7
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      DNA barcoding of fish fauna from low order streams of Tapajós River basin

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          The Amazon basin harbors a megadiverse fish fauna spread in an intricate network of big rivers and small streams. The Amazonian streams are home of many small sized fishes that remains poorly documented. In order to accelerate the scientific knowledge on these important aquatic systems we adopted a modern integrative approach joining morphology and molecular tools to investigate the ichthyofauna assemblages from low order streams situated on the lower Tapajós River Basin. Cytochrome c Oxidase I (COI) DNA barcodes from 252 specimens collected from 10 stream sites were obtained. The combined analysis revealed 29 species, 21 genera and 11 families. Cryptic diversity was evidenced in Knodus sp.1, Aequidens epae and Copella callolepis, in which deep genetic divergence were detected (intraspecific distances: 20.48%, 7.99% and 3.77%, respectively). The putative new species showed closer relationships with their counterparts occurring in the Tapajós-Xingu water drainages.

          Related collections

          Most cited references36

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          Fish biodiversity and conservation in South America.

          The freshwater and marine fish faunas of South America are the most diverse on Earth, with current species richness estimates standing above 9100 species. In addition, over the last decade at least 100 species were described every year. There are currently about 5160 freshwater fish species, and the estimate for the freshwater fish fauna alone points to a final diversity between 8000 and 9000 species. South America also has c. 4000 species of marine fishes. The mega-diverse fish faunas of South America evolved over a period of >100 million years, with most lineages tracing origins to Gondwana and the adjacent Tethys Sea. This high diversity was in part maintained by escaping the mass extinctions and biotic turnovers associated with Cenozoic climate cooling, the formation of boreal and temperate zones at high latitudes and aridification in many places at equatorial latitudes. The fresh waters of the continent are divided into 13 basin complexes, large basins consolidated as a single unit plus historically connected adjacent coastal drainages, and smaller coastal basins grouped together on the basis of biogeographic criteria. Species diversity, endemism, noteworthy groups and state of knowledge of each basin complex are described. Marine habitats around South America, both coastal and oceanic, are also described in terms of fish diversity, endemism and state of knowledge. Because of extensive land use changes, hydroelectric damming, water divergence for irrigation, urbanization, sedimentation and overfishing 4-10% of all fish species in South America face some degree of extinction risk, mainly due to habitat loss and degradation. These figures suggest that the conservation status of South American freshwater fish faunas is better than in most other regions of the world, but the marine fishes are as threatened as elsewhere. Conserving the remarkable aquatic habitats and fishes of South America is a growing challenge in face of the rapid anthropogenic changes of the 21st century, and deserves attention from conservationists and policy makers.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            Identifying Canadian Freshwater Fishes through DNA Barcodes

            Background DNA barcoding aims to provide an efficient method for species-level identifications using an array of species specific molecular tags derived from the 5′ region of the mitochondrial cytochrome c oxidase I (COI) gene. The efficiency of the method hinges on the degree of sequence divergence among species and species-level identifications are relatively straightforward when the average genetic distance among individuals within a species does not exceed the average genetic distance between sister species. Fishes constitute a highly diverse group of vertebrates that exhibit deep phenotypic changes during development. In this context, the identification of fish species is challenging and DNA barcoding provide new perspectives in ecology and systematics of fishes. Here we examined the degree to which DNA barcoding discriminate freshwater fish species from the well-known Canadian fauna, which currently encompasses nearly 200 species, some which are of high economic value like salmons and sturgeons. Methodology/Principal Findings We bi-directionally sequenced the standard 652 bp “barcode” region of COI for 1360 individuals belonging to 190 of the 203 Canadian freshwater fish species (95%). Most species were represented by multiple individuals (7.6 on average), the majority of which were retained as voucher specimens. The average genetic distance was 27 fold higher between species than within species, as K2P distance estimates averaged 8.3% among congeners and only 0.3% among concpecifics. However, shared polymorphism between sister-species was detected in 15 species (8% of the cases). The distribution of K2P distance between individuals and species overlapped and identifications were only possible to species group using DNA barcodes in these cases. Conversely, deep hidden genetic divergence was revealed within two species, suggesting the presence of cryptic species. Conclusions/Significance The present study evidenced that freshwater fish species can be efficiently identified through the use of DNA barcoding, especially the species complex of small-sized species, and that the present COI library can be used for subsequent applications in ecology and systematics.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              Can DNA barcoding accurately discriminate megadiverse Neotropical freshwater fish fauna?

              Background The megadiverse Neotropical freshwater ichthyofauna is the richest in the world with approximately 6,000 recognized species. Interestingly, they are distributed among only 17 orders, and almost 80% of them belong to only three orders: Characiformes, Siluriformes and Perciformes. Moreover, evidence based on molecular data has shown that most of the diversification of the Neotropical ichthyofauna occurred recently. These characteristics make the taxonomy and identification of this fauna a great challenge, even when using molecular approaches. In this context, the present study aimed to test the effectiveness of the barcoding methodology (COI gene) to identify the mega diverse freshwater fish fauna from the Neotropical region. For this purpose, 254 species of fishes were analyzed from the Upper Parana River basin, an area representative of the larger Neotropical region. Results Of the 254 species analyzed, 252 were correctly identified by their barcode sequences (99.2%). The main K2P intra- and inter-specific genetic divergence values (0.3% and 6.8%, respectively) were relatively low compared with similar values reported in the literature, reflecting the higher number of closely related species belonging to a few higher taxa and their recent radiation. Moreover, for 84 pairs of species that showed low levels of genetic divergence ( 2%), pointing to at least 23 strong candidates for new species. Conclusions Our study is the first to examine a large number of freshwater fish species from the Neotropical area, including a large number of closely related species. The results confirmed the efficacy of the barcoding methodology to identify a recently radiated, megadiverse fauna, discriminating 99.2% of the analyzed species. The power of the barcode sequences to identify species, even with low interspecific divergence, gives us an idea of the distribution of inter-specific genetic divergence in these megadiverse fauna. The results also revealed hidden genetic divergences suggestive of reproductive isolation and putative cryptic speciation in some species (23 candidates for new species). Finally, our study constituted an important contribution to the international Barcoding of Life (iBOL.org) project, providing barcode sequences for use in identification of these species by experts and non-experts, and allowing them to be available for use in other applications.
                Bookmark

