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PANGAEA tech-keyword 'deNBIMolEcolStaticandURL' (25 data sets)

Mostrando recursos 1 - 20 de 26

  1. Supplementary aDNA sequences from a Pleistocene ground squirrel midden, Yukon

    Langeveld, Bram W; Mol, D; Zazula, G D; Gravendeel, B; Eurlings, M; Groenenberg, D; van Reenen, G B A; van Geel, B
    Data consists of sequence data of plants and fungi from a Pleistocene ground squirrel midden (collected from a small placer goldmine on Little Blanche Creek, Klondike area near Dawson City, Yukon Territory, Canada; coordinates: 63°50'35"N 139°05'41"W). Three subsamples from this midden were sequenced with various primers, which yielded genetic products of various sizes. This resulted in six different tables, explained below. From the midden itself other subsamples were studied for macro- and microfossils of plants and fungi.

  2. Metabarcoding approach for non-indigenous species surveillance in marine coastal waters

    Zaiko, Anastasija; Samuiloviene, Aurelija; Ardura, Alba; Garcia-Vazquez, Eva
    In this study, high-throughput sequencing (HTS) metabarcoding was applied for the surveillance of plankton communities within the southeastern (SE) Baltic Sea coastal zone. These results were compared with those from routine monitoring survey and morphological analyses. Four of five nonindigenous species found in the samples were identified exclusively by metabarcoding. All of them are considered as invasive in the Baltic Sea with reported impact on the ecosystem and biodiversity. This study indicates that, despite some current limitations, HTS metabarcoding can provide information on the presence of exotic species and advantageously complement conventional approaches, only requiring the same monitoring effort as...

  3. Genetic data from Staurosira (Fragilariophyceae) sedimentary DNA

    Stoof-Leichsenring, Kathleen Rosmarie; Herzschuh, Ulrike; Pestryakova, Ludmila A; Klemm, Juliane; Epp, Laura Saskia; Tiedemann, Ralf
    Genetic investigations on eukaryotic plankton confirmed the existence of modern biogeographic patterns, but analyses of palaeoecological data exploring the temporal variability of these patterns have rarely been presented. Ancient sedimentary DNA proved suitable for investigations of past assemblage turnover in the course of environmental change, but genetic relatedness of the identified lineages has not yet been undertaken. Here, we investigate the relatedness of diatom lineages in Siberian lakes along environmental gradients (i.e. across treeline transects), over geographic distance and through time (i.e. the last 7000 years) using modern and ancient sedimentary DNA. Our results indicate that closely-related Staurosira lineages occur...

  4. AFLP data based on presence (1) and absence (0) of AFLP loci (A4-F171) in Gonyostomum semen

    Sassenhagen, Ingrid
    Many recent studies have found genetically differentiated populations in microorganisms despite potentially high dispersal. We designed a study to specifically examine the importance of physical dispersal barriers, i.e. geographic distance and lack of hydrological connectivity, in restricting gene flow and enhancing divergence in limnic microorganisms. We focused on the nuisance microalga Gonyostomum semen, which has recently expanded in northern Europe and differentiated into genetically distinct populations. Gonyostomum semen was sampled from six lakes distributed in two adjacent watersheds, which thereby comprised, both connected and non-connected lakes. The individual isolates were genotyped by Amplified Fragment Length Polymorphism. Several lake populations were...

  5. Total V9 rDNA information organized at the OTU level (Database W5)

    De Vargas, Colomban; Tara Oceans Consortium, Coordinators; Tara Oceans Expedition, Participants
    The present data set provides a tab separated text file compressed in a zip archive. The file includes metadata for each TaraOceans V9 rDNA OTU including the following fields: md5sum = identifier of the representative (most abundant) sequence of the swarm; cid = identifier of the OTU; totab = total abundance of barcodes in this OTU; TARA_xxx = number of occurrences of barcodes in this OTU in each of the 334 samples;rtotab = total abundance of the representative barcode; pid = percentage identity of the representative barcode to the closest reference sequence from V9_PR2; lineage = taxonomic path assigned to...

  6. Total V9 rDNA information organized at the metabarcode level (Database W4)

    De Vargas, Colomban; Tara Oceans Consortium, Coordinators; Tara Oceans Expedition, Participants
    The present data set provides a tab separated text file compressed in a zip archive. The file includes metadata for each TaraOceans V9 rDNA metabarcode including the following fields: md5sum = unique identifier; lineage = taxonomic path associated to the metabarcode; pid = % identity to the closest reference barcode from V9_PR2; sequence = nucleotide sequence of the metabarcode; refs = identity of the best hit reference sequence(s); TARA_xxx = number of occurrences of this barcode in each of the 334 samples; totab = total abundance of the barcode ; cid = identifier of the OTU to which the barcode...

