Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
132
datasets available to search
ShareScore release 0.9.0
Dataset results
132 results for “Freshwater diatoms”
rbcL reference sequences of marine and freshwater diatoms
<p>This database has been modified from the R-syst::Diatom rbcL database, version 9, accessed on 3.18.2021. (see Rimet et al.2016 for details)</p> <p>Sequences of mostly <em>Pseudo-nitzschia</em> from the Gulf of Trieste and some others missing from the database were added.</p> <p>The names of the sequences in the .fasta file are formatted in a way that they can be used directly in dada2 for taxonomic classification. </p> <p>This database represents a comprehensive marine diatom sequence archive. </p>
Data for: Resolving marine–freshwater transitions by diatoms through a fog of gene tree discordance
<p>Despite the obstacles facing marine colonists, most lineages of aquatic organisms have colonized and diversified in freshwaters repeatedly. These transitions can trigger rapid morphological or physiological change and, on longer timescales, lead to increased rates of speciation and extinction. Diatoms are a lineage of ancestrally marine microalgae that have diversified throughout freshwater habitats worldwide. We generated a phylogenomic dataset of genomes and transcriptomes for 59 diatom taxa to resolve freshwater transitions in one lineage, the Thalassiosirales. Although most parts of the species tree were consistently resolved with strong support, we had difficulties resolving a Paleocene radiation, which affected the placement of one freshwater lineage. This and other parts of the tree were characterized by high levels of gene tree discordance caused by incomplete lineage sorting and low phylogenetic signal. Despite differences in species trees inferred from concatenation versus summary methods and codons versus amino acids, traditional methods of ancestral state reconstruction supported six transitions into freshwaters, two of which led to subsequent species diversification. Evidence from gene trees, protein alignments, and diatom life history together suggest that habitat transitions were largely the product of homoplasy rather than hemiplasy, a condition where transitions occur on branches in gene trees not shared with the species tree. Nevertheless, we identified a small set of putatively hemiplasious genes, many of which have been associated with shifts to low salinity, indicating that hemiplasy played a small but potentially important role in freshwater adaptation. Accounting for differences in evolutionary outcomes, in which some taxa became locked into freshwaters while others were able to return to the ocean or become salinity generalists, might help further distinguish different sources of adaptive mutation in freshwater diatoms.</p>
Data for: Resolving marine–freshwater transitions by diatoms through a fog of gene tree discordance
Open the record for dataset details and reuse information.
Data from: Geo-climatic factors drive diatom community distribution in tropical South American freshwaters
1.Patterns that maintain and generate biodiversity of macro-organisms in the Neotropics are widely discussed in the scientific literature, yet the spatial ecology of microorganisms is largely unknown. The unique character of the tropical Andes and adjacent Amazon lowlands generates a wide gradient of environmental conditions to advance our understanding of what drives community assembly and diversity processes. 2.We analyzed the distribution patterns of benthic diatoms (unicellular siliceous algae) as a model group of microbial passive dispersers, including predictors that describe limnological and geo-climatic gradients for a total of 113 waterbodies (0–28ºS and 58–80ºW), including lakes and streams. Complementary multivariate statistical analyses were performed to correlate i) community composition, and ii) diatom species richness with environmental and spatial factors to infer niche-based and dispersal-based assembly processes, respectively. 3.Results showed that two gradients structured both diatom assemblages and waterbodies, namely climate and landscape configuration. Variance partitioning revealed that broad-scale spatial variables (distance-based Moran's Eigenvectors) outperformed the two environmental components (limnological and geo-climatic), suggesting dispersal-assembled communities. However, diatom assemblages were structured by geo-climatic (regional) factors in certain lakes in the northern and central Andes, although their effects were partially manifested via local variables after the geographical distances were factored out. In a similar way, climatic and topographic structuring homogenized lake and stream communities within ecoregions, as indicated by the strong overlap between the two community types and the weak correlation between biota and limnological variables. Notably, a significant increase in diatom species richness was related to increased water connectivity, interpreted to indicate that a decrease in the remoteness of the system increase species number. 4.Synthesis. We emphasize the strength of macroecological gradients (landscape configuration and climatic factors) in affecting both diatom diversity and community composition in the South American tropics. In this context, our results and the commonalities of ecoregion patterning with groups of macroorganisms (vegetation), suggest the need to integrate microbial ecology into a macroecology framework to unravel mechanisms behind diversity gradients.
Supporting data for Bryłka et al., 2023 Gene duplication, shifting selection, and functional diversification of silicon transporter proteins in marine and freshwater diatoms.
