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Fig. 1 in Short communication First record of eyeless specimens of Gammarus roeselii Gervais 1835 (Amphioda, Gammaridae) in a small stream of the sub-lacustrine Ticino River basin (Lombardy, Northern Italy)
Fig. 1 - The non-native amphipod Gammarus roeselii Gervais 1835 (from Paganelli et al., 2015).
Woerthersee sediment core data for the publication "Validation of seismic hazard curves using a calibrated 14 ka lacustrine record in the Eastern Alps, Austria"
<p>This dataset comprises sediment core data of Wörthersee, a lake in the Eastern European Alps, Austria. Together with a dataset comprising the seismic data (10.5281/zenodo.6479186), this is the basis for the publication Daxer et al. "Validation of seismic hazard curves using a calibrated 14 ka lacustrine record in the Eastern Alps, Austria".</p> <p>The files contain the following data:</p> <ul> <li>Core images Long Cores.zip: Core images of the Wörthersee Kullenberg-type long cores acquired with an ITRAX core scanner</li> <li>Core images Short Cores.zip: Core images of the Wörthersee gravity short cores (hammer-coring or trigger cores of the Kullenberg system) acquired with an ITRAX core scanner; provided as .tif files</li> <li>CT data WOER18-L5-X-Dicom.zip: X-ray computed tomography data acquired with a Siemens SOMATOM Definition AS (voxel size 0.2 x 0.2 x 0.3 mm); provided in DICOM format</li> <li>MSCL data.zip: Data acquired with a Geotek Multi-sensor core logger (e.g. magnetic susceptibility and gamma density); provided as Excel spreadsheets</li> <li>XRF data.zip: X-ray fluorescence data acquired with a ITRAX core scanner; provided in .csv format</li> </ul>
Data from: Drivers of contemporary lacustrine fish species richness in the glacial Lake Agassiz basin
<p><strong>Aim</strong>: Biological communities are the result of a stepwise spatiotemporal filtering process, driven by large-scale historical and local contemporary determinants. The biogeographical pattern and species richness of North American fishes are predominantly determined by historical processes of past glaciations and postglacial dispersal and by contemporary environmental and ecological processes. Here, we evaluate the effects of postglacial dispersal through glacial Lake Agassiz and habitat heterogeneity, as represented by lake surface area, on contemporary freshwater fish species richness patterns of northwestern Ontario lakes.</p> <p><strong>Location</strong>: Northwestern Ontario, Canada</p> <p><strong>Taxon</strong>: Freshwater fishes</p> <p><strong>Methods</strong>: We applied the theory of island biogeography and species-area curves to examine the effects of isolation from the past dispersal corridor of glacial Lake Agassiz and habitat heterogeneity on species richness across 264 contemporary lakes in northwestern Ontario, Canada. While controlling for correlations among the predictor variables, generalized linear models were constructed between species richness, as the response variable and the explanatory variables of lake elevation and surface area and connection to the dispersal corridor of Lake Agassiz.</p> <p><strong>Results</strong>: Differential cover by glacial Lake Agassiz led to variation in fish species richness across contemporary lake basins and species richness is higher in lakes that were covered by Lake Agassiz relative to basins remaining outside of the boundaries of the glacial lake. Lake surface area is the strongest predictor of species richness, while lake elevation is the strongest factor predicting isolation as species richness decreases with increasing altitudes.</p> <p><strong>Main Conclusions</strong>: Habitat heterogeneity and postglacial colonization have led to differences in fish richness within the same geographical region. Fish species richness increases with lake surface area and decreases with elevation, likely driven by greater niche diversity facilitating the assembly of more diverse communities and isostatic rebound and fluctuating levels of Lake Agassiz isolating lakes at high elevations from the dispersal route earlier during the colonization process, respectively. These patterns underscore the importance of incorporating historical and environmental community determinants in biodiversity studies.</p>
Lacustrine speciation associated with chromosomal inversion in a lineage of riverine fishes
