Review: Progress and potential of DNA barcoding for species identification of fish species

Imtiaz, Ayesha; Nor, Siti Azizah Mohd; Naim, Darlina Md.

doi:10.13057/biodiv/d180415

Cited by 32 publications

(24 citation statements)

References 91 publications

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“…The species identification is considered success when the barcoding gap was detected (Meyer and Paulay 2005;Meier et al 2008). This method also successfully assessed the power of COI as DNA barcoding marker in another insect species such as ladybird beetles (Coleoptera: Coccinellidae) (Wang et al 2019), fish species (Imtiaz et al 2017;Bramandito et al 2018), coffee pollinator insects (Sitompul et al 2018), Xyleborus sp. (Coleoptera: Scolytinae) (Chang et al 2014) or even a general soil insect (Nyamwasa et al 2017).…”

Section: Discussionmentioning

confidence: 98%

Molecular identification and population genetic study of Elaeidobius kamerunicus Faust. (Coleoptera: Curculionidae) from Indonesia, Malaysia and Cameroon based on mitochondrial gene

et al. 2020

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Abstract. Tambunan VB, Apriyanto A, Ajambang W, Etta CE, Sahari B, Buchori D, Hidayat P. 2020. Molecular identification and population genetic study of Elaeidobius kamerunicus Faust. (Coleoptera: Curculionidae) from Indonesia, Malaysia and Cameroon based on mitochondrial gene. Biodiversitas 21: 3263-3270. Oil palm pollinating weevil Elaeidobius kamerunicus is a very important insect pollinator in oil palm plantation. However, there is still lack of information about molecular identification and population genetic study in this species. The purpose of this study was to explore the effectiveness of oil palm pollinating weevil identification using mitochondrial DNA of COI gene and to assess its genetic variation between different locations and countries. We sequenced the DNA barcode of 36 individuals of this species using the mtDNA Cytochrome Oxidase I (COI) gene to explore their genetic variation, identity and phylogenetic relationship. The COI gene sequences generated from this study were successful in identifying E. kamerunicus. Phylogenetic analysis also revealed 3 well-supported monophyletic haplogroups of E. kamerunicus population. In addition, genetic differentiation analysis revealed that most populations from Indonesia were different from Malaysian and Cameroonian populations indicating that there was a genetic variation between the population samples from these countries. The overall E. kamerunicus used in this study were geographically structured in two regions; outside Indonesia region (Cameroon and Malaysia) and Indonesia region. These results demonstrate the feasibility of using COI gene sequence for molecular identification and population genetic study of E. kamerunicus species.

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Section: Discussionmentioning

confidence: 98%

Molecular identification and population genetic study of Elaeidobius kamerunicus Faust. (Coleoptera: Curculionidae) from Indonesia, Malaysia and Cameroon based on mitochondrial gene

et al. 2020

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“…Partial COI allows the genetic identification of species in numerous taxa. Divergence, which appeared by mutation over time, between different individual's sequences is low for individuals of the same species and high between individuals of a different species (Imtiaz et al 2017;Md-Zain et al 2018a;Md-Zain et al 2018b;Roesma et al 2019;Nuryanto et al 2019). This paper also provides a description based on morphometric, meristic, and molecular data (COI) of S. auxilimentus from Sangihe Island, North Sulawesi, Indonesia.…”

Section: Introductionmentioning

confidence: 99%

Short Communication: Presence of the vulnerable freshwater goby Sicyopus auxilimentus (Gobiidae, Sicydiinae) on Sangihe Island, Indonesia