                Author and article information

                Contributors
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: InvestigationRole: Methodology
                Role: Formal analysisRole: InvestigationRole: MethodologyRole: SupervisionRole: ValidationRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: ResourcesRole: ValidationRole: Writing – review & editing
                Role: ConceptualizationRole: SupervisionRole: ValidationRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                21 December 2018
                2018
                : 13
                : 12
                : e0209430
                Affiliations
                [1 ] Laboratório de Genética & Biodiversidade, Instituto de Ciências da Educação, Universidade Federal do Oeste do Pará, Santarém, Pará, Brazil
                [2 ] Programa de Pós Graduação em Recursos Naturais da Amazônia, Universidade Federal do Oeste do Pará, Santarém, Pará, Brazil
                [3 ] Coleção Ictiológica, Instituto de Ciências e Tecnologia das Águas, Universidade Federal do Oeste do Pará, Santarém, Pará, Brazil
                [4 ] Núcleo de Apoio a Pesquisa no Pará, Instituto Nacional de Pesquisas da Amazônia, Santarém, Pará, Brazil
                University of Hyogo, JAPAN
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                [¤]

                Current address: Universidade Federal do Oeste do Pará, Rua Vera Paz, s/n (Campus Tapajós), Salé, Santarém, Pará, Brasil.

                ‡ These authors also contributed equally to this work.

                Author information
                http://orcid.org/0000-0003-1393-6492
                http://orcid.org/0000-0003-2849-0382
                Article
                PONE-D-18-16456
                10.1371/journal.pone.0209430
                6303048
                30576366
                44a8ffcd-f58c-49dd-ba42-cb0f4488aa51
                © 2018 Guimarães et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 21 June 2018
                : 5 December 2018
                Page count
                Figures: 4, Tables: 3, Pages: 16
                Funding
                Funded by: CNPq
                Award ID: BrBOL Proc.564953/2010-5
                Award Recipient :
                Funded by: CAPES
                Award ID: Pro-Amazônia (AUXPE 3318/2013)
                Award Recipient :
                MPAS received Mastership from Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES); KLAG received Scholarship PIBIC/CNPq/UFOPA. This research is part of the Project 09 associated to the Brazilian Barcoding of Life (BrBOL-PRJ09 to JIRP) granted by CNPq. Supplemental funds were provided from CAPES-PROAmazônia (AUXPE-3318/2013 to LRRR). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Vertebrates
                Fish
                Freshwater Fish
                Biology and life sciences
                Molecular biology
                Molecular biology techniques
                DNA barcoding
                Research and analysis methods
                Molecular biology techniques
                DNA barcoding
                Biology and life sciences
                Evolutionary biology
                Evolutionary systematics
                Molecular systematics
                DNA barcoding
                Biology and life sciences
                Taxonomy
                Evolutionary systematics
                Molecular systematics
                DNA barcoding
                Computer and information sciences
                Data management
                Taxonomy
                Evolutionary systematics
                Molecular systematics
                DNA barcoding
                Biology and Life Sciences
                Taxonomy
                Computer and Information Sciences
                Data Management
                Taxonomy
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Processes
                Speciation
                Species Delimitation
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Systematics
                Phylogenetics
                Animal Phylogenetics
                Biology and Life Sciences
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Animal Phylogenetics
                Computer and Information Sciences
                Data Management
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Animal Phylogenetics
                Biology and Life Sciences
                Zoology
                Animal Phylogenetics
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Processes
                Speciation
                Cryptic Speciation
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Research and Analysis Methods
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Earth Sciences
                Marine and Aquatic Sciences
                Bodies of Water
                Rivers
                Ecology and Environmental Sciences
                Aquatic Environments
                Freshwater Environments
                Rivers
                Earth Sciences
                Marine and Aquatic Sciences
                Aquatic Environments
                Freshwater Environments
                Rivers
                Custom metadata
                All relevant data are within the paper and its Supporting Information files. Detailed protocols were uploaded and publicly shared to protocols.io platform.

                Uncategorized
                Uncategorized

                Comments

                Comment on this article

                scite_
                0
                0
                0
                0
                Smart Citations
                0
                0
                0
                0
                Citing PublicationsSupportingMentioningContrasting
                View Citations

                See how this article has been cited at scite.ai

                scite shows how a scientific paper has been cited by providing the context of the citation, a classification describing whether it supports, mentions, or contrasts the cited claim, and a label indicating in which section the citation was made.

                Similar content143

                Cited by9

                Most referenced authors768