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Fig. 6 in Application of the physical habitat simulation for fish species to assess environmental flows in an Atlantic Forest Stream in South-eastern Brazil
Fig. 6. Weighted usable area (WUA) in the upper and lower reach of the riacho São Pedro, for the three fish species.
Fig. 4 in Application of the physical habitat simulation for fish species to assess environmental flows in an Atlantic Forest Stream in South-eastern Brazil
Fig. 4. Habitat suitability curves for depth (m), mean water column velocity (m/s) and type of substrate for the three fish species in the riacho São Pedro. Substrate types are; 1- large boulder, 2- boulder, 3- cobble, 4- gravel, 5- fine gravel, 6- sand and 7- vegetation.
Fig. 3 in Application of the physical habitat simulation for fish species to assess environmental flows in an Atlantic Forest Stream in South-eastern Brazil
Fig. 3. Frequencies of habitat availability by classes of depth (m), mean velocity (m/s) and type of substrate (1- large boulder; 2- boulder; 3- cobble; 4- gravel; 5- fine gravel; 6- sand and 7- vegetation), obtained by direct survey in the riacho São Pedro.
Fig. 1 in Application of the physical habitat simulation for fish species to assess environmental flows in an Atlantic Forest Stream in South-eastern Brazil
Fig. 1. Map of the rio Guandu basin, with indication of the studied reach in riacho São Pedro. Solid dash = small substation of CEDAE (Water and Sewer Treatment Works of Rio de Janeiro State). WTP: Water Treatment Plant.
Fig. 2 in Application of the physical habitat simulation for fish species to assess environmental flows in an Atlantic Forest Stream in South-eastern Brazil
Fig. 2. Isometric view of the cross-sections in the two target reaches of the riacho São Pedro. Grey color indicates water; solid line indicates the contour of the cross-section (in wet areas and banks).
Data from: The effect of external flow on 3D orientation of a microscopic sessile suspension feeder, Vorticella convallaria
<p><em>Vorticella convallaria</em> are microscopic sessile suspension feeders that live attached to substrates in aquatic environments. They feed using a self‐generated current and help maintain the health of aquatic ecosystems and wastewater treatment facilities by consuming bacteria and detritus. Their environmental impact is mediated by their feeding rate. In ambient flow, feeding rates are highly dependent on an individual's orientation relative to the substrate and the flow. Here, we investigate how this orientation is impacted by flow speed. Furthermore, we examined whether individuals actively avoid orientations unfavorable for feeding. We exposed individuals to unidirectional laminar flow at shear rates of 0, 0.5, 1.0, and 1.5 s<sup>−1</sup>, and recorded their 3D orientation using a custom biplanar microscope. We determined that <em>V. convallaria</em> orientation became progressively tilted downstream as the shear rate increased, but individuals were still able to actively reorient. Additionally, at higher shear rates, individuals spent a larger fraction of their time in orientations with reduced feeding rates. Our shear rates correspond to freestream flows on the scale of mm s<sup>−1</sup> to cm s<sup>−1</sup> in natural environments.</p>
Data from: Understanding species boundaries that arise from complex histories: Gene flow across the speciation continuum in the spotted whiptail lizards
<p>Gene flow between diverging lineages challenges the resolution of species boundaries and the understanding of evolutionary history in recent radiations. Here, we integrate phylogenetic and coalescent tools to resolve reticulate patterns of diversification and use a perspective focused on evolutionary mechanisms to distinguish interspecific and intraspecific taxonomic variation. We use this approach to resolve the systematics for one of the most intensively studied but difficult to understand groups of reptiles: the spotted whiptail lizards of the genus <em>Aspidoscelis </em>(<em>A. gularis </em>complex). Whiptails contain the largest number of unisexual species known within any vertebrate group and the spotted whiptail complex has played a key role in the generation of this diversity through hybrid speciation. Understanding lineage boundaries and the evolutionary history of divergence and reticulation within this group is therefore key to understanding the generation of unisexual diversity in whiptails. Despite this importance, long-standing confusion about their systematics has impeded understanding of which gonochoristic species have contributed to the formation of unisexual lineages. Using reduced representation genomic data, we resolve patterns of divergence and gene flow within the spotted whiptails and clarify patterns of hybrid speciation. We find evidence that biogeographically structured ecological and environmental variation has been important in morphological and genetic diversification, as well as the maintenance of species boundaries in this system. Our study elucidates how gene flow among lineages and the continuous nature of speciation can bias the practice of species delimitation and lead taxonomists operating under different frameworks to different conclusions (here we propose that a two species arrangement best reflects our current understanding). In doing so, this study provides conceptual and methodological insights into approaches to resolving diversification patterns and species boundaries in rapid radiations with complex histories, as well as long-standing taxonomic challenges in the field of systematic biology.</p>
