1
|
Canoglu H, Aksu I, Turan D, Bektas Y. DNA barcoding of the genus Alburnoides Jeitteles, 1861 (Actinopterygii, Cyprinidae) from Anatolia, Turkey. ZOOSYST EVOL 2023. [DOI: 10.3897/zse.99.94333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
The present study investigated the ability of DNA barcoding to reliably identify the endemic freshwater species in Turkey, known as biodiversity hotspots. The barcode region (652 bp) of the mitochondrial cytochrome c oxidase subunit I (COI) was used to barcode 153 individuals from 13 morphologically identified species of the genus Alburnoides. Based on the Kimura two-parameter (K2P) evolution model, the average interspecific distance (0.0595) was 31-fold higher than the average intraspecific distance (0.0019). There was a clear-cut barcode gap (0.0158–0.0187) between maximum intraspecific distance (A. tzanevi and A. velioglui) and minimum nearest-neighbour distance (A. freyhofi and A. kurui) for Anatolian Alburnoides species and a common genetic threshold of 0.0158 sequence divergence was defined for species delimitation. The multiple species delimitation methods (ABGD, ASAP, GMYC and bPTP) revealed a total of 11 molecular operational taxonomic units (MOTUs) for 13 morphospecies. Neighbour-joining (NJ), Maximum Likelihood (ML) and Bayesian Inference (BI) tree analysis indicated that all haplotypes were clustered into two major clades, which corresponded to eleven Alburnoides species clusters, with strong bootstrap support. Furthermore, all the specimens clustered in concurrence with the morpho-taxonomic status of the species, except for two species (A. coskuncelebii and A. emineae) that were morphologically differentiated, but showed overlap in variation for COI-based DNA barcode data with other species. Overall, present results identified that COI-based DNA barcoding is effective for species identification and cataloguing of genus Alburnoides in Turkey.
Collapse
|
2
|
Kiwele Mutambala P, Abwe E, Schedel FDB, Chocha Manda A, Schliewen UK, Vreven EJWMN. A new Parakneria Poll 1965 (Gonorhynchiformes: Kneriidae), 'Mikinkidi' from the Upper Lufira Basin (Upper Congo: DRC): Evidence from a morphologic and DNA barcoding integrative approach. JOURNAL OF FISH BIOLOGY 2023; 102:4-26. [PMID: 36444901 DOI: 10.1111/jfb.15206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 08/27/2022] [Indexed: 06/16/2023]
Abstract
A new species, Parakneria alytogrammus, is described from the main stream of the Upper Lufira River. This species is easily distinguished from its congeners from the Congo Basin by its unique colouration, consisting of a low number of transversal bands on each of the caudal-fin lobes, 2 (vs. 3-5) and the presence of an uninterrupted lateral mid-longitudinal black band in fresh and preserved specimens (vs. absent). In addition, the new species differs from its Upper Lualaba congeners by the narrow width of its pectoral-fin base, 4.8-5.6% LS [vs. wider, 8.2-10.1% for P. lufirae, 8.6% LS for P. damasi (holotype), and 7.6-7.9% LS for P. thysi]. Finally, it differs from the only species currently known from the Luapula-Mweru system, P. malaissei, by having a short post-dorsal distance, 36.4-36.6% LS (vs. longer, 38.6-41.1% LS ) and a short post-pelvic distance of 40.0-40.6% LS (vs. longer, 41.4-44.1% LS ). Mitochondrial DNA-haplotypes of P. alytogrammus sp. nov. form a clade, which is sister to the P. thysi clade, and from which it diverges by a genetic (Kimura 2-parameter and uncorrected p) distance of 0.7% in the COI-barcoding locus. The Upper Lufira, one of the sub-basins of the Upper Congo Basin, remains poorly explored relative to its fish fauna. In contrast, the region is well explored with regard to its mineral wealth. Unfortunately, mining exploitation is carried out in the region without proper concern for the environment. Thus, the discovery of this new species for science calls for increased protection and aquatic biodiversity exploration in this mining region.
