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Figure 15 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 15: Depth distribution of fish abundance by species (individuals per unit effort) in benthic habitats to 50 m deep according to CEN benthic nets.
Figure 26 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 26: Depth distribution of catch per unit effort (CPUE; horizontal axis) for native fish species living in the deeper zones of the deep, northern perialpine lakes: Coregonus spp (yellow), Salvelinus spp (red), Cottus spp (grey/brown) and Lota lota (light grey). CPUE is the average of catches in deep-set vertical nets and benthic CEN nets. CPUE is square-root transformed to increase the visibility of the smaller values in the profundal zone. Note that the scale of the horizontal axis (CPUE) differs among the lakes. Whereas Lota lota has pelagic eggs and larvae and does hence not have to recruit locally, all other species recruit locally. Boxes at the bottom of the figure show the total phosphorus of the lake at the time of Projet Lac sampling (upper value) and the maximum measured total phosphorus value that had been experienced by the lake in the past (lower value in bold). The panels for Constance and Zurich show the data for the deeper lake in each of the pairs (i.e. Upper Constance and Lower Zurich).
Figure 23 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 23: Fish biomass (CEN gillnets) in the shallow sunlit zone near the lake floor to around 12 m was higher in lakes with more phosphorus. In the deeper parts of the lakes (below 50 m), benthic fish biomass was highest in the lakes with very low phosphorus. Dashed lines are shown for statistically significant relationships (surface: p-value = 0.003, R2 = 0.74; middle: p-value = 0.63, R2 = 0.02, deep: p-value = 0.014, R2 = 0.467). Horizontal axis is displayed on a log scale.
Figure 14 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 14: Whole-lake average fish biomass per unit net area in vertical nets was lower in deeper lakes due to their proportionally larger volume of less productive habitat. Note that vertical and horizontal axes are on a log scale. Lakes that have returned from a period of eutrophic conditions with hypoxia in the hypolimnion in at least part of the lake to meso- or oligotropic conditions are indicated in blue, while yellow points indicate re-oligotrophied lakes that have lost profundal fish species.
Figure 10 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 10: Uniqueness of the fish communities of all lakes and catchments. Uniqueness index for each lake was calculated as the sum of the inverse of the number of lakes where each species in the lake was recorded.
Figure 17 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 17: Habitat associations of fishes in the littoral zone in late summer/autumn based on sampling in 28 perialpine lakes. Grey lines indicate that the species was recorded (electrofishing and shallow-set vertical nets) more often in this littoral habitat than in other habitats. The thickness of the line reflects how much more frequently than random the species was recorded in the habitat. Associations were averaged among lakes and shown only where the association was positive in more than half of the lakes in which a species was recorded. Only fish species recorded in the littoral zone of at least three lakes are shown. Three species were recorded in at least three lakes, but had no clear habitat association (Carassius gibelio, Rhodeus amarus, Telestes muticellus). Lineages of Barbatula spp and forms of Perca fluviatilis could unfortunately not be differentiated in the analysis. Inflows and outflows are excluded to focus on the lacustrine habitats. Note that some of these species may have their strongest associations with other habitats outside the littoral (e.g. the sublittoral, profundal or pelagic), but such habitat occurrences could not be included in this analysis. See [47] for more information on the calculation of habitat association.
Figure 6 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 6: Species-abundance distributions (SADs) for each of 35 perialpine lakes and 1 lowland lake. These SADs result from combining partial SADs obtained by sampling with the CEN netting protocol, the VERT netting protocol and the electrofishing protocol (for all partial SADs see Appendix B Figure 69). Abundances are log2-transformed. Normal distributions are indicated by a thin line in each plot. The qualitative fit to the expected distribution is indicated by coloured circles: dark green = good fit, light green = modest fit, orange = poor fit, red = very poor fit. Colour of bars indicates drainage systems: green = Rhone, red = Rhine, orange = Po, blue = Danube. Note the systematic difference between Rhine lakes (9 good, 3 modest, 4 poor, 1 very poor) and Po lakes (0 good, 1 modest, 2 poor, 6 very poor). This difference cannot be due to differences in sampling effort because Maggiore and Lugano were among the best sampled lakes, but both have very poor fits to the expected distributions. Lake Aulnes is a lowland lake in the southern Rhone drainage that we sampled but did not otherwise consider in this report.
Figure 1 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 1: Map of lakes surveyed by Projet Lac with major river networks and catchments indicated by background colour. Note that the Aare-Rhine includes the subcatchments of the Reuss and Limat rivers. Data source: Federal Office of Topography swisstopo 2020.
Figure 19 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 19: Opposing relationships with total phosphorus for the biomass of the two most common fish taxa among the large and deep lakes (average depth> 50 m). Data are whole-lake average biomass (in grams) of fish per vertical net battery. Note that the horizontal axis is on a log scale. Regression statistics for Coregonus are p-value = 0.005, R2 = 0.57 and perch are p-value = 0.004, R2 = 0.58. Shaded regions show thresholds for total phosphorus of 10 μg / L and 5 μg / L.
