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PANGAEA - Publishing Network for Geoscientific & Environmental Data (840.077 recursos)

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

Mostrando recursos 1 - 20 de 66

  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. 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.

  3. 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...

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  20. 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...

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