/78642</dc:identifier>
	<dc:identifier>10.14710/ik.ijms.31.3.323-332</dc:identifier>
	<dc:source xml:lang="en-US">ILMU KELAUTAN: Indonesian Journal of Marine Sciences; Vol 31, No 3 (2026): Ilmu Kelautan; 323-332</dc:source>
	<dc:source>2406-7598</dc:source>
	<dc:source>0853-7291</dc:source>
	<dc:language>eng</dc:language>
	<dc:relation>https://ejournal.undip.ac.id/index.php/ijms/article/view/78642/pdf</dc:relation>
	<dc:relation>https://ejournal.undip.ac.id/index.php/ijms/article/downloadSuppFile/78642/24778</dc:relation>
	<dc:rights xml:lang="en-US">Copyright (c) 2026 ILMU KELAUTAN: Indonesian Journal of Marine Sciences</dc:rights>
	<dc:rights xml:lang="en-US">https://creativecommons.org/licenses/by-sa/4.0</dc:rights>
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