Assessing the species composition of tropical eels (Anguillidae) in Aceh Waters, Indonesia, with DNA barcoding gene
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Abstract

The objective of the present study was to evaluate the species diversity of eels native to Aceh waters based on genetic data. Sampling was conducted in western coast waters of Aceh Province, Indonesia, from July to August 2016. Genomic DNA was extracted from the samples, a genomic region from the 5’ region of the cox1 gene was amplified and sequenced, and this was then used to analyse genetic variation. The genetic sequences were blasted into the NCBI database. Based on this analysis there were three valid species of eels that occurred in Aceh waters, namely Anguilla marmorata, A. bicolor bicolor, and A. bengalensis bengalensis.

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Identification of Astyanax altiparanae (Teleostei, Characidae) in the Iguaçu River, Brazil, based on mitochondrial DNA and RAPD markers

Sônia M.A.P. Prioli, Alberto J. Prioli, Horácio Júlio Jr … (2002)

Astyanax fishes are among the most important food-web components of South America rivers. In the Iguaçu River basin, the Astyanax genus is represented mainly by endemic species. For millions of years, that hydrographic basin has been geographically isolated from the Paraná River basin by the Iguaçu Falls. Recently, a species from the Upper Paraná River basin identified as Astyanax bimaculatus was revised and described as a new species named Astyanax altiparanae Garutti & Britski, 2000. Fauna endemism and geographic isolation triggered interest in investigations to evaluate the identification and genetic relatedness among two A. altiparanae populations from the Upper Paraná River basin and the population identified as A. bimaculatus in the Iguaçu River, upstream from the Iguaçu Falls. Mitochondrial DNA sequences and RAPD markers revealed high genetic diversity within each population, as well as low genetic distance, high gene flow, and high mitochondrial DNA similarity among all three populations. In conjunction with morphological similarities, these results demonstrated that the population presently known as Astyanax bimaculatus in the Iguaçu River should actually be stated as Astyanax altiparanae. Furthermore, it could be inferred that the A. altiparanae population is not endemic and most likely it was recently introduced in the Iguaçu River basin, maintaining the ancestral genetic identity.

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Illegal trade of regulated and protected aquatic species in the Philippines detected by DNA barcoding.

Angelli Marie Jacynth M Asis, Joanne Lacsamana, Mudjekeewis Santos (2016)

Illegal trade has greatly affected marine fish stocks, decreasing fish populations worldwide. Despite having a number of aquatic species being regulated, illegal trade still persists through the transport of dried or processed products and juvenile species trafficking. In this regard, accurate species identification of illegally traded marine fish stocks by DNA barcoding is deemed to be a more efficient method in regulating and monitoring trade than by morphological means which is very difficult due to the absence of key morphological characters in juveniles and processed products. Here, live juvenile eels (elvers) and dried products of sharks and rays confiscated for illegal trade were identified. Twenty out of 23 (87%) randomly selected "elvers" were identified as Anguilla bicolor pacifica and 3 (13%) samples as Anguilla marmorata. On the other hand, 4 out of 11 (36%) of the randomly selected dried samples of sharks and rays were Manta birostris. The rest of the samples were identified as Alopias pelagicus, Taeniura meyeni, Carcharhinus falciformis, Himantura fai and Mobula japonica. These results confirm that wild juvenile eels and species of manta rays are still being caught in the country regardless of its protected status under Philippine and international laws. It is evident that the illegal trade of protected aquatic species is happening in the guise of dried or processed products thus the need to put emphasis on strengthening conservation measures. This study aims to underscore the importance of accurate species identification in such cases of illegal trade and the effectivity of DNA barcoding as a tool to do this.

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Species identification using genetic tools: the value of nuclear and mitochondrial gene sequences in whale conservation.

