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  • 1
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 13, No. 1 ( 2022-05-18)
    Abstract: There is still limited consensus on the evolutionary history of species-rich temperate alpine floras due to a lack of comparable and high-quality phylogenetic data covering multiple plant lineages. Here we reconstructed when and how European alpine plant lineages diversified, i.e., the tempo and drivers of speciation events. We performed full-plastome phylogenomics and used multi-clade comparative models applied to six representative angiosperm lineages that have diversified in European mountains (212 sampled species, 251 ingroup species total). Diversification rates remained surprisingly steady for most clades, even during the Pleistocene, with speciation events being mostly driven by geographic divergence and bedrock shifts. Interestingly, we inferred asymmetrical historical migration rates from siliceous to calcareous bedrocks, and from higher to lower elevations, likely due to repeated shrinkage and expansion of high elevation habitats during the Pleistocene. This may have buffered climate-related extinctions, but prevented speciation along elevation gradients as often documented for tropical alpine floras.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2553671-0
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  • 2
    In: Ecological Modelling, Elsevier BV, Vol. 483 ( 2023-09), p. 110424-
    Type of Medium: Online Resource
    ISSN: 0304-3800
    RVK:
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2023
    detail.hit.zdb_id: 191971-4
    detail.hit.zdb_id: 2000879-X
    SSG: 12
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  • 3
    In: Frontiers in Plant Science, Frontiers Media SA, Vol. 12 ( 2021-6-7)
    Abstract: Mountain environments are marked by an altitudinal zonation of habitat types. They are home to a multitude of terrestrial green algae, who have to cope with abiotic conditions specific to high elevation, e.g., high UV irradiance, alternating desiccation, rain and snow precipitations, extreme diurnal variations in temperature and chronic scarceness of nutrients. Even though photosynthetic green algae are primary producers colonizing open areas and potential markers of climate change, their overall biodiversity in the Alps has been poorly studied so far, in particular in soil, where algae have been shown to be key components of microbial communities. Here, we investigated whether the spatial distribution of green algae followed the altitudinal zonation of the Alps, based on the assumption that algae settle in their preferred habitats under the pressure of parameters correlated with elevation. We did so by focusing on selected representative elevational gradients at distant locations in the French Alps, where soil samples were collected at different depths. Soil was considered as either a potential natural habitat or temporary reservoir of algae. We showed that algal DNA represented a relatively low proportion of the overall eukaryotic diversity as measured by a universal Eukaryote marker. We designed two novel green algae metabarcoding markers to amplify the Chlorophyta phylum and its Chlorophyceae class, respectively. Using our newly developed markers, we showed that elevation was a strong correlate of species and genus level distribution. Altitudinal zonation was thus determined for about fifty species, with proposed accessions in reference databases. In particular, Planophila laetevirens and Bracteococcus ruber related species as well as the snow alga Sanguina genus were only found in soil starting at 2,000 m above sea level. Analysis of environmental and bioclimatic factors highlighted the importance of pH and nitrogen/carbon ratios in the vertical distribution in soil. Capacity to grow heterotrophically may determine the Trebouxiophyceae over Chlorophyceae ratio. The intensity of freezing events (freezing degree days), proved also determinant in Chlorophyceae distribution. Guidelines are discussed for future, more robust and precise analyses of environmental algal DNA in mountain ecosystems and address green algae species distribution and dynamics in response to environmental changes.
