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818 results for “Neutrality”
Robot swarms neutralize harmful Byzantine robots using a blockchain-based token economy
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Obuasi case study data: Performance of neutral SNP barcodes to determine genetic diversity and structure of Plasmodium falciparum in Africa
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Data from: where the minor things are: a pan-eukaryotic survey suggests neutral processes may dominate minor spliceosomal intron evolution
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Converting non-neutralizing SARS-CoV-2 antibodies targeting conserved epitopes into broad-spectrum inhibitors through receptor blockade
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CLIC Calorimeter 3D images: Neutral Pion showers at Random Angle
<p>Energy deposits from single-particle showers in the ECAL+HCAL calorimeters of the CLIC detector</p> <p>Simulation performed with GEANT4 (https://geant4.web.cern.ch) and DD4HEP software (https://dd4hep.web.cern.ch/dd4hep/)</p> <p>Neutral Pions entering the detector at variable energy and direction</p> <p>See https://arxiv.org/abs/1912.06794 for details</p>
MD simulations of bilayers containing POPC and Cholesterol: 52POPC_76CHL_31Nwat_neutral (lipid14)
<p>NMRLipids III CholXray project (nmrlipids.blogspot.fi)</p> <p>Gromacs 5.0.4, lipid14 FF (Madej et al. JPCB 2015, 119, 12424), 1 atm, 303K, 200ns</p> <p>128 lipids (52 POPC, 76 CHL), N_wat/lipid = 31, 24496 Atoms</p>
MD simulations of bilayers containing POPC and Cholesterol: 64POPC_64CHL_31Nwat_neutral (lipid14)
<p>NMRLipids III CholXray project (nmrlipids.blogspot.fi)</p> <p>Gromacs 5.0.4, lipid14 FF (Madej et al. JPCB 2015, 119, 12424), 1 atm, 303K, 200ns</p> <p>128 lipids (64 POPC, 64 CHL), N_wat/lipid = 31, 25216 Atoms</p>
MD simulations of bilayers containing POPC and Cholesterol: 84POPC_44CHL_31Nwat_neutral (lipid14)
<p>NMRLipids III CholXray project (nmrlipids.blogspot.fi)</p> <p>Gromacs 5.0.4, lipid14 FF (Madej et al. JPCB 2015, 119, 12424), 1 atm, 303K, 200ns</p> <p>128 lipids (84 POPC, 44 CHL), N_wat/lipid = 31, 26416 Atoms</p>
MD simulations of bilayers containing POPC and Cholesterol: 108POPC_20CHL_31Nwat_neutral (lipid14)
<p>NMRLipids III CholXray project (nmrlipids.blogspot.fi)</p> <p>Gromacs 5.0.4, lipid14 FF (Madej et al. JPCB 2015, 119, 12424), 1 atm, 303K, 200ns</p> <p>128 lipids (108 POPC, 20 CHL), N_wat/lipid = 31, 27856 Atoms</p>
Increasing importance of niche versus neutral processes in the assembly of plant–herbivore networks during succession
<p>Recent studies suggest that the assembly of trophic interaction networks is the result of both niche (deterministic and selective) and neutral (stochastic) processes, but we know little about their relative importance. Succession following disturbance offers a good opportunity to address this question. Studies of single-trophic guilds suggest that, shortly after a disturbance, such as a fire, neutral assembly processes (e.g. colonisation events) dominate whereas niche processes (selection) become more and more important as succession proceeds. Building on these observations, we predict similar changes in interaction networks during succession, with a shift from stochastic toward selective interactions. To test this, we studied succession of plant–herbivorous insect networks in South Africa after a fire. We sampled a total of 385 herbivorous arthropod species and 92 plant species. For different successional stages and spatial grain sizes, we used network descriptors to estimate plant–herbivore specificity and partner fidelity of plant and herbivore species across networks (i.e. localities). We compared the observed network descriptors to neutral models, and then differentiated selective species (associated with similar partner species in different networks) from neutral species (associated at random with their partners). Our results suggest that specialisation, partner fidelity and the proportion of selective species of plants and herbivores increased with succession, which is consistent with the hypothesis that niche-based processes prevail over neutral processes as succession proceeds. However, in all the successional stages, the majority of species were neutral species, which pinpoints the importance of opportunistic interactions in the assembly of trophic networks. </p>
Dataset for: Majority of olfactory-receptor neurons have individually neutral effects on behavior
<p><strong>Summary</strong></p> <p>Animals use olfactory receptors to navigate danger, mates, and food. However, for complex olfactory systems, it is unknown what proportion of olfactory-receptor neurons (ORNs) can individually drive avoidance or attraction. Similarly it is unclear what rules govern behavioral responses to ORN-activity combinations. We used optogenetic analysis in Drosophila to map the behavior elicited by nearly all ORN classes; just one-fifth of ORNs drove either avoidance or attraction. Although wind and hunger are closely linked to olfaction, neither context had much effect on single-ORN-class behavior. Various models have been used to explain the way multiple ORNs combine their behavioral influences, including several simple pooling rules. To assess these, we activated two-way combinations and compared patterns of single- and double-ORN responses: these comparisons were inconsistent with simple pooling. We conclude that the majority of ORN types have neutral behavioral effects individually, but participate in broad, odor-elicited ensembles with potent behavioral effects arising from complex interactions.</p>
