51
views
0
recommends
+1 Recommend
1 collections
    0
    shares

      Publish your biodiversity research with us!

      Submit your article here.

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

      A DNA barcode-assisted annotated checklist of the spider (Arachnida, Araneae) communities associated to white oak woodlands in Spanish National Parks

      research-article

      Read this article at

      ScienceOpenPublisherPMC
      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

          Abstract
          Background

          A large scale semi-quantitative biodiversity assessment was conducted in white oak woodlands in areas included in the Spanish Network of National Parks, as part of a project aimed at revealing biogeographic patterns and identify biodiversity drivers. The semi-quantitative COBRA sampling protocol was conducted in sixteen 1-ha plots across six national parks using a nested design. All adult specimens were identified to species level based on morphology. Uncertain delimitations and identifications due to either limited information of diagnostic characters or conflicting taxonomy were further investigated using DNA barcode information.

          New information

          We identified 376 species belonging to 190 genera in 39 families, from the 8,521 adults found amongst the 20,539 collected specimens. Faunistic results include the discovery of 7 new species to the Iberian Peninsula, 3 new species to Spain and 11 putative new species to science. As largely expected by environmental features, the southern parks showed a higher proportion of Iberian and Mediterranean species than the northern parks, where the Palearctic elements were largely dominant. The analysis of approximately 3,200 DNA barcodes generated in the present study, corroborated and provided finer resolution to the morphologically based delimitation and identification of specimens in some taxonomically challenging families. Specifically, molecular data confirmed putative new species with diagnosable morphology, identified overlooked lineages that may constitute new species, confirmed assignment of specimens of unknown sexes to species and identified cases of misidentifications and phenotypic polymorphisms.

          Related collections

          Most cited references59

          • Record: found
          • Abstract: not found
          • Article: not found

          Gene Trees in Species Trees

            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Approaching a state shift in Earth's biosphere.

            Localized ecological systems are known to shift abruptly and irreversibly from one state to another when they are forced across critical thresholds. Here we review evidence that the global ecosystem as a whole can react in the same way and is approaching a planetary-scale critical transition as a result of human influence. The plausibility of a planetary-scale 'tipping point' highlights the need to improve biological forecasting by detecting early warning signs of critical transitions on global as well as local scales, and by detecting feedbacks that promote such transitions. It is also necessary to address root causes of how humans are forcing biological changes.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

              Introduction The PCR-based analysis of homologous genes has become one of the most powerful approaches for species detection and identification, particularly with the recent availability of Next Generation Sequencing platforms (NGS) making it possible to identify species composition from a broad range of environmental samples. Identifying species from these samples relies on the ability to match sequences with reference barcodes for taxonomic identification. Unfortunately, most studies of environmental samples have targeted ribosomal markers, despite the fact that the mitochondrial Cytochrome c Oxidase subunit I gene (COI) is by far the most widely available sequence region in public reference libraries. This is largely because the available versatile (“universal”) COI primers target the 658 barcoding region, whose size is considered too large for many NGS applications. Moreover, traditional barcoding primers are known to be poorly conserved across some taxonomic groups. Results We first design a new PCR primer within the highly variable mitochondrial COI region, the “mlCOIintF” primer. We then show that this newly designed forward primer combined with the “jgHCO2198” reverse primer to target a 313 bp fragment performs well across metazoan diversity, with higher success rates than versatile primer sets traditionally used for DNA barcoding (i.e. LCO1490/HCO2198). Finally, we demonstrate how the shorter COI fragment coupled with an efficient bioinformatics pipeline can be used to characterize species diversity from environmental samples by pyrosequencing. We examine the gut contents of three species of planktivorous and benthivorous coral reef fish (family: Apogonidae and Holocentridae). After the removal of dubious COI sequences, we obtained a total of 334 prey Operational Taxonomic Units (OTUs) belonging to 14 phyla from 16 fish guts. Of these, 52.5% matched a reference barcode (>98% sequence similarity) and an additional 32% could be assigned to a higher taxonomic level using Bayesian assignment. Conclusions The molecular analysis of gut contents targeting the 313 COI fragment using the newly designed mlCOIintF primer in combination with the jgHCO2198 primer offers enormous promise for metazoan metabarcoding studies. We believe that this primer set will be a valuable asset for a range of applications from large-scale biodiversity assessments to food web studies.
                Bookmark