Figure 22 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 22: Whole-lake average number of European perch (Perca fluviatilis) per vertical net battery compared to total phosphorus concentration in large and deep lakes (average depth> 50 m). The left panel shows the relationship for all perch caught in the lake (p-value = 0.022, R2 = 0.42). The right panel shows the relationship for only perch larger than 20 cm (length from snout to the tip of the tail; p-value = 0.003, R2 = 0.6). Note that the horizontal axis is on a log scale. Dashed red lines indicate statistically significant relationships.
Food web rewiring drives long-term compositional differences and late-disturbance interactions at the community level
<p><strong>Abstract</strong></p> <p>Ecological communities are constantly exposed to multiple natural and anthropogenic disturbances. Multivariate composition (if recovered) has been found to need significantly more time to be regained after pulsed disturbance compared to univariate diversity metrics and functional endpoints. However, the mechanisms driving the different recovery times of communities to single and multiple disturbances remain unexplored. Here, we apply for the first time quantitative ecological network analyses to try to elucidate the mechanisms driving long-term community composition dissimilarity and late-stage disturbance interactions at the community level. For this, we evaluate the effects of two pesticides, nutrients enrichment and their interactions in outdoor mesocosms containing a complex freshwater community. We found changes in interactions strength to be strongly related to compositional changes and identified post-disturbance interaction strength rewiring to be responsible for most of the observed compositional changes. Additionally, we found pesticides interactions to be significant in the long term only when both interactions strength and food web architecture are reshaped by the disturbances. We suggest that quantitative network analysis has the potential to unveil ecological processes that prevent long-term community recovery.</p> <p><strong>Significance Statement</strong></p> <p>Multiple anthropogenic disturbances affect the structure and functioning of communities. Recent evidence highlighted that, after pulse disturbance, the functioning a community performs may be recovered fast due to functional redundancy, whereas community multivariate composition needs longer time. Yet, the mechanisms that drive the different community recovery times have not been quantified empirically. We use quantitative food web analysis to assess the influence of species interactions on community recovery. We found species interactions strength to be the main mechanism driving differences between structural and functional recovery. Additionally, we show that interactions between multiple disturbances appear in the long term only when both species interaction strength and food web architecture change significantly.</p> <p>Please see the "readme" sheet in the datafile for a description of the file structure and treatments abreviations.</p>
Bacterial community composition of bulk soil from date palm (Phoenix dactylifera) farm depend on irrigation water salinity
<p>Non-saline and saline ground water irrigation is extensively used in the arid regions of United Arab Emirates (UAE) for date palm (<em>Phoenix</em> <em>dactylifera</em>) cultivation without knowing its effect on bulk soil bacterial communities. Bulk soil acts as a supply base for microbes and nutrients that are accessed by date palm roots. We collected soil samples from date farms across UAE and performed V3-V4 16s rRNA metabarcoding analysis to understand how bulk soil bacterial diversity and communities respond to irrigation water sources (non-saline and saline groundwater irrigation). There was no significant variation in bulk bacterial diversity (Shannon diversity, richness as well as evenness). But bulk bacterial communities differed between irrigation water sources and irrigation water electrical conductivity was the significant factor that explained a part of community variation. Out of total 5089 OTUs, saline bulk soil harbored only 21.3% of total OTUs compared to 31.5% OTUs in non-saline bulk soil, while 47.15% OTUs shared between both types of irrigation. Proteobacteria abundance was higher in saline bulk soil, while Actinobacteriota abundance was enhanced in non-saline bulk soil. Similar selection was observed at genus level, wherein saline bulk soil showed increase in abundance of <em>Subgroup_10, Nitrospira </em>and<em> Mycobacterium</em>, whereas <em>Microvirga, Ammoniphilus, Nitrospira</em> and <em>Lysinibacillus </em>were elevated in non-saline bulk soil. Saline (<em>Novibacillus</em> and <em>Bauldea</em>) and non-saline bulk soil (<em>Microvirga</em>, <em>Marmoricola</em>, <em>Domibacillus</em>, <em>Oceanobacillus</em>, <em>Bhargavaea</em> and <em>Solirubrobacter</em>) showed significant selection of indicator taxa (P < 0.05). This indicate that bacterial communities colonizing bulk soil differ depending on irrigation water source and it is affected by irrigation water EC.</p>
Fig. 3 in Communities Of Ditylenchus Destructor Satellite Species Of Nematodes In Infected Potato Tubers: Species Composition Of Phytonematode Complex And The Structure Of Their Infracommunities
Fig. 3. The dynamics of the ratio of the total number of various trophoecological group nematodes during the disease of potato tubers caused by D. destructor.
Fig. 1 in Communities Of Ditylenchus Destructor Satellite Species Of Nematodes In Infected Potato Tubers: Species Composition Of Phytonematode Complex And The Structure Of Their Infracommunities
Fig. 1. Ditylenchus destructor (Thorne, 1945) potato nematode: A — female; B — head end of the female; C — spicules; D — male; E — head end of the male; F, G — lateral field by the Thorne, 1945.