A test of island biogeographic theory applied to estimates of gene flow in a Fijian bird is largely consistent with neutral expectations
<p>Islands were key to the development of allopatric speciation theory because they are a natural laboratory of repeated barriers to gene flow caused by open water gaps. Despite their proclivity for promoting divergence, little empirical work has quantified the extent of gene flow among island populations. Following classic island biogeographic theory, two metrics of interest are relative island size and distance. Fiji presents an ideal system for studying these dynamics, with four main islands that form two large-small pairs. We sequenced thousands of ultraconserved elements (UCEs) of the Fiji bush-warbler<i> Horornis ruficapilla</i>, a passerine distributed on these four Fijian islands, and performed a demographic analysis to test hypotheses of the effects of island size and distance on rates of gene flow. Our demographic analysis inferred low levels of gene flow from each large island to its small counterpart and little or none in the opposite direction. The difference in the distance between these two island pairs manifested itself in lower levels of gene flow between more distant islands. Both findings are generally concordant with classic island biogeography. The amount of reduction in gene flow based on distance was consistent with predictions from island biogeographic equations, while the reduction from small to large islands was possibly greater than expected. These findings offer a hypothesis and framework to guide future study of inter-island gene flow in archipelagos as the study of island biogeography progresses into the genomic era.</p>
Data from: Habitat fragmentation differentially shapes neutral and immune gene variation in a tropical bird species
<p>Habitat fragmentation is a major cause of biodiversity loss, responsible for an alteration of intraspecific patterns of neutral genetic diversity and structure. Although neutral genetic variation can be informative for demographic inferences, it may be a poor predictor of adaptive genetic diversity and thus of the consequences of habitat fragmentation on selective evolutionary processes. In this context, we contrasted patterns of genetic diversity and structure of neutral loci (microsatellites) and immune genes (i.e., toll-like receptors) in an understorey bird species, the wedge-billed woodcreeper <i>Glyphorynchus spirurus</i>. The objectives were (1) to investigate forest fragmentation effects on population genetic diversity, (2) to disentangle the relative role of demography (genetic drift and migration) and selection, and (3) to assess whether immunogenetic patterns could be associated with variation of ectoparasite (i.e., ticks) pressures. Our results revealed an erosion of neutral genetic diversity and a substantial genetic differentiation among fragmented populations, resulting from a decrease in landscape connectivity and leading to the divergence of distinct genetic pools at a small spatial scale. Patterns of genetic diversity observed for TLR4 and TLR5 were concordant with neutral genetic patterns, whereas those observed for TLR3 and TLR21 were discordant. This result underlines that the dominant evolutionary force shaping immunogenetic diversity (genetic drift vs. selection) may be different depending on loci considered. Finally, tick prevalence was higher in fragmented environments. We discussed the hypothesis that pathogen selective pressures may contribute to maintain adaptive genetic diversity despite the negative demographic effect of habitat fragmentation on neutral genetic diversity.</p>
Data from: Niche divergence versus neutral processes: combined environmental and genetic analyses identify contrasting patterns of differentiation in recently diverged pine species
Background and Aims: Solving relationships of recently diverged taxa, poses a challenge due to shared polymorphism and weak reproductive barriers. Multiple lines of evidence are needed to identify independently evolving lineages. This is especially true of long-lived species with large effective population sizes, and slow rates of lineage sorting. North American pines are an interesting group to test this multiple approach. Our aim is to combine cytoplasmic genetic markers with environmental information to clarify species boundaries and relationships of the species complex of Pinus flexilis, Pinus ayacahuite, and Pinus strobiformis. Methods: Mitochondrial and chloroplast sequences were combined with previously obtained microsatellite data and contrasted with environmental information to reconstruct phylogenetic relationships of the species complex. Ecological niche models were compared to test if ecological divergence is significant among species. Key Results and Conclusion: Separately, both genetic and ecological evidence support a clear differentiation of all three species but with different topology, but also reveal an ancestral contact zone between P. strobiformis and P. ayacahuite. The marked ecological differentiation of P. flexilis suggests that ecological speciation has occurred in this lineage, but this is not reflected in neutral markers. The inclusion of environmental traits in phylogenetic reconstruction improved the resolution of internal branches. We suggest that combining environmental and genetic information would be useful for species delimitation and phylogenetic studies in other recently diverged species complexes.
