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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) · pp. 323–332

DOI
10.14710/ik.ijms.31.3.323-332
ISSN
2406-7598, 0853-7291
Published
2026-09-10
Publisher
Marine Science Department Diponegoro University
Language
eng
License
creativecommons.org/licenses/by-sa/4.0

Abstract

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.

Keywords

Collaboration network of the authors

40 authors · 127 co-authorship links · 9 across different organisations · showing the 40 most connected

Hover or tap a name to highlight its co-authors. Double-click to open the author's page.

  • University of Brawijaya
  • Universitas Papua
  • Musamus Merauke University
  • Cenderawasih University
  • Affiliation unknown
  • Different organisations
  • Same organisation
  • Affiliation unknown
  • Thicker line = more joint articles · bigger circle = more articles
Show as table
Co-authorOrganisationJoint articles
Risky Hadi WibowoAffiliation unknown6
Abdul Hamid A. TohaUniversitas Papua6
Ridwan SalaUniversitas Papua5
Daniel Frikli MokodonganAffiliation unknown5
Debora Christin PurbaniAffiliation unknown5
Destia Fitri AriyaniUniversity of Brawijaya3
Nisa Rachmania MubarikAffiliation unknown2
Iman RusmanaAffiliation unknown2
Maggy Thenawidjaya SuhartonoAffiliation unknown2
Welly DarwisAffiliation unknown2
Putri Hezekiel Claracia SimanjuntakAffiliation unknown2
Lalu Panji Imam AgamawanCenderawasih University1
Dandi SalekyMusamus Merauke University1
Febriyana Novita DamayantiUniversity of Brawijaya1
Agoes SoeprijantoUniversity of Brawijaya1
Surya Dewa RamadhanUniversity of Brawijaya1
Maheno Sri WidodoUniversity of Brawijaya1
Rakhmad Ndaru PratamaUniversity of Brawijaya1
Corazon Ell Merilia Papuani MayorUniversitas Papua1
Alberth W. RenyaanUniversitas Papua1
Dian Fita LestariAffiliation unknown1
Santi Nurul KamilahAffiliation unknown1
Fepta AryantiAffiliation unknown1
Jarulis JarulisAffiliation unknown1
Sarwo Sucitra AminAffiliation unknown1
Athina RousselyAffiliation unknown1
Faiz MuttaqyAffiliation unknown1
Atin Nur AuliaAffiliation unknown1
Ade Surya PutraAffiliation unknown1
Annisa Prastika SupriyantoAffiliation unknown1
Rochmah SupriatiAffiliation unknown1

Affiliations come from OpenAlex; journal OAI-PMH metadata carries none. Authors without an OpenAlex ID are matched by name, which can merge or split people.

Metadata source: OAI-PMH (metadata jurnal) http://ejournal.undip.ac.id/index.php/ijms/oai, first harvested 8 Nov 2026, last seen 8 Nov 2026.
Original metadata (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>
</oai_dc:dc>