  7. List of size fractionated eukaryotic plankton community samples and associated metadata (Database W1)

    De Vargas, Colomban; Tara Oceans Expedition, Participants; Tara Oceans Consortium, Coordinators
    The present data set provides an Excel file in a zip archive. The file lists 334 samples of size fractionated eukaryotic plankton community with a suite of associated metadata (Database W1). Note that if most samples represented the piconano- (0.8-5 µm, 73 samples), nano- (5-20 µm, 74 samples), micro- (20-180 µm, 70 samples), and meso- (180-2000 µm, 76 samples) planktonic size fractions, some represented different organismal size-fractions: 0.2-3 µm (1 sample), 0.8-20 µm (6 samples), 0.8 µm - infinity (33 samples), and 3-20 µm (1 sample). The table contains the following fields: a unique sample sequence identifier; the sampling station...

  8. Supplemental Data - Bioremediation of polluted air from an industrial plant using rotating biofilter reactor-based technology

    Bonadei, Martina; Donà, Mattia; Balestrazzi, Alma; Bruni, Gabriele; Carbonera, Daniela
    Two microbial isolates (HDB, Hydrogen-Degrading Bacteria) obtained from industrial wastewater were inoculated into the rotating biofilter reactor 'Biowheel 2.0' and tested for the ability to purify gaseous flows containing benzene and non-methane volatile organic compounds (NMVOCs) released at an industrial plant. Different classes of gaseous flow were tested, namely 'cold box', 'in shell', and 'mix', all of them associated with the industrial process of 'mold-casting'. A significant increase in Removal Efficiency (RE) was recorded for benzene and NMVOCs in the inoculated 'Biowheel 2.0' biofilter, compared to uninoculated control. For each type of gaseous flow, odor impact was evaluated in the...

  9. New possibilities arise for studies of hybridization: SNP-based markers for the multi-species Daphnia longispina complex derived from transcriptome data

    Rusek, Jakub; Ayan, Gokce; Turko, Patrick; Tellenbach, Christoph; Giessler, Sabine; Spaak, Piet; Wolinska, Justyna
    In order to trace population community dynamics and reticulate evolution in hybrid species complexes, long-term comparative studies of natural populations are necessary and thus, tools for fine-scale genetic analyses are needed. In the present study, we developed species-diagnostic SNP markers for hybridizing freshwater crustaceans: the multispecies Daphnia longispina complex. Specifically, we took advantage of transcriptome data from a key species of this hybrid complex, the annotated genome of a related Daphnia species and well-defined reference genotypes from three parental species. Altogether eleven nuclear loci with several species-specific SNP sites were identified in sequence alignments of 22 individuals of three parental...

  10. Defence chemistry modulation by light and temperature (results in 4 excel files, zipped)

    Saha, Mahasweta; Rempt, Martin; Stratil, Stephanie B; Wahl, Martin; Pohnert, Georg; Weinberger, Florian
    The goals of this study were (1) to investigate whether Fucus vesiculosus regulates the production of its antifouling defence chemicals against microfoulers in response to light limitation and temperature shifts and (2) to investigate if different surface concentrations of defence compounds shape epibacterial communities. F. vesiculosus was incubated in indoor mesocosms at five different temperature conditions (5 to 25°C) and in outdoor mesocosms under six differently reduced sunlight conditions (0 to 100%), respectively. Algal surface concentrations of previously identified antifouling compounds - dimethylsulphopropionate (DMSP), fucoxanthin and proline - were determined and the bacterial community composition was characterized by in-depth sequencing...

  11. PumaPlex 1.0: Data generated during the development of the SNP markers and SNP genotypes of pumas

    Fitak, Robert; Naidu, Ashwin; Thompson, Ron; Culver, Melanie
    Pumas are one of the most studied terrestrial mammals because of their widespread distribution, substantial ecological impacts, and conflicts with humans. Extensive efforts, often employing genetic methods, are undertaken to manage this species. However, the comparison of population genetic data is difficult because few of the microsatellite loci chosen are shared across research programs. Here, we describe the development of PumaPlex, a high-throughput assay to genotype 25 single nucleotide polymorphisms in pumas. We validated PumaPlex in more than 700 North American pumas (Puma concolor couguar), and demonstrated its ability to generate reproducible genotypes and accurately identify individuals. Furthermore, we compared...