Collapse
Affiliation(s)
- Pacifique Kiwele Mutambala
- Unité de Recherche en Biodiversité et Exploitation durable des Zones Humides, Faculté des Sciences Agronomiques, Université de Lubumbashi, Lubumbashi, Democratic Republic of the Congo
| | - Emmanuel Abwe
- Unité de Recherche en Biodiversité et Exploitation durable des Zones Humides, Faculté des Sciences Agronomiques, Université de Lubumbashi, Lubumbashi, Democratic Republic of the Congo
- Royal Museum for Central Africa, Section Vertebrates, Ichthyology, Tervuren, Belgium
- KU Leuven, Fish Diversity and Conservation, Leuven, Belgium
| | - Frederic D B Schedel
- Zoological Institute, University of Basel, Basel, Switzerland
- Faculty of Biology, LMU Munich, Munich, Germany
| | - Auguste Chocha Manda
- Unité de Recherche en Biodiversité et Exploitation durable des Zones Humides, Faculté des Sciences Agronomiques, Université de Lubumbashi, Lubumbashi, Democratic Republic of the Congo
| | - Ulrich K Schliewen
- Department of Ichthyology, SNSB-Bavarian State Collection of Zoology, Munich, Germany
| | - Emmanuel J W M N Vreven
- Royal Museum for Central Africa, Section Vertebrates, Ichthyology, Tervuren, Belgium
- KU Leuven, Fish Diversity and Conservation, Leuven, Belgium
| |
Collapse
|
3
|
Bektas Y, Aksu İ, Kaya C, Bayçelebi E, Turan D. DNA barcoding and species delimitation of the genus Oxynoemacheilus (Teleostei: Nemacheilidae) in Anatolia. JOURNAL OF FISH BIOLOGY 2022; 101:505-514. [PMID: 35607971 DOI: 10.1111/jfb.15114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
The DNA barcoding approach was used for the determination of evolutionary relationships and species delimitation of the genus Oxynoemacheilus (Teleostei: Nemacheilidae). The COI barcode region (615 bp amplicon) was used to barcode 444 individuals from 64 morphologically identified species in the genus Oxynoemacheilus and 189 haplotypes were identified. The average of the interspecific p distance (9.59%) was about 21-fold higher than the average intraspecific distance (0.44%). A general genetic threshold of 1.46% sequence divergence was defined for species delimitation. The multiple species delimitation methods (BCM, GMYC, bPTP and TCS) revealed a total of 62 molecular operational taxonomic units for 64 morphospecies with a new loach species from the BuyukMelen River. Neighbour-joining, maximum likelihood and Bayesian inference analyses indicated that all haplotypes were clustered into 62 clades, which corresponded to Oxynoemacheilus species, with strong bootstrap support (≥95%). Furthermore, all samples grouped in concurrence with the taxonomic status of the species except for species groups (O. germencicus-O. cinicus-O. mesudae and O. leontinae-O. namiri) that were showed intraspecific overlap in genetic diversity for COI-based barcodes. In conclusion, our analyses indicate that COI-based barcodes provide reliable species discrimination. Therefore, we currently recommend COI barcodes as the suitable barcode for genus Oxynoemacheilus.
Collapse
Affiliation(s)
- Yusuf Bektas
- Deparment of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - İsmail Aksu
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - Cüneyt Kaya
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - Esra Bayçelebi
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - Davut Turan
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| |
Collapse
|
4
|
Tsoupas A, Papavasileiou S, Minoudi S, Gkagkavouzis K, Petriki O, Bobori D, Sapounidis A, Koutrakis E, Leonardos I, Karaiskou N, Triantafyllidis A. DNA barcoding identification of Greek freshwater fishes. PLoS One 2022; 17:e0263118. [PMID: 35081163 PMCID: PMC8791500 DOI: 10.1371/journal.pone.0263118] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 01/12/2022] [Indexed: 11/18/2022] Open
Abstract
Biodiversity is a key factor for the functioning and efficiency of an ecosystem. Greece, though covering a relatively small surface area, hosts a great deal of species diversity. This is especially true for freshwater fishes. In recent years, the traditional methods of species identification have been supplemented by the use of molecular markers. The present study therefore aims to extensively produce DNA barcodes for Greek freshwater fish species and investigate thoroughly if the presently accepted species classification is in agreement with molecular data. A 624-bases long fragment of the COI gene was sequenced, from 406 freshwater fish specimens belonging to 24 genera and originating from 18 lake and river sites. These sequences were used along with 596 sequences from the same genera, recovered from BOLD, for the construction of phylogenetic trees and the estimation of genetic distances between individuals. In total, 1002 sequences belonging to 72 species were analyzed. The method was found to be effective for 55 of 72 studied species. 17 closely related species with low interspecific genetic distances were observed, for which further study is proposed. It should also be noted that, in four cases, cryptic diversity was observed, where groups originally identified as one species exhibited genetic distance great enough to be separated into discrete species. Region specific haplotypes were also detected within populations of 14 species, giving the possibility to identify even the geographic origin of a species. Our findings are discussed in the light of the rich history of the Balkan peninsula and provide a significant steppingstone for the further study of Greek and European freshwater fish biodiversity.