Data from: Empirical evaluation of neutral interactions in host-parasite networks
While niche-based processes have been invoked extensively to explain the structure of interaction networks, recent studies propose that neutrality could also be of great importance. Under the neutral hypothesis, network structure would simply emerge from random encounters between individuals and thus would be directly linked to species abundance. We investigated the impact of species abundance distributions on qualitative and quantitative metrics of 113 host-parasite networks. We analysed the concordance between neutral expectations and empirical observations at interaction, species and network levels. We found that species abundance accurately predicts network metrics at all levels. Despite host-parasite systems being constrained by physiology and immunology, our results suggest that neutrality could also explain, at least partially, their structure. We hypothesize that trait-matching would determine potential interactions between species, while abundance would determine their realization.
Data from: Neutral and adaptive genomic signatures of rapid poleward range expansion
Many species are expanding their range polewards and this has been associated with rapid phenotypic change. Yet, it is unclear to what extent this reflects rapid genetic adaptation or neutral processes associated with range expansion, or selection linked to the new thermal conditions encountered. To disentangle these alternatives, we studied the genomic signature of range expansion in the damselfly Coenagrion scitulum using 4950 newly developed genomic SNPs and linked this to the rapidly evolved phenotypic differences between core and (newly established) edge populations. Most edge populations were genetically clearly differentiated from the core populations and all were differentiated from each other indicating independent range expansion events. In addition, evidence for genetic drift in the edge populations, and strong evidence for adaptive genetic variation in association with the range expansion was detected. We identified one SNP under consistent selection in four of the five edge populations and showed that the allele increasing in frequency is associated with increased flight performance. This indicates collateral, non-neutral evolutionary changes in independent edge populations driven by the range expansion process. We also detected a genomic signature of adaptation to the newly encountered thermal regimes, reflecting a pattern of countergradient variation. The latter signature was identified at a single SNP as well as in a set of covarying SNPs using a polygenic multilocus approach to detect selection. Overall, this study highlights how a strategic geographic sampling design and the integration of genomic, phenotypic and environmental data can identify and disentangle the neutral and adaptive processes that are simultaneously operating during range expansions.
Data from: Exploring neutral and adaptive processes in expanding populations of gilthead sea bream, Sparus aurata L., in the North-East Atlantic
Recent studies in empirical population genetics have highlighted the importance of taking into account both neutral and adaptive genetic variation in characterizing microevolutionary dynamics. Here we explore the genetic population structure and the footprints of selection in four populations of the warm-temperate coastal fish, the gilthead sea bream (Sparus aurata), whose recent northward expansion has been linked to climate change. Samples were collected at four Atlantic locations, including Spain, Portugal, France and the South of Ireland, and genetically assayed using a suite of species-specific markers, including 15 putatively neutral microsatellites and 23 Expressed Sequence Tag-linked (ESTs) markers, as well as a portion of the mitochondrial DNA (mtDNA) Control Region. Two of the putatively neutral markers, Bld-10 and Ad-10, bore signatures of strong directional selection, particularly in the newly established Irish population, though the potential 'surfing effect' of rare alleles at the edge of the expansion front was also considered. Analyses after the removal of these loci suggest low but significant population structure likely affected by some degree of gene flow counteracting random genetic drift. No signal of historic divergence was detected at mtDNA. BLAST searches conducted with all 38 markers used failed to identify specific genomic regions associated to adaptive functions. However, the availability of genomic resources for this commercially valuable species is rapidly increasing, bringing us closer to the understanding of the interplay between selective and neutral evolutionary forces, shaping population divergence of an expanding species in a heterogeneous milieu.