<p>These are supporting files used in the analysis in Bryłka et al., 2023 "<em>Gene duplication, shifting selection, and functional diversification of silicon transporter proteins in marine and freshwater diatoms". </em> All data newly generated from the Alverson lab.</p> <p> </p>
Evidence of local adaptation in a freshwater diatom indicates higher sensitivity to nutrient limitation as water temperature rises
Open the record for dataset details and reuse information.
Data from: Geo-climatic factors drive diatom community distribution in tropical South American freshwaters
Open the record for dataset details and reuse information.
Diatoms define a novel freshwater biogeography of the Antarctic
<p><span class="fontstyle0">Terrestrial biota in the Antarctic are more globally distinct and highly structured</span><br> <span class="fontstyle0">biogeographically than previously believed, but information on biogeographic patterns</span><br> <span class="fontstyle0">and endemism in freshwater communities is largely lacking. We studied biogeographic</span><br> <span class="fontstyle0">patterns of Antarctic freshwater diatoms based on the analysis of species occurrences in a</span><br> <span class="fontstyle0">dataset of 439 lakes spread across the Antarctic realm. Highly distinct diatom floras, both</span><br> <span class="fontstyle0">in terms of composition and richness, characterize Continental Antarctica, Maritime</span><br> <span class="fontstyle0">Antarctica and the sub-Antarctic islands, with marked biogeographic provincialism in</span><br> <span class="fontstyle0">each region. A total of 44% of all species is estimated to be endemic to the Antarctic, and</span><br> <span class="fontstyle0">most of them are confined to a single biogeographic region. The level of endemism</span><br> <span class="fontstyle0">significantly increases with increasing latitude and geographic isolation. Our results have</span><br> <span class="fontstyle0">implications for conservation planning, and suggest that successful dispersal of</span><br> <span class="fontstyle0">freshwater diatoms to and within the Antarctic is limited, fostering the evolution of</span><br> <span class="fontstyle0">highly endemic diatom floras</span><br> </p>
Data from: Diatoms do radiate: evidence for a freshwater species flock
Due to the ubiquity and high dispersal capacity of unicellular eukaryotes, their often extraordinary diversity found in isolated and long-lived ecosystems such as ancient lakes is typically attributed to multiple colonization events rather than to in situ speciation. However, respective evolutionary studies are very scarce and the often high number of species flocks in ancient lakes across multicellular taxa raises the question whether unicellular species, such as diatoms, may radiate as well. Here, we use an integrative approach that includes molecular data from benthic diatom species of the genus Aneumastus endemic to ancient Lake Ohrid, fossil data obtained from the sediment record of a recent deep-drilling project and biogeographical information to test if this group, indeed, constitutes a species flock. Molecular-clock and phylogenetic analyses indicate a young monophyletic group of several endemic species. Molecular, fossil and biogeographical data strongly suggest a rapid intra-lacustrine diversification, which was possibly triggered by the emergence of novel habitats. This finding is the first evidence for a species flock in diatoms and suggests that in situ speciation is also a relevant evolutionary process for unicellular eukaryotes in isolated ecosystems.
Data from: Hidden diversity in the freshwater planktonic diatom Asterionella formosa
Many freshwater and marine algal species are described as having cosmopolitan distributions. Whether these widely distributed morphologically similar algae also share a similar gene pool remains often unclear. In the context of island biogeography theory, stronger spatial isolation deemed typical of freshwater lakes should restrict gene flow and lead to higher genetic differentiation among lakes. Using nine microsatellite loci, we investigate the genetic diversity of a widely distributed freshwater planktonic diatom, Asterionella formosa, across different lakes in Switzerland and the Netherlands. We applied a hierarchical spatial sampling design to determine the geographical scale at which populations are structured. A subset of the isolates was additionally analysed using amplified fragment length polymorphism (AFLP) markers. Our results revealed complex and unexpected population structure in A. formosa with evidence for both restricted and moderate to high gene flow at the same time. Different genetic markers (microsatellites and AFLPs) analysed with a variety of multivariate methods consistently revealed that genetic differentiation within lakes was much stronger than among lakes, indicating the presence of cryptic species within A. formosa. We conclude that the hidden diversity found in this study is expected to have implications for the further use of A. formosa in biogeographical, conservation and ecological studies. Further research using species-level phylogenetic markers is necessary to place the observed differentiation in an evolutionary context of speciation.
FIGURES 12–15 in Taxonomy and valve ultrastructure of new and interesting freshwater fossil diatoms (Bacillariophyta) of Miocene age from the Espanola Formation of New Mexico, U.S.A. II. Description of a New Grunowia species with comments on the genus
FIGURES 12–15. Grunowia mannii Kociolek & Danz sp. nov. SEM. Valve interior. 12–14. Entire valves, showing differences in valve shape relative to length. Large fibulae and large portules over the raphe canal are evident. 15. View of central nodule showing small, helictoglossa-like center and discontinuous raphe branch. Scale bars = 5 µm (Fig. 12), 4 µm (Fig. 13), 3 µm (Fig. 14), 1 µm (Fig. 15).