<p>Geographic isolation is the primary driver of speciation in many vertebrate lineages. This trend is exemplified by North American darters, a clade of freshwater fishes where nearly all sister species pairs are allopatric and separated by millions of years of divergence. One of the only exceptions is the Lake Waccamaw endemic <em>Etheostoma perlongum</em> and its riverine sister species <em>E. maculaticeps</em>, which have no physical barriers to gene flow. Here we show that lacustrine speciation of <em>E. perlongum</em> is characterized by morphological and ecological divergence likely facilitated by a large chromosomal inversion. While <em>Etheostoma perlongum</em> is phylogenetically nested within the geographically widespread <em>E. maculaticeps</em>, there is a sharp genetic and morphological break coinciding with the lake-river boundary in the Waccamaw River system. Despite recent divergence, an active hybrid zone, and ongoing gene flow, analyses using a de novo reference genome reveal a 9 Mb chromosomal inversion with elevated divergence between <em>E. perlongum</em> and <em>E. maculaticeps</em>. This region exhibits striking synteny with known inversion supergenes in two distantly related fish lineages, suggesting deep evolutionary convergence of genomic architecture. Our results illustrate that rapid, ecological speciation with gene flow is possible even in lineages where geographic isolation is the dominant mechanism of speciation.</p>
Data from: Direct and indirect effects of a fishing ban on lacustrine fish community do not result in a full recovery
<ol> <li>Protected areas are increasingly being promoted as an important means of protecting freshwater biological diversity and ecological processes. A robust assessment of ecological changes in protected areas is fundamental to optimize conservation policies and adaptive management. China's efforts to establish aquatic reserves have attracted worldwide attention, especially the "10-year fishing ban" implemented in the Yangtze River basin.</li> <li>We focused on Liangzi Lake, a freshwater protected area in the Yangtze River basin, to understand the effect of a fishing ban occurring after a short period of overfishing. In this aim, the time series of fish community taxonomic and functional structure encompassing the overfishing period and a post-ban period have been analyzed. Fish community metrics with direct, indirect, and no responses to fishing bans were identified.</li> <li>The results indicate that in the early period of the fishing ban, the trophic level and body size structure of the fish community were in the way of recovery. However, species that prefer benthic habitats did not recover after fishing-induced habitat degradation. Functional traits were more sensitive than taxonomic indices and revealed subtle community changes, such as the recovery of some ecological functions, despite a non-recovering species richness.</li> <li> <em>Synthesis and applications.</em> This study provides a rare case of a freshwater protected area in which the effects of conservation measures are studied with a temporal survey. The effectiveness of the functional trait approach in the application of protected area assessment was demonstrated by revealing the recovery of trophic level and body size structure of fish communities after the implementation of the fishing ban and the inadequacy of habitat restoration efforts. We suggest that in freshwater protected areas, insistence on a fishing ban is necessary but not sufficient for full biodiversity recovery, and other measures are needed, such as habitat restoration and species-focused stocking.</li> </ol>
Data from: Direct and indirect effects of a fishing ban on lacustrine fish community do not result in a full recovery
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Lacustrine speciation associated with chromosomal inversion in a lineage of riverine fishes
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Data from: Drivers of contemporary lacustrine fish species richness in the glacial Lake Agassiz basin
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Historical, abiotic, and biotic drivers influence contemporary lacustrine fish community composition in the glacial Lake Agassiz basin
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Surface water chemistry:Scale Dependent Nutrient Interactions among Lacustrine Communities
E280 is a long-term study, initiated in 2013, to determine how nutrient retention vs. export in the uplands affects downslope aquatic communities. Experimental work will focus on stoichiometry and patterns of nutrient limitation at different observational scales. Our proposed work will test the hypothesis that with increasing spatial and temporal scale, interactions among limiting nutrients diminish and single factor limitation is increasingly prevalent.
