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DNA Barcoding on Indian Ocean Squid, Uroteuthis duvaucelii (D'Orbigny, 1835) (Cephalopoda: Loliginidae) from the Java Sea, Indonesia

Jurnal Ilmiah Perikanan dan Kelautan · Vol. 14 No. 2 (2022) · hlm. 231–245

DOI
10.20473/jipk.v14i2.33448
ISSN
2528-0759, 2085-5842
Terbit
2022-08-30
Penerbit
Faculty of Fisheries and Marine Universitas Airlangga
Bahasa
eng
Lisensi
creativecommons.org/licenses/by-nc-sa/4.0

Abstrak

Highlight ResearchThe possibility of U. duvauceli be a polymorph cryptic species is further reinforced by the results of the present study.Phylogenetic analysis showed two separate clusters though did not perfectly segregate north to the south waters.Individuals in cluster II from the south coast showed the highest polymorphism levels by 40 segregating sites (S), compared to only 2-4 sites in that of cluster IFrequencies of A, C, G, and T in mitochondrial DNA of all specimens skewed toward A and T, with T being the most preferred and G being the least preferred nucleotideAll specimens showed no amino acid frequency for glutamic acid. Further, all four individuals in cluster II (south coast) were also have no amino acid frequencies for aspartic acid and valine as well.AbstractUroteuthis duvauceli (D' Orbigny, 1835) also known as the Indian Ocean Squid is a highly important commercial marine organism along the Java coast, Indonesia. Based on genetic variation this species-complex are polymorphic and cryptic. In the present study, the genetic diversity and stock structure of loliginid squid U. duvauceli is investigated using a mitochondrial gene cytochrome oxidase subunit I (COI). Samples were collected by hand-jigging onboard of an 8hp small fisher-boat equipped with a few lamps during May to August 2015, May 2016 and August to November 2018. Sample collection started at dusk until midnight. The attractor was a weighed-quill attached to nylon string, manually immersed into the water and pulled quickly and continuously for about 3-5 minutes at each effort. The determination was conducted with BLAST. Phylogenetic analysis showed two separate clusters with 100% bootstrap value, in which cluster II from Palabuhanratu has divergences of 5.9 - 7.0%, compared to cluster I. Genetic variations exist within and among individuals over the locations. Palabuhanratu individuals have the highest polymorphism levels compared to other locations as shown by 40 segregating sites (S). Frequencies of A, C, G, and T in mtDNA of the 20 specimens U. duvauceli are biased toward A and T, with T being the most favoured and G being the least favoured nucleotide. All specimen showed no amino acid frequency for glutamic acid and all four individuals in cluster II (south coast) also have no amino acid frequencies for aspartic acid and valine as well.

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  • Diponegoro University
  • Ministry of Marine Affairs and Fisheries
  • University of the Ryukyus
  • Alasmarya Islamic University
  • Universitas PGRI Ronggolawe
  • University of Tripoli
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Rekan penulisOrganisasiArtikel bersama
Widianingsih WidianingsihDiponegoro University12
Wilis Ari SetyatiDiponegoro University6
Hadi EndrawatiDiponegoro University4
Nining NursalimDiponegoro University4
Rudhi PribadiDiponegoro University4
Muhammad ZainuriDiponegoro University4
Ambariyanto AmbariyantoDiponegoro University4
Diah Permata WijayantiDiponegoro University4
Ervia YudiatiDiponegoro University3
Ita WidowatiDiponegoro University3
Muggi BachtiarUniversity of the Ryukyus2
Widianingsih WidianingsihAfiliasi tidak diketahui2
Valentina R. IrianiDiponegoro University2
Marita Ika JoesidawatiUniversitas PGRI Ronggolawe2
Ni Kadek Dita CahyaniDiponegoro University2
Sri RedjekiDiponegoro University2
Sutrisno AnggoroDiponegoro University2
Mostafa Imhmed IghwerbAlasmarya Islamic University2
Ria AzizahDiponegoro University2
Agus SabdonoDiponegoro University2
Hermin Pancasakti KusumaningrumDiponegoro University2
Elis IndrayantiDiponegoro University2
Ali DjunaediDiponegoro University2
Ocky Karna RadjasaDiponegoro University2
Jasiel Junior KarosekaliDiponegoro University1
Almay Atsiil Harits SyamDiponegoro University1
S. SubagiyoDiponegoro University1
Henna Rya AbdurachimAfiliasi tidak diketahui1
Husna El IksirohDiponegoro University1
Heri YantiAfiliasi tidak diketahui1
Nuril AzharDiponegoro University1
Rabia Omar AlghazeerUniversity of Tripoli1
Tri KaryawatiDiponegoro University1
Esti RudianaDiponegoro University1
Anastasia Dian RDiponegoro University1