  12. Gene expression profiling in gills of the great spider crab Hyas araneus in respond to ocean acidification and warming, supplementary data

    Harms, Lars; Frickenhaus, Stephan; Schiffer, Melanie; Mark, Felix Christopher; Storch, Daniela; Held, Christoph; Lucassen, Magnus
    Hypercapnia and elevated temperatures resulting from climate change may have adverse consequences for many marine organisms. While diverse physiological and ecological effects have been identified, changes in those molecular mechanisms, which shape the physiological phenotype of a species and limit its capacity to compensate, remain poorly understood. Here, we use global gene expression profiling through RNA-Sequencing to study the transcriptional responses to ocean acidification and warming in gills of the boreal spider crab Hyas araneus exposed medium-term (10 weeks) to intermediate (1,120 µatm) and high (1,960 µatm) PCO2 at different temperatures (5°C and 10°C). The analyses reveal shifts in steady...

  13. Experiment effects on marine bacterial community composition: diversity analysis

    Krause, Evamaria

  14. Historical genetic data set as flat file (zipped)

    Pavlova, Alexandra; Selwood, Peter; Harrisson, Katherine A; Murray, Neil; Quin, Bruce; Menkhorst, Peter; Smales, Ian; Sunnucks, Paul

  15. Contemporary genetic data set as flat file (zipped)

    Pavlova, Alexandra; Selwood, Peter; Harrisson, Katherine A; Murray, Neil; Quin, Bruce; Menkhorst, Peter; Smales, Ian; Sunnucks, Paul

  16. Phased haplotype files for 15 nuclear genes in NEXUS format (zipped)

    Pavlova, Alexandra; Selwood, Peter; Harrisson, Katherine A; Murray, Neil; Quin, Bruce; Menkhorst, Peter; Smales, Ian; Sunnucks, Paul

  17. Supplementary material

    Cornils, Astrid; Held, Christoph

  18. Impacts of seawater acidification on mantle gene expression patterns of the Baltic Sea blue mussel: implications for shell formation and energy metabolism, link to supplementary material

    Hüning, Anne K; Melzner, Frank; Thomsen, Jörn; Gutowska, Magdalena A; Krämer, Lars; Frickenhaus, Stephan; Rosenstiel, Philip; Pörtner, Hans-Otto; Philipp, Eva E R; Lucassen, Magnus
    Marine organisms have to cope with increasing CO2 partial pressures and decreasing pH in the oceans. We elucidated the impacts of an 8-week acclimation period to four seawater pCO2 treatments (39, 113, 243 and 405 Pa/385, 1,120, 2,400 and 4,000 µatm) on mantle gene expression patterns in the blue mussel Mytilus edulis from the Baltic Sea. Based on the M. edulis mantle tissue transcriptome, the expression of several genes involved in metabolism, calcification and stress responses was assessed in the outer (marginal and pallial zone) and the inner mantle tissues (central zone) using quantitative real-time PCR. The expression of genes...

  19. Molecular and biochemical analyses of wounding in mesocarp of peach (Prunus persica L. Batsch) ripe fruits

    Tosetti, Roberta; Tadiello, Alice; Zaffalon, Valerio; Giorgi, Federico M; Guidi, Lucia; Trainotti, Livio; Tonutti, Pietro
    The physiological and molecular responses of ripe fruit to wounding were evaluated in two peach (Prunus persica) varieties ('Glohaven', GH, melting and 'BigTop', BT, slow melting nectarine) by comparing mesocarp samples from wedges (as in minimal processing) and whole fruit as the control. Slight differences between the two varieties were detected in terms of ethylene production, whereas total phenol and flavonoid concentrations, and PPO and POD enzyme activities showed a general increase in wounded GH but not in BT. This was associated with the better appearance of the BT wedges at the end of the experimental period (72 h). Microarray...

  20. Diversity of zooplankton assemblages at Station L4, Western English Channel, measured using next generation DNA sequencing

    Parry, Helen E; Lindeque, Pennie K; Harmer, Rachel A
    Background: Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel Next Generation Sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify the richness and diversity of a mixed zooplankton assemblage from a productive monitoring site in the Western English Channel. Methodology/Principle...

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