Beyond gene flow: (non)-parallelism of secondary contact in a pair of highly differentiated sibling species
<p>Replicated secondary contact zones can provide insights on the barriers to gene flow that are important during speciation and can reveal to which degree secondary contact may result in similar evolutionary outcomes. Here, we studied two secondary contact zones between highly differentiated Alpine butterflies<em> </em>of the genus <em>Erebia</em> using whole-genome re-sequencing data. We assessed the genomic relationships between populations and species and find hybridization to be rare, with no to little current or historical introgression in either contact zone. There are large similarities between the contact zones, consistent with an allopatric origin of interspecific differentiation, with no indications for ongoing reinforcing selection. Consistent with expected reduced effective population size, we further find that scaffolds related to the Z-chromosome show increased differentiation compared to the already high levels across the entire genome, which could also hint towards a contribution of the Z chromosome to species divergence in this system. Finally, we detected the presence of the endosymbiont <em>Wolbachia</em>, which can cause reproductive isolation between its hosts, in all <em>E. cassioides</em>, while it appears to be fully or largely absent in contact zone populations of <em>E. tyndarus</em>. We discuss how this rare pattern may have arisen and how it may have affected the dynamics of speciation upon secondary contact.</p>
Рис. 6. Структура сообществ зообентоса оз. УΑыΛь и впаΑающих в него рек и ручьев, июΛь 2021 г. Fig. 6. The structure of zoobenthic communities of Udyl Lake and rivers and streams flowing into it, July 2021 in Quantitative zoobenthos characteristics of the Udyl Lake basin (Udyl Nature Reserve, Khabarovsky Region)
Рис. 6. Структура сообществ зообентоса оз. УΑыΛь и впаΑающих в него рек и ручьев, июΛь 2021 г. Fig. 6. The structure of zoobenthic communities of Udyl Lake and rivers and streams flowing into it, July 2021
Fig. 3 in Limited gene flow among Cydia pomonella (Lepidoptera: Tortricidae) populations in two isolated regions in China: Implications for utilization of the SIT
Fig. 3. Dendrogram generated by NJ analysis representing the genetic distance among populations of Cydia pomonella. The topology was tested by bootstrap analysis with 1,000 replicates. The scale bar represents 2.0% genetic distance. The sampling locations include JinTa (JJT), YinDa (JYD), XiDong (JXD) and ZongZai (JZZ) of Jiuquan Region, and Luo Tuocheng (ZLT), NiJiaying (ZNJ), MinYong (ZMY) and XiaoMan (ZXM) of Zhangye Region.
Fig. 1 in Limited gene flow among Cydia pomonella (Lepidoptera: Tortricidae) populations in two isolated regions in China: Implications for utilization of the SIT
Fig. 1. Sampling regions and locations of Cydia pomonella in Hexi Corridor of China. (I) map of China, the Hexi Corridor is indicated in the dash box; (II) enlarged map of Hexi Corridor, the 2 sampling regions are indicated as (A) Jiuquan region and (B) Zhangye region; (III) enlarged map of the sampling regions and sampling locations. The sampling locations includes JinTa (JJT), YinDa (JYD), XiDong (JXD), and ZongZai (JZZ) of the Jiuquan Region, and Luo Tuocheng (ZLT), NiJiaying (ZNJ), MinYong (ZMY) and XiaoMan (ZXM) of the Zhangye Region.
Fig. 2 in Limited gene flow among Cydia pomonella (Lepidoptera: Tortricidae) populations in two isolated regions in China: Implications for utilization of the SIT
Fig. 2. Bayesian clustering analysis by use of STRUCTURE, which indicates the presence of 2 clusters. Proportion of membership coefficient for 8 Cydia pomonella populations falling into the 2 clusters is depicted by 2 different shades of gray, respectively. The sampling locations include JinTa (JJT), YinDa (JYD), XiDong (JXD) and ZongZai (JZZ) of Jiuquan Region, and Luo Tuocheng (ZLT), NiJiaying (ZNJ), MinYong (ZMY) and XiaoMan (ZXM) of Zhangye Region.
Fig. 4 in Drainage Network Morphology Influences Population Structure and Gene Flow of the Andean Water Frog (Anura: Telmatobiidae) of the Atacama Desert, Northern Chile.
Fig. 4. Results of the Geneland analysis. A: Bar plot of posterior probability density according to the number of clusters; B: posterior probability maps for the delimited clusters.
Fig. 3 in Drainage Network Morphology Influences Population Structure and Gene Flow of the Andean Water Frog (Anura: Telmatobiidae) of the Atacama Desert, Northern Chile.