Collapse
Affiliation(s)
- Alexandros Tsoupas
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Papavasileiou
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Styliani Minoudi
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Konstantinos Gkagkavouzis
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Olga Petriki
- Faculty of Sciences, Department of Zoology, Laboratory of Ichthyology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitra Bobori
- Faculty of Sciences, Department of Zoology, Laboratory of Ichthyology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- * E-mail: (DB); (AT)
| | - Argyrios Sapounidis
- Department of Inland Waters and Lagoons, Fisheries Research Institute, Hellenic Agricultural Organization “DEMETER”, Nea Peramos, Kavala, Greece
| | - Emmanouil Koutrakis
- Department of Inland Waters and Lagoons, Fisheries Research Institute, Hellenic Agricultural Organization “DEMETER”, Nea Peramos, Kavala, Greece
| | - Ioannis Leonardos
- Department of Biological Applications and Technologies, Laboratory of Zoology, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Nikoleta Karaiskou
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Alexandros Triantafyllidis
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
- * E-mail: (DB); (AT)
| |
Collapse
|
5
|
Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1846485. [PMID: 35059459 PMCID: PMC8766189 DOI: 10.1155/2022/1846485] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/06/2021] [Indexed: 01/04/2023]
Abstract
DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.
Collapse
|
6
|
Epitashvili G, Geiger M, Astrin JJ, Herder F, Japoshvili B, Mumladze L. Towards retrieving the Promethean treasure: a first molecular assessment of the freshwater fish diversity of Georgia. Biodivers Data J 2020; 8:e57862. [PMID: 33177949 PMCID: PMC7599205 DOI: 10.3897/bdj.8.e57862] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 09/24/2020] [Indexed: 11/24/2022] Open
Abstract
In this study, we provide a first estimation of the molecular diversity of the freshwater fishes of Georgia. In addition to field collections, we integrated DNA barcode data obtained from recent works and public databases (BOLD and NCBI GenBank). Currently, the DNA barcode reference library for freshwater fishes of Georgia comprises 352 DNA barcodes for 50 species, 36 genera and 15 families (52% of total Georgian freshwater fish diversity), from which 162 DNA barcodes belonging to 41 species were newly generated as part of this study. A total of 22 species are reported from the Caspian Sea basin and 31 from the Black Sea basin. Amongst the studied taxa, seven species were found with large interspecific divergences (> 2%) while 11 species were found to share DNA barcodes within our dataset. In the course of the study, we found the first evidence of the existence of Gymnocephaluscernua (Linnaeus, 1758) and also confirm the second occurrence of invasive Rhinogobiuslindbergi (Berg, 1933) in Georgia. Based on the evaluation of currently-available barcode data for Georgian fishes, we highlighted major gaps and research needs to further progress DNA-based biodiversity studies in Georgia. Though this study lays a solid base for DNA, based biodiversity assessment and monitoring approaches, further efforts within the recently started CaBOL (Caucasus Barcode Of Life) project are needed to obtain reference data for the species still lacking DNA barcodes.
Collapse
Affiliation(s)
- Giorgi Epitashvili
- Institute of Zoology, Ilia State University, Tbilisi, Georgia Institute of Zoology, Ilia State University Tbilisi Georgia
| | - Matthias Geiger
- Zoological Research Museum A. Koenig, Bonn, Germany Zoological Research Museum A. Koenig Bonn Germany
| | - Jonas J Astrin
- Zoological Research Museum A. Koenig, Bonn, Germany Zoological Research Museum A. Koenig Bonn Germany
| | - Fabian Herder
- Zoological Research Museum A. Koenig, Bonn, Germany Zoological Research Museum A. Koenig Bonn Germany
| | - Bella Japoshvili
- Institute of Zoology, Ilia State University, Tbilisi, Georgia Institute of Zoology, Ilia State University Tbilisi Georgia
| | - Levan Mumladze
- Institute of Zoology, Ilia State University, Tbilisi, Georgia Institute of Zoology, Ilia State University Tbilisi Georgia
| |
Collapse
|
7
|
Levin BA, Gandlin AA, Simonov ES, Levina MA, Barmintseva AE, Japoshvili B, Mugue NS, Mumladze L, Mustafayev N, Pashkov AN, Roubenyan HR, Shapovalov MI, Doadrio I. Phylogeny, phylogeography and hybridization of Caucasian barbels of the genus Barbus (Actinopterygii, Cyprinidae). Mol Phylogenet Evol 2019; 135:31-44. [DOI: 10.1016/j.ympev.2019.02.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/11/2019] [Accepted: 02/27/2019] [Indexed: 11/25/2022]
|
8
|
Turanov SV, Kartavtsev YP, Shapovalov ME. The First Attempt at Studying the Species Diversity of Fish in Lake Khanka Using DNA Barcoding Techniques. RUSS J GENET+ 2019. [DOI: 10.1134/s102279541904015x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
9
|
Barbieri R, Vukić J, Šanda R, Kapakos Y, Zogaris S. Alburnoides economoui, a new species of spirlin from Central Greece and redescription of Alburnoides thessalicus (Actinopterygii: Cyprinidae). Biologia (Bratisl) 2017. [DOI: 10.1515/biolog-2017-0113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|