Employing DNA barcoding as taxonomy and conservation tools for fish species censuses at the southeastern Mediterranean, a hot-spot area for biological invasion

Karahan, Arzu
PAZ, Guy
Kıdeyş, Ahmet Erkan
Goren, Menachem
This study evaluates the utility of DNA barcoding (mitochondrial cytochrome oxidase subunit I; COI) as a biodiversity and conservation applied tool for identifying fish fauna from the southeastern Mediterranean (the continental coast of Israel), a hot-spot area for biological invasion, also with an eye to establish the foundation for follow-up studies that will use environmental DNA (eDNA) tracks of native and invasive species, and for the application of eDNA concepts and methodologies in nature conservation. We established a dataset of 280 DNA barcodes, representing 110 marine fish species (all identified by a taxonomist), belonging to 75 native and 35 Lessepsian migratory species that were tested within and against the BOLD system database. Most of the query sequences showed 98% matches with reference DNA barcodes in the BOLD system excluding two Trachurus species, three Dasyatis pastinaca and two Rhinobatos rhino batos individuals. Relatively high intraspecific genetic distances were observed in two Elasmobranchii species (8.83%-18%), suggesting possible cryptic species. In contrast, relatively low interspecific genetic distances were found between two Actinopterygii species (1.54%). Gobiidae family members were observed as being the most scattered on the Bayesian tree. Out of the 110 fish species, 48 were taxonomically discordant with the BOLD BINs (4 at the family level, 15 at the genus level and 29 at the species level), 53 were concordant and 9 were singletons. Discordancy was noted for some Dip lodus and Fistularia species during the BOLD BIN analysis. Apogon queketti, Champsodon nudivittis and Cheilodipterus novemstriatus were uploaded to the BOLD system for the first time. We elucidated 177 haplotypes, 122 for the native fish species and 55 for the Lessepsian species. The results will allow the evaluation of invasive species success and will help developing improved policies for the conservation of Mediterranean biodiversity. (C) 2017 Elsevier GmbH. All rights reserved.


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DNA sequencing analysis of the mitochondrial DNA cytochrome oxidase H (COII) region was used to examine genetic variation in the termite genus Reticulitermes Holmgren. We examined 21 species and subspecies from three continents. Sequencing of a 677-bp region of a 780-bp amplicon from 41 individuals and from 17 sequences obtained from GenBank revealed 221 polymorphic sites within the genus. Tajima-Nei distances from species ranged from 0.9 to 12.7%, and parsimony and maximum likelihood analysis revealed seve...
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Random amplified polymorphic DNA (RAPD) fragments were used to assess genetic relationships among Cicer spp. growing in Turkey. Seven 10-mer primers selected from a 50 random oligonucleotide primer set, depending on their ability to amplify genomic DNA in all species, were used to detect RAPD variation in 43 wild and cultivated accessions representing ten species. These primers yielded 95 reproducible amplification products, 92 of which were polymorphic. Pairwise,genetic distances of accessions estimated ac...
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Topoisomerase II alpha (Topo IIα) is one of the essential enzymes in cell viability. It is required for cell cycle progression due to its role in regulating the topological constraints during DNA replication and transcription. Due to its role, Topo IIα became one of the extensively exploited targets in chemotherapy, and there is an on-going research in design of small molecules targeting topoisomerase’s catalytic activity at different stages using different mechanisms. Within the scope of this thesis first,...
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Microarray is a technology that enables simultaneously analysis of thousands of genes in DNA structure depending on the advances in biochemistry. With this technology, it has become possible to diagnose and treat heredity diseases by analyzing thousands of gene expression levels. This study proposes an artificial intelligence method, Adaptive neuro-fuzzy inference system (ANFIS), to classify cancer gene expression profiles. The findings obtained with the proposed ANFIS approach are compared with the results...
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Citation Formats
A. Karahan, G. PAZ, N. STERN, A. E. Kıdeyş, M. Goren, and B. RİNKEVİCH, “Employing DNA barcoding as taxonomy and conservation tools for fish species censuses at the southeastern Mediterranean, a hot-spot area for biological invasion,” JOURNAL FOR NATURE CONSERVATION, pp. 1–9, 2017, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/30175.