Plant DNA metabarcoding records from three cores of lacustrine lakes along a open larch forest-forest tundra-tundra transect at the Omoloy region, north-eastern Siberia
<p>Here, we provide the raw plant DNA metabarcoding data archived in three Siberian lake sediment cores spanning the mid-Holocene to the present (7.6-0 cal ka BP), from northern typical tundra to southern open larch forest in the Omoloy region.</p> <p>There are three cores:</p> <ol> <li> <strong>14-OM-20B</strong>, Lat. / °: 70.53, Lon. / °: 132.91, Ele. / m a.s.l.: 52, Modern vegetation: open larch forest, Lake area / km2: 0.26, Maximal depth / m: 3.4</li> <li> <strong>14-OM-02B</strong>, Lat. / °: 70.72, Lon. / °: 132.67, Ele. / m a.s.l.: 58, Modern vegetation: forest tundra, Lake area / km2: 0.08, Maximal depth / m: 3.5</li> <li> <strong>14-OM-12A</strong>, Lat. / °: 70.96, Lon. / °: 132.57, Ele. / m a.s.l.: 60, Modern vegetation: tundra, Lake area / km2: 0.09, Maximal depth / m: 4.5</li> </ol> <p>Three lake sediment cores, 14OM12A (33 cm long), 14OM02B (49.5 cm long) and 14OM20B (86 cm long), were recovered from three sites using a UWITEC gravity corer (6 cm internal diameter) equipped with a hammer tool in July 2014.</p> <p>From the three cores, 16 bulk organic carbon samples were selected because of the lack of macrofossil remains and radiocarbon dated using accelerator mass spectrometry (AMS) at Poznań radiocarbon laboratory of Adam Mickiewicz University, Poland. In addition, 30 freeze-dried samples per core at 0.25 or 0.5 cm intervals between 0 and 15 cm were analysed for 210Pb/137Cs at the Liverpool University Environmental Radioactivity Laboratory. (The dating table has been submitted to PANGAEA)</p> <p>In this project, we analyse pollen (has been submitted to PANGAEA, doi: 10.1594/PANGAEA.922550) and sedaDNA from three lake sediment cores from the Omoloy region in north-eastern Siberia (northern Yakutia), which are currently surrounded by different vegetation types ranging from typical tundra to open larch forest. First, our aim is to compare sedaDNA with the pollen data to see whether both methods track the same pattern with respect to compositional changes and diversity changes across the northern Russian treeline zone or are complementary to each other. Second, we reconstruct the mid- to late-Holocene changes of vegetation composition along a north–south transect. Third, we use the sedaDNA data to reconstruct variations in species richness and relate this to vegetation and climate change.</p>
Data from: Juvenile divergence in adaptive traits among seven sympatric fish eco-morphs arises before moving to different lacustrine habitats
Identifying the mechanisms initiating sympatric diversification in vertebrates has remained a conceptual challenge. Here we analyze an assemblage of sympatric charr (Salvelinus malma) morphs from landlocked Lake Kronotskoe basin as a model to uncover the divergence pathways in freshwater fishes during the early life history stages. All morphs have distinct developmental biology, but a similar developmental rate retardation compared to the ancestor. Our study reveals that adult morphological differences, which acquire functionality at maturation, originate in the early juvenile stages due to heterochrony in skeletogenesis and allometric changes triggered by variation in metabolic activity. The craniofacial differences among the morphs result from asynchronous development of several skeletal modules. The accelerated ossification of teeth-armed bones occurs in predatory feeding morphs, while cranial cover ossification is promoted in benthivorous morphs. These contrasting growth patterns have led to seven phenotypes that span a range far beyond the ancestral variability. The most distinct morphs are a riverine-spawning, epilimnetic predator and a lacustrine-spawning, profundal benthic feeder. Taken together, we argue that the adaptive morphological differentiation in these sympatric freshwater fishes is driven by diverging patterns in ossification rate and metabolic activity against a background of uneven somatic growth. This divergence is primarily associated with basic environmental differences on the nursery grounds that might be unrelated to resource use. This non-heritable phenotype divergence is then exposed to natural selection that could result in further adaptive genetic changes.