                Author and article information

                Contributors
                Journal
                Biodivers Data J
                Biodivers Data J
                Biodiversity Data Journal
                Biodiversity Data Journal
                Biodiversity Data Journal
                Pensoft Publishers
                1314-2828
                2018
                29 November 2018
                : 6
                : e29443
                Affiliations
                [1 ] Department of Evolutionary Biology, Ecology and Environmental Sciences & Biodiversity Research Institute (IRBio), Universitat de Barcelona, Av. Diagonal 643, E-08028, Barcelona, Spain Department of Evolutionary Biology, Ecology and Environmental Sciences & Biodiversity Research Institute (IRBio), Universitat de Barcelona, Av. Diagonal 643, E-08028 Barcelona Spain
                [2 ] Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History, University of Helsinki; PO Box 17, 00014, Helsinki, Finland Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History, University of Helsinki; PO Box 17, 00014 Helsinki Finland
                [3 ] Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History, University of Helsinki; PO Box 17, 00014, Helsinki, Finland Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History, University of Helsinki; PO Box 17, 00014 Helsinki Finland
                [4 ] cE3c - Centre for Ecology, Evolution and Environmental Changes, University of the Azores; Rua Capitão João d´Ávila, Pico da Urze, 9700-042 , Angra do Heroísmo, Terceira, Azores, Portugal cE3c - Centre for Ecology, Evolution and Environmental Changes, University of the Azores; Rua Capitão João d´Ávila, Pico da Urze, 9700-042 Angra do Heroísmo, Terceira, Azores Portugal
                [5 ] Department of Functional and Evolutionary Ecology, Estación Experimenta de Zonas Áridas (EEZA, CSIC); Carretera de Sacramento, s/n. La Cañada de San Urbano 04120, Almeria, Spain Department of Functional and Evolutionary Ecology, Estación Experimenta de Zonas Áridas (EEZA, CSIC); Carretera de Sacramento, s/n. La Cañada de San Urbano 04120 Almeria Spain
                [6 ] Department of Genetics, Microbiology and Statistics, & Biodiversity Research Institute (IRBio), Universitat de Barcelona, Av. Diagonal 643, E-08028, Barcelona, Spain Department of Genetics, Microbiology and Statistics, & Biodiversity Research Institute (IRBio), Universitat de Barcelona, Av. Diagonal 643, E-08028 Barcelona Spain
                [7 ] Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiologíıa, C/Astrofísico Francisco Sánchez 3, La Laguna, Tenerife, Canary Islands, Spain Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiologíıa, C/Astrofísico Francisco Sánchez 3 La Laguna, Tenerife, Canary Islands Spain
                [8 ] Department of Functional and Evolutionary Ecology, Estación Experimenta de Zonas Áridas (EEZA, CSIC); Carretera de Sacramento, s/n. La Cañada de San Urbano 04120, Almeria, Spain Department of Functional and Evolutionary Ecology, Estación Experimenta de Zonas Áridas (EEZA, CSIC); Carretera de Sacramento, s/n. La Cañada de San Urbano 04120 Almeria Spain
                [9 ] Department of Entomology and Nematology, University of California, Davis, CA 95616, Davis, United States of America Department of Entomology and Nematology, University of California, Davis, CA 95616 Davis United States of America
                [10 ] Laboratory of Systematic Entomology in the Department of Applied Biology of Chungnam National University, Daejeon, Korea, South Laboratory of Systematic Entomology in the Department of Applied Biology of Chungnam National University Daejeon Korea, South
                [11 ] CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vila do Conde, Portugal CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto Vila do Conde Portugal
                Author notes
                Corresponding author: Miquel A. Arnedo ( marnedo@ 123456gmail.com ).

                Academic editor: Gergin Blagoev

                Author information
                https://orcid.org/0000-0003-4352-5301
                https://orcid.org/0000-0002-5859-9656
                Article
                Biodiversity Data Journal 9788
                10.3897/BDJ.6.e29443
                6284012
                fcc142e2-5ffe-4b42-8db8-2bdd80fb3a2a
                Luís Crespo, Marc Domènech, Alba Enguídanos, Jagoba Malumbres-Olarte, Pedro Cardoso, Jordi Moya-Laraño, Cristina Frías-López, Nuria Macías-Hernández, Eva De Mas, Paola Mazzuca, Elisa Mora, Vera Opatova, Enric Planas, Carles Ribera, Marcos Roca-Cusachs, Dolores Ruiz, Pedro Sousa, Vanina Tonzo, Miquel Arnedo

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 31 August 2018
                : 08 November 2018
                Page count
                Figures: 20, Tables: 2, References: 84
                Funding
                This study was funded by the Organismo Autónomo de Parques Nacionales (OAPN #485/2012). Additional support was provided by 2014SGR1604 from the Catalan Government.
                Categories
                Taxonomic Paper
                Animalia
                Chelicerata
                Araneae
                Arachnida
                Arthropoda
                Invertebrata
                Ecology & Environmental sciences
                Systematics
                Molecular biology
                Biodiversity & Conservation
                Zoology & Animal Biology
                Neogene
                Iberian Peninsula
                Spain

                dna barcoding,faunistics,cobra protocol,mediterranean region,iberian peninsula, dictynidae , gnaphosidae , linyphiidae , philodromidae

                Comments

                Comment on this article