    Type of Medium: Online Resource
    ISSN: 1664-462X
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
    detail.hit.zdb_id: 2687947-5
    detail.hit.zdb_id: 2613694-6
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  • 4
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 12, No. 1 ( 2022-06-17)
    Abstract: High-throughput DNA sequencing is becoming an increasingly important tool to monitor and better understand biodiversity responses to environmental changes in a standardized and reproducible way. Environmental DNA (eDNA) from organisms can be captured in ecosystem samples and sequenced using metabarcoding, but processing large volumes of eDNA data and annotating sequences to recognized taxa remains computationally expensive. Speed and accuracy are two major bottlenecks in this critical step. Here, we evaluated the ability of convolutional neural networks (CNNs) to process short eDNA sequences and associate them with taxonomic labels. Using a unique eDNA data set collected in highly diverse Tropical South America, we compared the speed and accuracy of CNNs with that of a well-known bioinformatic pipeline (OBITools) in processing a small region (60 bp) of the 12S ribosomal DNA targeting freshwater fishes. We found that the taxonomic labels from the CNNs were comparable to those from OBITools, with high correlation levels for the composition of the regional fish fauna. The CNNs enabled the processing of raw fastq files at a rate of approximately 1 million sequences per minute, which was about 150 times faster than with OBITools. Given the good performance of CNNs in the highly diverse ecosystem considered here, the development of more elaborate CNNs promises fast deployment for future biodiversity inventories using eDNA.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2615211-3
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  • 5
    In: Molecular Ecology Resources, Wiley, Vol. 21, No. 7 ( 2021-10), p. 2565-2579
    Abstract: Bioinformatic analysis of eDNA metabarcoding data is a crucial step toward rigorously assessing biodiversity. Many programs are now available for each step of the required analyses, but their relative abilities at providing fast and accurate species lists have seldom been evaluated. We used simulated mock communities and real fish eDNA metabarcoding data to evaluate the performance of 13 bioinformatic programs and pipelines to retrieve fish occurrence and read abundance using the 12S mt rRNA gene marker. We used four indices to compare the outputs of each program with the simulated samples: sensitivity, F‐measure, root‐mean‐square error (RMSE) on read relative abundances, and execution time. We found marked differences among programs only for the taxonomic assignment step, both in terms of sensitivity, F‐measure and RMSE. Running time was highly different between programs for each step. The fastest programs with best indices for each step were assembled into a pipeline. We compared this pipeline to pipelines constructed from existing toolboxes (OBITools, Barque, and QIIME 2). Our pipeline and Barque obtained the best performance for all indices and appear to be better alternatives to highly used pipelines for analysing fish eDNA metabarcoding data when a complete reference database is available. Analysis on real eDNA metabarcoding data also indicated differences for taxonomic assignment and execution time only. This study reveals major differences between programs during the taxonomic assignment step. The choice of algorithm for the taxonomic assignment can have a significant impact on diversity estimates and should be made according to the objectives of the study.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 2406833-0
    SSG: 12
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  • 6
    In: Plants, MDPI AG, Vol. 9, No. 4 ( 2020-04-01), p. 432-
    Abstract: Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was 〉 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications.
    Type of Medium: Online Resource
    ISSN: 2223-7747
    Language: English
    Publisher: MDPI AG
    Publication Date: 2020
    detail.hit.zdb_id: 2704341-1
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  • 7
    In: Frontiers in Ecology and Evolution, Frontiers Media SA, Vol. 11 ( 2023-7-12)
    Abstract: Connected landscapes can increase the effectiveness of protected areas by facilitating individual movement and gene flow between populations, thereby increasing the persistence of species even in fragmented habitats. Connectivity planning is often based on modeling connectivity for a limited number of species, i.e., “connectivity umbrellas”, which serve as surrogates for co-occurring species. Connectivity umbrellas are usually selected a priori , based on a few life history traits and often without evaluating other species. Methods We developed a quantitative method to identify connectivity umbrellas at multiple scales. We demonstrate the approach on the terrestrial large mammal community (24 species) in continental Europe at two scales: 13 geographic biomes and 36 ecoregions, and evaluate the interaction of landscape characteristics on the selection of connectivity umbrellas. Results We show that the number, identity, and attributes of connectivity umbrellas are sensitive to spatial scale and human influence on the landscape. Multiple species were selected as connectivity umbrellas in 92% of the geographic biomes (average of 4.15 species) and 83% of the ecoregions (average of 3.16 species). None of the 24 species evaluated is by itself an effective connectivity umbrella across its entire range. We identified significant interactions between species and landscape attributes. Species selected as connectivity umbrellas in regions with low human influence have higher mean body mass, larger home ranges, longer dispersal distances, smaller geographic ranges, occur at lower population densities, and are of higher conservation concern than connectivity umbrellas in more human-influenced regions. More species are required to meet connectivity targets in regions with high human influence (average of three species) in comparison to regions with low human influence (average of 1.67 species). Discussion We conclude that multiple species selected in relation to landscape scale and characteristics are essential to meet connectivity goals. Our approach enhances objectivity in selecting which and how many species are required for connectivity conservation and fosters well-informed decisions, that in turn benefit entire communities and ecosystems.