Data from: Spatial and temporal patterns of neutral and adaptive genetic variation in the endangered African wild dog (Lycaon pictus)
Deciphering patterns of genetic variation within a species is essential for understanding population structure, local adaptation and differences in diversity between populations. Whilst neutrally evolving genetic markers can be used to elucidate demographic processes and genetic structure, they are not subject to selection and therefore are not informative about patterns of adaptive variation. As such, assessments of pertinent adaptive loci, such as the immunity genes of the Major Histocompatibility Complex (MHC), are increasingly being incorporated into genetic studies. In this study we combined neutral (microsatellite, mtDNA) and adaptive (MHC class II DLA-DRB1 locus) markers to elucidate the factors influencing patterns of genetic variation in the African wild dog (Lycaon pictus); an endangered canid that has suffered extensive declines in distribution and abundance. Our genetic analyses found all extant wild dog populations to be relatively small (Ne < 30). Furthermore, through coalescent modelling, we detected a genetic signature of a recent and substantial demographic decline, which correlates with human expansion, but contrasts with findings in some other African mammals. We found strong structure of wild dog populations, indicating the negative influence of extensive habitat fragmentation and loss of gene flow between habitat patches. Across populations we found that the spatial and temporal structure of microsatellite and MHC diversity were correlated, and strongly influenced by demographic stability and population size, indicating the effects of genetic drift in these small populations. Despite this correlation, we detected signatures of selection at the MHC, implying that selection has not been completely overwhelmed by genetic drift.
Data from: Acoustic monitoring of coastal dolphins and their response to naval mine neutralization exercises
To investigate the potential impacts of naval mine neutralization exercises (MINEX) on odontocete cetaceans, a long-term passive acoustic monitoring study was conducted at a US Navy training range near Virginia Beach, USA. Bottom-moored acoustic recorders were deployed in 2012–2016 near the epicentre of MINEX training activity and were refurbished every 2–4 months. Recordings were analysed for the daily presence/absence of dolphins, and dolphin acoustic activity was quantified in detail for the hours and days before and after 31 MINEX training events. Dolphins occurred in the area year-round, but there was clear seasonal variability, with lower presence during winter months. Dolphins exhibited a behavioural response to underwater detonations. Dolphin acoustic activity near the training location was lower during the hours and days following detonations, suggesting that animals left the area and/or reduced their signalling. Concurrent acoustic monitoring farther away from the training area suggested that the radius of response was between 3 and 6 km. A generalized additive model indicated that the predictors that explained the greatest amount of deviance in the data were the day relative to the training event, the hour of the day and circumstances specific to each training event.
Data from: Evolutionary neutrality of mtDNA introgression: evidence from complete mitogenome analysis in roe deer
Introgressive hybridization offers a unique platform for studying the molecular basis of natural selection acting on mitogenomes. Most of the mtDNA protein-coding genes are extremely conserved; however, some of the observed variations have potentially adaptive significance. Here, we evaluated whether the evolution of mtDNA in closely related roe deer species affected by widespread mtDNA introgression is neutral or adaptive. We characterized and compared 16 complete mitogenomes of European (Capreolus capreolus) and Siberian (C. pygargus) roe deer, including four of Siberian origin introgressed into European species. The average sequence divergence of species-specific lineages was estimated at 2.8% and varied across gene classes. Only 21 of 315 fixed differences identified in protein-coding genes represented nonsynonymous changes. Only three of them were determined to have arisen in the C. pygargus lineage since the time to the most recent common ancestor (TMRCA) of both Capreolus species, reflecting a decelerated evolutionary ratio. The almost four-fold higher dN/dS ratio described for the European roe deer lineage is constrained by overall purifying selection, especially pronounced in the ND4 and ND5 genes. We suggest that the highly divergent C. capreolus lineage could have maintained a capability for genomic incorporation of the well-preserved and almost ancestral type of mtDNA present in C. pygargus. Our analyses did not indicate any signs of positive selection for Siberian roe deer mtDNA, suggesting that the present widespread introgression is evolutionarily neutral.
ScienceDex guides
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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.