Hasan

Valen²,

Islamy

et al. 2021

Biodiversitas

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Abstract. Hasan V, Valen FS, Islamy RA, Widodo MS, Saptadjaja AM, Islam I. 2021. Short Communication: Presence of the vulnerable freshwater goby Sicyopus auxilimentus (Gobiidae, Sicydiinae) on Sangihe Island, Indonesia. Biodiversitas 22: 571-579. A single specimen of freshwater goby Sicyopus auxilimentus was photographed and collected using fish traps between 8 and 15 September 2019 in the Laine waterfall, Sangihe island district, North Sulawesi Province, Indonesia. S. auxilimentus is amphidromous that live in both freshwater and marine environments. This species is currently listed as Vulnerable (VU) within the IUCN Red List Status. The specimen was identified as male S. auxilimentus based on the coloration of the preserved specimen: background yellowish; scale edges brown; posterior flanks and caudal peduncle orange; first dorsal fin black, second dorsal fin dusky black; pectoral fin slightly brown; ventral fin slightly dusky; anal fin blackish; caudal fin dusky brown. Specific morphological features were as follows: the base of the first dorsal fin was not connected to the second dorsal fin base; distance between the base of first and second dorsal fin was generally less than half of eye diameter; ventral fin rays were fused to belly only between fifth rays; posterior margin of caudal fins rays was rounded; scales were all ctenoid; scales appeared on the caudal peduncle, and between anal and second dorsal fins; anterior to which, scales became widely spaced and did not imbricate. Meristic characters were as follows: first dorsal fin rays VI; second dorsal fin rays I+9; ventral fin rays I+5; pectoral-fin rays 14; anal-fin rays I+9; caudal-fin rays 13; scales in lateral series 13; scales in zigzag series 7; scales in transverse series backward 7; scales in transerves series forward 4. This finding is considered the first record in Sulawesi and the fifth from Indonesian waters after findings in Halmahera, Java, Bali and Lombok. This record enhances the understanding of the distribution of S. auxilimentus in Indonesian waters. Monitoring is needed to assess the possibility of Sangihe Island being a growth ground, spawning ground, and/or on the migration route of S. auxilimentus. In the Laine waterfall, Sangihe island, freshwater conditions were as follows: salinity 3.5 psu, temperature 23-25°C, and dissolved oxygen 7.7-9.2 mg/l, which were ideal habitat for S. auxilimentus. S. auxilimentus from Sangihe Island, had 0.000 genetic distance than from S. auxilimentus from Bali, while the next closest genetic distance was S. zosterophorus at genetic distance of 0.090. In addition to onsite conservation, domestication programs are needed to increase commercial availability without depending on natural catches.

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“…Furthermore, the number of individual for some species investigated in this study was limited with only four individuals (N. peronii and N. nemurus). It is also well understood that the quantitative data such as geometric morphometrics does not predict true phylogeny as what the molecular data can suggests (Imtiaz et al 2017). However, the question of discrimination among taxa on basis of shape differences can be resolved on the basis of the geometric taxonomy as demonstrated in this current study.…”

Section: Pairwise Differences Among Taxamentioning

confidence: 77%

Geometric morphometrics species discrimination within the Genus Nemipterus from Malaysia and its surrounding seas

Imtiaz¹,

Naim

2018

Biodiversitas

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Imtiaz A, Md Naim D. 2018. Geometric morphometrics species discrimination within the Genus Nemipterus from Malaysia and its surrounding seas. Biodiversitas 19: 2316-2322. High demand of fish protein diet and exposure of marine fish to a challenging marine environment has increased the importance of advanced fisheries research especially in Malaysian waters, particularly research related to taxonomy, biology, diversity, population structure as well as phylogenetic histories of commercially important marine fish species to ensure continuous supply of fish and fish products. This current research aimed to explore the potential of geometric morphometrics method to discriminate among taxa of genus Nemipterus through body size and shape differences. A total of 171 individuals representing ten species of genus Nemipterus collected from Malaysia and its surrounding seas were examined. The resulting homologous landmarks were subjected to generalized procustes analysis followed by principal component analysis. Principle component scores were further investigated to cross-validated discriminant analysis to determine the efficacy of landmarks in discriminating by taxon. Our finding shows that species within the genus Nemipterus can be differentiated using geometric morphometrics method as strongly depicted by canonical variance analysis. This current study is the first report utilizing geometric morphometrics approach conducted on the genus Nemipterus from Malaysian waters.

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Review: Progress and potential of DNA barcoding for species identification of fish species

Cited by 32 publications

References 91 publications

Molecular identification and population genetic study of Elaeidobius kamerunicus Faust. (Coleoptera: Curculionidae) from Indonesia, Malaysia and Cameroon based on mitochondrial gene

Molecular identification and population genetic study of Elaeidobius kamerunicus Faust. (Coleoptera: Curculionidae) from Indonesia, Malaysia and Cameroon based on mitochondrial gene

Short Communication: Presence of the vulnerable freshwater goby Sicyopus auxilimentus (Gobiidae, Sicydiinae) on Sangihe Island, Indonesia

Geometric morphometrics species discrimination within the Genus Nemipterus from Malaysia and its surrounding seas

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