Data from: Do genetic drift and accumulation of deleterious mutations preclude adaptation? Empirical investigation using RADseq in a northern lacustrine fish
Understanding genomic signatures of divergent selection underlying long-term adaptation in populations located in heterogeneous environments is a key goal in evolutionary biology. In this study, we investigated neutral, adaptive and deleterious genetic variation using 7,192 SNPs in 31 Lake Trout (Salvelinus namaycush) populations (n = 673) from Québec, Canada. Average genetic diversity was low, weakly shared among lakes, and positively correlated to lake size, indicating a major role for genetic drift subsequent to lake isolation. Putatively deleterious mutations were on average at lower frequencies than the other SNPs, and their abundance relative to the entire polymorphism in each population was positively correlated to inbreeding, suggesting that the effectiveness of purifying selection was negatively correlated to inbreeding, as predicted from theory. Despite evidence for pronounced genetic drift and inbreeding, several outlier loci were associated with temperature and found in or close to genes with biologically relevant functions notably related to heat-stress and immune responses. Outcomes of gene-temperature associations were influenced by the inclusion of the most inbred populations, in which allele frequencies deviated the most from model predictions. This result illustrates challenge in identifying gene-environment associations in cases of high genetic drift and restricted gene flow and suggests limited adaptation in populations experiencing higher inbreeding. We discuss the relevance of these findings for the conservation and management, notably regarding stocking and genetic rescue, of Lake Trout populations and other species inhabiting highly fragmented habitats.
Data from: Changes in Eocene plant diversity and composition of the vegetation: the lacustrine archive of Messel (Germany)
Based on high resolution palynological analysis of 680 samples from a core, short-term changes in plant diversity and floristic composition within the Paleogene greenhouse have been detected in the lacustrine succession of a Lower to Middle Eocene maar lake at Messel (Federal State of Hesse, Germany). The microfloristic data show that taxonomic diversity increased rapidly within some decades during recolonization of a volcanically devastated area around the lake. With the establishment of a climax vegetation at the end of recolonization the maximum in palynological diversity was reached in the crater area. During the following 640 Kyr the composition of the palynospectrum changed only gradually. However, different richness and evenness estimations show that alpha and gamma diversity decreased up to 35% which can be related to the establishment of an equilibrium stage within the climax vegetation that led to the dominance of an assemblage of self-replacing species. Nevertheless, time series analysis of alpha diversity changes within the climax vegetation reveals that orbitally controlled climate change of Milankovitch and Sub-Milanovitch order influenced the diversity of the vegetation resulting in a rise of beta diversity. Based on the composition of the vegetation and comparison to modern analogues our analysis now proves that Eocene paratropical plant diversity increased during periods of slightly higher temperature and precipitation. Therefore, both composition and diversity of the vegetation was highly susceptible to minor-scale short-term changes in climate even during equable greenhouse conditions.