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Sumber metadata: OAI-PMH (metadata jurnal) https://e-journal.unair.ac.id/index.php/JIPK/oai, pertama di-harvest 9 Nov 2026, terakhir terlihat 9 Nov 2026.
Metadata asli (oai_dc) 
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	<dc:title xml:lang="en-US">DNA Barcoding on Indian Ocean Squid, Uroteuthis duvaucelii (D'Orbigny, 1835) (Cephalopoda: Loliginidae) from the Java Sea, Indonesia</dc:title>
	<dc:creator>Norma Afiati</dc:creator>
	<dc:creator>Subagiyo, Subagiyo</dc:creator>
	<dc:creator>Handayani, Christina Retna</dc:creator>
	<dc:creator>Hartati, Retno</dc:creator>
	<dc:creator>Kholilah, Nenik</dc:creator>
	<dc:subject xml:lang="en-US">Uroteuthis duvauceli</dc:subject>
	<dc:subject xml:lang="en-US">mtDNA</dc:subject>
	<dc:subject xml:lang="en-US">COI</dc:subject>
	<dc:subject xml:lang="en-US">Java Sea</dc:subject>
	<dc:subject xml:lang="en-US">Indonesia</dc:subject>
	<dc:description xml:lang="en-US">Highlight ResearchThe possibility of U. duvauceli be a polymorph cryptic species is further reinforced by the results of the present study.Phylogenetic analysis showed two separate clusters though did not perfectly segregate north to the south waters.Individuals in cluster II from the south coast showed the highest polymorphism levels by 40 segregating sites (S), compared to only 2-4 sites in that of cluster IFrequencies of A, C, G, and T in mitochondrial DNA of all specimens skewed toward A and T, with T being the most preferred and G being the least preferred nucleotideAll specimens showed no amino acid frequency for glutamic acid. Further, all four individuals in cluster II (south coast) were also have no amino acid frequencies for aspartic acid and valine as well.AbstractUroteuthis duvauceli (D' Orbigny, 1835) also known as the Indian Ocean Squid is a highly important commercial marine organism along the Java coast, Indonesia. Based on genetic variation this species-complex are polymorphic and cryptic. In the present study, the genetic diversity and stock structure of loliginid squid U. duvauceli is investigated using a mitochondrial gene cytochrome oxidase subunit I (COI). Samples were collected by hand-jigging onboard of an 8hp small fisher-boat equipped with a few lamps during May to August 2015, May 2016 and August to November 2018. Sample collection started at dusk until midnight. The attractor was a weighed-quill attached to nylon string, manually immersed into the water and pulled quickly and continuously for about 3-5 minutes at each effort. The determination was conducted with BLAST. Phylogenetic analysis showed two separate clusters with 100% bootstrap value, in which cluster II from Palabuhanratu has divergences of 5.9 - 7.0%, compared to cluster I.  Genetic variations exist within and among individuals over the locations. Palabuhanratu individuals have the highest polymorphism levels compared to other locations as shown by 40 segregating sites (S). Frequencies of A, C, G, and T in mtDNA of the 20 specimens U. duvauceli are biased toward A and T, with T being the most favoured and G being the least favoured nucleotide. All specimen showed no amino acid frequency for glutamic acid and all four individuals in cluster II (south coast) also have no amino acid frequencies for aspartic acid and valine as well.</dc:description>
	<dc:publisher xml:lang="en-US">Faculty of Fisheries and Marine Universitas Airlangga</dc:publisher>
	<dc:date>2022-08-30</dc:date>
	<dc:type>info:eu-repo/semantics/article</dc:type>
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	<dc:identifier>https://e-journal.unair.ac.id/JIPK/article/view/33448</dc:identifier>
	<dc:identifier>10.20473/jipk.v14i2.33448</dc:identifier>
	<dc:source xml:lang="en-US">Jurnal Ilmiah Perikanan dan Kelautan; Vol. 14 No. 2 (2022): JURNAL ILMIAH PERIKANAN DAN KELAUTAN; 231-245</dc:source>
	<dc:source>2528-0759</dc:source>
	<dc:source>2085-5842</dc:source>
	<dc:language>eng</dc:language>
	<dc:relation>https://e-journal.unair.ac.id/JIPK/article/view/33448/17273</dc:relation>
	<dc:relation>https://e-journal.unair.ac.id/JIPK/article/view/33448/40880</dc:relation>
	<dc:rights xml:lang="en-US">Copyright (c) 2022 Jurnal Ilmiah Perikanan dan Kelautan</dc:rights>
	<dc:rights xml:lang="en-US">http://creativecommons.org/licenses/by-nc-sa/4.0</dc:rights>
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