Fig. 5 in Communities Of Ditylenchus Destructor Satellite Species Of Nematodes In Infected Potato Tubers: Species Composition Of Phytonematode Complex And The Structure Of Their Infracommunities
Fig. 5. Occurrence of various species of phytonematodes during successive stages of the pathological process.
Fig. 1 in Species Composition And Structure Of The Communities Of Plant-Parasitic And Free-Living Soil Nematodes In The Greenhouses Of Botanical Gardens Of Ukraine
Fig. 1. Dendrogram of similarity of the nematode communities in the greenhouses of botanical gardens of Ukraine (amalgamation by the method of complete linkage). Explanation of the abbreviations is given in table 2. Рис. 1. Дендрограмма сходства нематодных сообществ в оранжереях ботанических садов Украины (объединение по методу полной связи). Расшифровка сокращений дана в таблице 2.
Fig. 2 in Species Composition And Structure Of The Communities Of Plant-Parasitic And Free-Living Soil Nematodes In The Greenhouses Of Botanical Gardens Of Ukraine
Fig. 2. Dendrogram of similarity of plant-parasitic nematodes' communities in the greenhouses of botanical gardens of Ukraine (amalgamation by the method of complete linkage). Explanation of the abbreviations is given in table 2.
Plant management but not fertilization mediates soil carbon emission and microbial community composition in subtropical Eucalyptus plantations
<p><span>The diversity of </span><span>plant functional group</span><span>s</span><span> in plantations affects soil carbon, but we have limited understanding of the underlying mechanisms for how plant management affects soil carbon dynamics. Here, we conducted a 3-year manipulation experiment of plant functional groups that included understory removal, tree root trenching, and fertilization treatments in 2-year-old and 6-year-old <em>Eucalyptus</em> plantations in the subtropical region. The results showed that soil respiration was significantly suppressed by understory removal (-38%), tree root trenching (-41%), and their interactions (-54%), but that fertilization alone and in interactions had no significant effect. The Chao1 indices for soil bacterial and fungal diversity significantly decreased with understory removal in the 2-year-old plantation and with tree root trenching in the 6-year-old plantation. Soil bacterial and fungal communities were also affected by understory removal and tree root trenching. Soil respiration, physicochemical characteristics, microbial diversity, and community composition were significantly affected by plantation age. Reductions in soil carbon emissions were associated with reductions in plant functional groups and soil microbial groups, while increases in soil respiration were associated with soil physicochemical factors, soil temperature, and plantation age. Our findings highlight that plant managements are of great significance to the soil carbon emission processes in afforested plantations.</span></p>
spectre: An R package to estimate spatially-explicit community composition using sparse data
<p>An understanding of how biodiversity is distributed across space is key to much of ecology and conservation. Many predictive modelling approaches have been developed to estimate the distribution of biodiversity over various spatial scales. Community modelling techniques may offer many benefits over single-species modelling. However, techniques capable of estimating precise species makeups of communities are highly data intensive and thus often limited in their applicability. Here we present an R package, spectre, which can predict regional community composition at a fine spatial resolution using only sparsely sampled biological data. The package can predict the presence and absence of all species in an area, both known and unknown, at the sample site scale. Underlying the spectre package is a min-conflicts optimisation algorithm that predicts species' presences and absences throughout an area using estimates of α-, β-, and γ-diversity. We demonstrate the utility of the spectre package using a spatially-explicit simulated ecosystem to assess the accuracy of the package's results. spectre offers a simple-to-use tool with which to accurately predict community compositions across varying scales, facilitating further research and knowledge acquisition into this fundamental aspect of ecology.</p>
Diversity and composition of macroinvertebrate communities in a rare inland salt marsh
<p>Inland salt marshes are rare habitats in the Great Lakes region of North America, formed on salt deposits from the Silurian period. These patchy habitats are abiotically stressful for the freshwater invertebrates that live there, and provide an opportunity to study the relationship between stress and diversity. We used morphological and COI metabarcoding data to assess changes in diversity and composition across both space (a transect from the salt seep to an adjacent freshwater area) and time (three sampling seasons). Richness was significantly lower at the seep site with both datatypes, while metabarcoding data additionally showed reduced richness at the freshwater transect end, consistent with a pattern where intermediate levels of stress show higher diversity. We found complementary, rather than redundant, patterns of community composition using the two datatypes: not all taxa were equally sequenced with the metabarcoding protocol. We identified taxa that are abundant at the salt seep of the marsh, including biting midges (<i>Culicoides</i>) and ostracods (<i>Heterocypris</i>). We conclude that (as found in other studies) molecular and morphological work should be used in tandem to identify the biodiversity in this rare habitat. Additionally, salinity may be a driver of community membership in this system, though further ecological research is needed to rule out alternate hypotheses.</p>
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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.