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

Date

2017-04-01

Author

Karahan, Arzu
PAZ, Guy
STERN, Nir
Kıdeyş, Ahmet Erkan
Goren, Menachem
RİNKEVİCH, Baruch

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

198
views

0
downloads

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.

Subject Keywords

Mediterranean fish, DNA barcode, Taxonomy, Invasive species, Conservation

URI

https://hdl.handle.net/11511/30175

Journal

JOURNAL FOR NATURE CONSERVATION

DOI

https://doi.org/10.1016/j.jnc.2017.01.004

Collections

Graduate School of Marine Sciences, Article

Suggestions

OpenMETU
Core

A comparative genetic analysis of the subterranean termite genus Reticulitermes (Isoptera : Rhinotermitidae) Austin, JW; Szalanski, AL; Uva, P; Bagneres, AG; Kence, Aykut (Oxford University Press (OUP), 2002-11-01) 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...
Evaluation of genotype imputation for ancient genomes from regions underrepresented in the reference panel Çubukcu, Hande; Yet, İdil; Kılınç, Gülşah Merve (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) Genotype imputation decreases the need for producing high coverage genomes since it allows to generate diploid genotypes from low coverage genome sequencing data. GLIMPSE is a recently developed software for imputing low-coverage genomes and it outperforms other softwares regarding runtime and accuracy. Imputation of low coverage ancient genomes using GLIMPSE has revealed high levels of accuracy for alleles with frequency of minimum 0.02 for genomes well represented in the reference panel. However the accur...
Analysis of genetic relationships among perennial and annual Cicer species growing in Turkey using RAPD markers Sudupak, MA; Akkaya, Mahinur; Kence, A (2002-12-01) 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...
Insights into the action mechanism of azacyanines: their Topoisomerase IIα inhibition potential and nucleic acid selectivity Güloğlu, Sercan; Persil Çetinkol, Özgül; Department of Biochemistry (2018) 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,...
A mechanistic insight into selective de novo DNA methylation regulated by base-specific hydrogen bonding profile Barlas , Ayşe Berçin; Karaca , Ezgi (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) The mammalian DNA methylation regulates diverse biological processes at the epigenetic level, such as ageing, embryonic development, reprogramming, chromatin modification, and X chromosome inactivation. Abnormalities in the DNA methylation disrupts integral molecular signaling mechanisms, leading to the severe diseases, especially cancer. DNA methylation occurs mainly at CpG islands through the transfer of a methyl group from S-adenosyl-L-methionine (SAM) to the 5' carbon of the target cytosine. De novo met...

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.