FIGURES 1–7 in Taxonomy and valve ultrastructure of new and interesting freshwater fossil diatoms (Bacillariophyta) of Miocene age from the Espanola Formation of New Mexico, U.S.A. II. Description of a New Grunowia species with comments on the genus
FIGURES 1–7. Grunowia mannii Kociolek & Danz sp. nov. LM. Size diminution series. Fig. 1 represents an initial valve. The holotype is presented in fig. 4. Scale bar = 10 µm.
FIGURES 8–11 in Taxonomy and valve ultrastructure of new and interesting freshwater fossil diatoms (Bacillariophyta) of Miocene age from the Espanola Formation of New Mexico, U.S.A. II. Description of a New Grunowia species with comments on the genus
FIGURES 8–11. Grunowia mannii Kociolek & Danz sp. nov. SEM of valve exterior. 8, 9. Valve view showing characteristic shape and distinctly-elevated, raphe-bearing keel. 10. Apex of the valve showing raphe end extending onto the mantle. 11. Central portion of the valve, with raphe branches interrupted. Scale bars = 5 µm (Figs 8, 9), 3 µm (Fig. 10), 2 µm (Fig. 11).
FIGURES 1–15 in An unusual freshwater diatom with bilobate ends from the Mid-Miocene of East Antarctica: Staurosirella tigris sp. nov. (Fragilariaceae, Bacillariophyta)
FIGURES 1–15. Staurosirella tigris sp. nov., LM pictures taken from the holotype population (sample WD 19, BR-4689). 1. Frustule in girdle view. 2–15. Several valves in valve face view in decreasing valve length. Fig. 15 most likely represents a teratological valve. Scale bar = 10 µm.
FIGURES 16–20 in An unusual freshwater diatom with bilobate ends from the Mid-Miocene of East Antarctica: Staurosirella tigris sp. nov. (Fragilariaceae, Bacillariophyta)
FIGURES 16–20. Staurosirella tigris sp. nov., SEM pictures taken from the holotype population (sample WD 19, BR-4689). 16. External view of an entire valve. 17. External detail of the valve margin showing the conical spines with hollow bases and the linear areolae. 18. External detail of the apical pore fields. 19. Internal detail showing part of the valvocopula and the copulae. 20. Internal detail of a valve apex showing the apical pore fields and some vimines with small or remnant volae. Scale bars = 10 µm (Figs 16, 19), 5 µm (Figs 18, 20), 1 µm (Fig. 17).
FIGURES 8–15 in Pinnularia dongzhenensis sp. nov., a new freshwater diatom species (Bacillariophyceae) from Dongzhen Reservoir, Fujian Province, China
FIGURES 8–15. Pinnularia dongzhenensis sp. nov., SEM external views of P. dongzhenensis sp. nov.. 8, 9. General view of valve. 10, 11. Central area showing proximal raphe fissures bent in the same direction. 12, 13. Details of alveoli with rows of rounded areolae. 14, 15. Detail of the sickle–shaped raphe fissure at pole, and each alveolus with rows of rounded areolae. Scale bars = 10 μm (Figs 8, 9), 2 μm (Figs 10–15).
FIGURES 1–7 in Pinnularia dongzhenensis sp. nov., a new freshwater diatom species (Bacillariophyceae) from Dongzhen Reservoir, Fujian Province, China
FIGURES 1–7. LM micrographs of the type population of Pinnularia dongzhenensis from Dongzhen Reservoir. Scale bar = 10 μm.
Supplementary data to the manuscript "Morphology and metabarcoding! A test with stream diatoms from Mexico highlights the complementarity of methods", submitted to Freshwater Science by D. Mora, N. Abarca, S. Proft, J. Grau, N. Enke, J. Carmona, O. Skibbe, R. Jahn and J. Zimmermann.
<p>Demultiplexed fastq files for 18 samples, accompanied by a table including sample numbers in the manuscript and sample numbers in the fastq files.</p>
Data and code for Freshwater diatoms diversify and turn over faster than marine in both planktonic and benthic habitats
<p>Data and R scripts to run the analyses in the diatom muhisse paper. See also the 'Running MuHiSSE' vignette in the R package hisse.</p>
FIGURES 3–26 in Geissleria triundulata sp.nov., a new freshwater diatom (Cymbellaceae, Bacillariophyta) from the Mula-Mutha River Basin, India
FIGURES 3–26. Geissleria triundulata sp.nov., light microscope images showing size diminution series: (3) holotype specimen. Scale bar = 10 μm. 3776/ 51.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.