    Type of Medium: Online Resource
    ISSN: 2296-701X
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2745634-1
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  • 8
    In: Journal of Ecology, Wiley, Vol. 109, No. 2 ( 2021-02), p. 1041-1054
    Abstract: Species range limits are thought to result from a decline in demographic performance at range edges. However, recent studies reporting contradictory patterns in species demographic performance at their edges cast doubt on our ability to predict climate change demographic impacts. To understand these inconsistent demographic responses, we need to shift the focus from geographic to climatic edges and analyse how species responses vary with climatic constraints at the edge and species' ecological strategy. Here we parameterised integral projection models with climate and competition effects for 27 tree species using forest inventory data from over 90,000 plots across Europe. Our models estimate size‐dependent climatic responses and evaluate their effects on two life trajectory metrics: life span and passage time—the time to grow to a large size. Then we predicted growth, survival, life span and passage time at the hot and dry or cold and wet edges and compared them to their values at the species climatic centre to derive indices of demographic response at the edge. Using these indices, we investigated whether differences in species demographic response between hot and cold edges could be explained by their position along the climate gradient and functional traits related to their climate stress tolerance. We found that at cold and wet edges of European tree species, growth and passage time were constrained, whereas at their hot and dry edges, survival and life span were constrained. Demographic constraints at the edge were stronger for species occurring in extreme conditions, that is, in hot edges of hot‐distributed species and cold edges of cold‐distributed species. Species leaf nitrogen content was strongly linked to their demographic responses at the edge. In contrast, we found only weak links with wood density, leaf size and xylem vulnerability to embolism. Synthesis . Our study presents a more complicated picture than previously thought with demographic responses that differ between hot and cold edges. Predictions of climate change impacts should be refined to include edge and species characteristics.
    Type of Medium: Online Resource
    ISSN: 0022-0477 , 1365-2745
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2021
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    detail.hit.zdb_id: 2004136-6
    SSG: 12
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  • 9
    In: Global Change Biology, Wiley, Vol. 26, No. 1 ( 2020-01), p. 119-188
    Abstract: Plant traits—the morphological, anatomical, physiological, biochemical and phenological characteristics of plants—determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits—almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
    Type of Medium: Online Resource
    ISSN: 1354-1013 , 1365-2486
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2020313-5
    SSG: 12
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  • 10
    In: Global Ecology and Biogeography, Wiley, Vol. 32, No. 9 ( 2023-09), p. 1485-1494
    Abstract: Although dispersal ability is one of the key features determining the spatial dynamics of plant populations and the structure of plant communities, it is also one of the traits for which we still lack data for most species. We compiled a comprehensive dataset of seed dispersal distance classes and predominant dispersal modes for most European vascular plants. Our seed dispersal dataset can be used in functional biogeography, dynamic vegetation modelling and ecological studies at local to continental scales. Main Types of Variables Contained Species were classified into seven ordered classes with similar dispersal distances estimated based on the predominant dispersal mode, the morphology of dispersal units (diaspores or propagules), life form, plant height, seed mass, habitat and known dispersal by humans. We evaluated our results by comparing them with dispersal distances calculated using the ‘dispeRsal’ function in R. Spatial Location Europe. Time Period Present. Major Taxa and Level of Measurement The seed dispersal dataset contains information on dispersal distance classes and the predominant dispersal mode for 10,327 most frequent and locally dominant European vascular plant species. Software Format Data are available in .csv format.
    Type of Medium: Online Resource
    ISSN: 1466-822X , 1466-8238
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 1479787-2
    detail.hit.zdb_id: 2021283-5
    SSG: 12
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