Fig. 3. Pairwise FST between localities of Telmatobius pefauri obtained using mitochondrial (A) and microsatellite (B) data. The colour scale corresponding to the values of FST is shown to the right of each matrix. Significant (Bonferroni corrected) comparisons showing p <0.05, p <0.01 and p <0.001 are denoted by *, ** and ***, respectively.
Fig. 2 in Drainage Network Morphology Influences Population Structure and Gene Flow of the Andean Water Frog (Anura: Telmatobiidae) of the Atacama Desert, Northern Chile.
Fig. 2. Median-joining network based on the fragment of the analysed control region. Table 1. Indices of mitochondrial diversity, nuclear diversity, and inbreeding coefficients (FIS) by locality
Fig. 1 in Drainage Network Morphology Influences Population Structure and Gene Flow of the Andean Water Frog (Anura: Telmatobiidae) of the Atacama Desert, Northern Chile.
Fig. 1. Study area, distribution of Telmatobius pefauri. Localities, 1: Socoroma (Socoroma River); 2: Murmuntani; 3: Copaquilla; 4: Chapiquiña; 5: Belén; 6: Lupica; 7: Saxamar. Localities 2 and 3 belong to the Seco River drainage; localities 4–7 belong to the Tignamar River drainage. Basin limits are indicated with dashed lines. The inset map shows the study area (highlighted by a red box) in relation to South America. SAAD = South American Arid Diagonal.
Fig. 5 in Drainage Network Morphology Influences Population Structure and Gene Flow of the Andean Water Frog (Anura: Telmatobiidae) of the Atacama Desert, Northern Chile.
Fig. 5. Scatter plot for the first two principal components obtained in the Principal Components Analysis using SSR data.
Database: Influence of large-scale freestream turbulence on bypass transition in air and organic vapour flows
<p>This is an open-access database of numerical simulations of freestream-turbulence induced transitions of zero-pressure-gradient flat plates boundary layers. The data have been collected at Arts et Metiers Institute of Technology, at DynFluid laboratory, in the period 2021-2024 within the REGAL-ORC project- REal GAs effects on Loss mechanisms of ORC turbine flows, a project in collaboration with FH Münster in Germany.</p> <p>Work related to the database is published in Journal of Fluid Mechanics, under the title: "Influence of large-scale freestream turbulence on bypass transition in air and organic vapour flows". The aims of this work was to investigate freestream-turbulence induced transitions, in particular under relatively large integral length scale, of air and organic vapors boundary layers.</p> <p>This version contains evolutions of averaged quantities in the streamwise direction, along with profiles and spectra in the boundary layer for all the different simulations performed. This database is supplemented with python codes to read the data and descriptions of the data in the headers and README files.</p>
Figure 5. Process flow of PSO-Classification of Human Emotion from Deap EEG Signal Using Hybrid Improved Neural Networks with Cuckoo Search
<p>PSO is used to identify the best solution from collection of solution. It is a computational<br> method that optimizes a problem by iteratively trying to improve a candidate solution with regard to<br> a given measure of quality. PSO optimizes a problem by having a population of candidate solutions,<br> here dubbed particles, and moving these particles around in the search-space according to simple<br> mathematical formulae over the particle's position and velocity. Each particle's movement is<br> influenced by its local best known position but, is also guided toward the best known positions in<br> the search-space, which are updated as better positions are found by other particles. This is expected<br> to move the swarm toward the best solutions. PSO is a metaheuristic as it makes few or no<br> assumptions about the problem being optimized and can search very large spaces of candidate<br> solutions. However, metaheuristic such as PSO do not guarantee an optimal solution is ever found.<br> The following Figure 5 explains the basic flow of PSO process.</p>
Figure.4. Proposed system's flow chart-Single Trial Classification of Evoked EEG Signals Due to RGB Colors
<p>In this paper we proved the possibility to perform a single trial classification the EEG signals which are evoked by the RGB color stimulus. The required time to do this process is much shorter than the time which is required by any other stimulus, such as imagery and spelling words, which is presented in the previous researches. This result proves the main idea behind using colors in the next generation of BCI systems, which is based on introducing more efficient and faster systems that are able to give a quicker response than any other time. As a future work, we are going to conduct a BCI application that controls a cursor movement on PC by using those signals. This is unlike earlier BCI systems where cursor controlled movement application is controlled by the imagination of foot and hand movement, but no one has controlled it with colored stimuli before. Such study would be used to simulate an environment where a disabled person would be expected to drive a vehicle in a virtual environment with a possible uniform background, in which the vehicle will either start and/or stop moving on appearance of Green and Red lights respectively.</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.