On following pages: 115. Reed Vole (Alexandromys fortis); 116. Sakhalin Vole (Alexandromys sachalinensis); 117. Mongolian Vole (Alexandromys mongolicus); 118. Middendorff's Vole (Alexandromys middendorffii; 119. Gromov's Vole (Alexandromys gromovi); 120. Lacustrine Vole (Alexandromys limnophilus); 121. Root Vole (Alexandromys oeconomus); 122. Taiwan Vole (Alexandromys kikuchii); 123. Japanese Grass Vole (Alexandromys montebell); 124. Afghan Vole (Microtus afghanus); 125. Bucharian Vole (Microtus bucharensis); 126. Juniper Vole (Microtus juldaschi); 127. Short-tailed Field Vole (Microtus agrestis); 128. Mediterranean Field Vole (Microtus lavernedii): 129. Portuguese Field Vole (Microtus rozianus); 130. Insular Vole (Microtus abbreviatus); 131. Singing Vole (Microtus miurus); 132. Rock Vole (Microtus chrotorrhinus); 133. Zempoaltepec Vole (Microtus umbrosus); 134. Tarabundi Vole (Microtus oaxacensis); 135. Guatemalan Vole (Microtus guatemalensis); 136. Woodland Vole (Microtus pinetorum); 137. Jalapan Vole (Microtus quasiater); 138. California Vole (Microtus californicus): 139. Beach Vole (Microtus brewer); 140. Mexican Vole (Microtus mexicanus); 141. Mogollon Vole (Microtus mogollonensis); 142. Prairie Vole (Microtus ochrogasten; 143. Taiga Vole (Microtus xanthognathus); 144. Cabrera''s Vole (Microtus cabrerae); 145. North American Water Vole (Microtus richardson); 146. Gray-tailed Vole (Microtus canicaudus). in Cricetidae
On following pages: 115. Reed Vole (Alexandromys fortis); 116. Sakhalin Vole (Alexandromys sachalinensis); 117. Mongolian Vole (Alexandromys mongolicus); 118. Middendorff's Vole (Alexandromys middendorffii; 119. Gromov's Vole (Alexandromys gromovi); 120. Lacustrine Vole (Alexandromys limnophilus); 121. Root Vole (Alexandromys oeconomus); 122. Taiwan Vole (Alexandromys kikuchii); 123. Japanese Grass Vole (Alexandromys montebell); 124. Afghan Vole (Microtus afghanus); 125. Bucharian Vole (Microtus bucharensis); 126. Juniper Vole (Microtus juldaschi); 127. Short-tailed Field Vole (Microtus agrestis); 128. Mediterranean Field Vole (Microtus lavernedii): 129. Portuguese Field Vole (Microtus rozianus); 130. Insular Vole (Microtus abbreviatus); 131. Singing Vole (Microtus miurus); 132. Rock Vole (Microtus chrotorrhinus); 133. Zempoaltepec Vole (Microtus umbrosus); 134. Tarabundi Vole (Microtus oaxacensis); 135. Guatemalan Vole (Microtus guatemalensis); 136. Woodland Vole (Microtus pinetorum); 137. Jalapan Vole (Microtus quasiater); 138. California Vole (Microtus californicus): 139. Beach Vole (Microtus brewer); 140. Mexican Vole (Microtus mexicanus); 141. Mogollon Vole (Microtus mogollonensis); 142. Prairie Vole (Microtus ochrogasten; 143. Taiga Vole (Microtus xanthognathus); 144. Cabrera''s Vole (Microtus cabrerae); 145. North American Water Vole (Microtus richardson); 146. Gray-tailed Vole (Microtus canicaudus).
Spatial patterns and quantification of lacustrine groundwater discharge determined based on 222Rn
<p>Shape of water pixels calculated by Modified Normalized Difference Water Index algorithm based on Landsat8 images</p>
Spatial patterns and quantification of lacustrine groundwater discharge determined based on 222Rn
<p>The field parameter [temperature (T), electrical conductivity (EC), pH, dissolved oxygen (DO), redox potential (Eh) and 222Rn concentration] were listed here. </p>
Spatial patterns and quantification of lacustrine groundwater discharge determined based on 222Rn
<p>The 132 bathymetric data from the lake while lake samples were taken on board. We created a bathymetric contour map in ArcGIS 10.2 using the natural neighborhood method to reflect the overall bathymetry of the lake through 116 randomly selected bathymetric data. The size of the Landsat 8 image was used as the basic unit (30*30 m) to divide the lake into 30*30 m areas and read data from 16 other bathymetric points that were not involved in the production of the bathymetric map.</p>
Spatial patterns and quantification of lacustrine groundwater discharge determined based on 222Rn
<p>Wind speed data were collected from the Shishou weather station monitored by the China Meteorological Network (http://data.cma.cn/dataService/cdcindex/datacode/A.0012.0001/show_value/normal.html).</p>
FIGURES 70–71 in Morphology of some fossil lacustrine centric species from the western United States assigned to the genus Cyclotella (Bacillariophyta), including four described as new
FIGURES 70–71: Cyclotella jonesii. LM. Figure 70 is of Morphotype 1. Figure 71 is of Morphotype 2. Scale bars = 10 µm.
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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.