S R Palumbi, Viviane Cipriano (2015)

DNA sequence analysis is a powerful tool for identifying the source of samples thought to be derived from threatened or endangered species. Analysis of mitochondrial DNA (mtDNA) from retail whale meat markets has shown consistently that the expected baleen whale in these markets, the minke whale, makes up only about half the products analyzed. The other products are either unregulated small toothed whales like dolphins or are protected baleen whales such as humpback, Bryde's, fin, or blue whales. Independent verification of such mtDNA identifications requires analysis of nuclear genetic loci, but this is technically more difficult than standard mtDNA sequencing. In addition, evolution of species-specific sequences (i.e., fixation of sequence differences to produce reciprocally monophyletic gene trees) is slower in nuclear than in mitochondrial genes primarily because genetic drift is slower at nuclear loci. When will use of nuclear sequences allow forensic DNA identification? Comparison of neutral theories of coalescence of mitochondrial and nuclear loci suggests a simple rule of thumb. The "three-times rule" suggests that phylogenetic sorting at nuclear loci is likely to produce species-specific sequences when mitochondrial alleles are reciprocally monophyletic and the branches leading to the mtDNA sequences of a species are three times longer than the average difference observed within species. A preliminary test of the three-times rule, which depends on many assumptions about the species and genes involved, suggests that blue and fin whales should have species-specific sequences at most neutral nuclear loci, whereas humpback and fin whales should show species-specific sequences at fewer nuclear loci. Partial sequences of actin introns from these species confirm the predictions of the three-times rule and show that blue and fin whales are reciprocally monophyletic at this locus. These intron sequences are thus good tools for the identification of these species and will afford a chance to identify putative hybrid blue/fin whales thought to have entered the retail market after 1989.

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Author and article information

Journal

Journal ID (nlm-ta): F1000Res

Journal ID (iso-abbrev): F1000Res

Journal ID (pmc): F1000Research

Title: F1000Research

Publisher: F1000Research (London, UK )

ISSN (Electronic): 2046-1402

Publication date (Electronic): 13 March 2017

Publication date Collection: 2017

Volume: 6

Electronic Location Identifier: 258

Affiliations

[1 ]Department of Aquaculture, Faculty of Marine and Fisheries, Syiah Kuala University, Banda Aceh, Indonesia

[2 ]School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia

[1 ]Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Tamil Nadu, India

[1 ]Genetic Fingerprinting Laboratory, National Fisheries Research and Development Institute, Quezon City, Philippines

[1 ]Department of Biology, University College of Taymma, University of Tabuk, Tabuk, Saudi Arabia

Author notes

[a ] muchlisinza@ 123456unsyiah.ac.id

ZAM is responsible for developing research proposal and study design and approved the final draft of the paper. ASB, NF, AAM, NF and AIU are responsible for sample collection, sample processing, and data analysis. MNS is responsible for manuscript sequence alignment and proofreading of the draft.

Competing interests: No competing interests were disclosed.

Author information

Zainal A. Muchlisin http://orcid.org/0000-0002-0858-1853

Nur Fadli http://orcid.org/0000-0001-6845-1383

Article

DOI: 10.12688/f1000research.10715.1

PMC ID: 5428524

SO-VID: 9368d15b-76b2-4f37-b409-f7156576e053

License:

This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

The author(s) is/are employees of the US Government and therefore domestic copyright protection in USA does not apply to this work. The work may be protected under the copyright laws of other jurisdictions when used in those jurisdictions.

History

Date accepted : 1 March 2017

Funding

Funded by: Syiah Kuala University

Award ID: 230/UN11.2/2016

This study was supported by Syiah Kuala University through the 2016 H index scheme (Contract number: 230/UN11.2/2016).

The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Assessing the species composition of tropical eels (Anguillidae) in Aceh Waters, Indonesia, with DNA barcoding gene cox1.

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Most cited references 12

Identification of Astyanax altiparanae (Teleostei, Characidae) in the Iguaçu River, Brazil, based on mitochondrial DNA and RAPD markers

Illegal trade of regulated and protected aquatic species in the Philippines detected by DNA barcoding.

Species identification using genetic tools: the value of nuclear and mitochondrial gene sequences in whale conservation.

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