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3,655 results for “Structural data”
Research data for "Origins of structural and electronic transitions in disordered silicon"
<p>This is a dataset related to the publication "Origins of structural and electronic transitions in disordered silicon" (<em>Nature</em> <strong>2021</strong>, <em>589</em>, 59–64). The paper is available online here: https://doi.org/10.1038/s41586-020-03072-z.</p> <p>Three separate .tar.gz archive files are provided:</p> <ul> <li>"coordinates": structural data in (extended) XYZ format including atomic information</li> <li>"ML_DOS_data": original data for the electronic DOS analysis (Fig. 3)</li> <li>"other_potentials": tests with further ML potential models (as described in the Methods section)</li> </ul>
Data from: Large-scale connectivity, cryptic population structure, and relatedness in Eastern Pacific olive ridley sea turtles (Lepidochelys olivacea)
<p>Endangered species are grouped into genetically discrete populations to direct conservation efforts. Mitochondrial Control Region (mtCR) haplotypes are used to elucidate deep divergences between populations, as compared to nuclear microsatellites that can detect recent structuring. When prior populations are unknown, it is useful to subject microsatellite data to clustering and/or ordination population inference. Olive ridley sea turtles (Lepidochelys olivacea) are the most abundant sea turtle, yet few studies have characterized olive ridley population structure. Recently, clustering results of olive ridleys in the Eastern Tropical Pacific Ocean suggested weak structuring (FST=0.02) between Mexico and Central America. We analyzed mtCR haplotypes, new microsatellite genotypes from Costa Rica, and pre-existing microsatellite genotypes from olive ridleys across the Eastern Tropical Pacific, to further explore population structuring in this region. We subjected inferred populations to multiple analyses to explore the mechanisms behind their structuring. We found 10 mtCR haplotypes from 60 turtles nesting at three sites in Costa Rica, but did not detect divergence between Costa Rican sites, or between Central America and Mexico. In Costa Rica, clustering suggested one population with no structuring, but ordination suggested four cryptic clusters with moderate structuring (FST=0.08, p<0.001). Across the Eastern Tropical Pacific, ordination suggested nine cryptic clusters with moderate structuring (FST=0.103, p<0.001) that largely corresponded to Mexican and Central American populations. All ordination clusters displayed significant internal relatedness relative to global relatedness (p<0.001) and contained numerous sibling pairs. This suggests that broadly dispersed family lineages have proliferated in Eastern Tropical Pacific olive ridleys and corroborates previous work showing basin-wide connectivity and shallow population structure in this region. The existence of broadly dispersed kin in Eastern Tropical Pacific olive ridleys has implications for management of olive ridleys in this region, and adds to our understanding of sea turtle ecology and life-history, particularly in light of the natal-homing paradigm.</p>
Data from: Bacterial epibiont communities of panmictic Antarctic krill are spatially structured
<p>Antarctic krill (<i>Euphausia superba</i>) are amongst the most abundant animals on Earth, with a circumpolar distribution in the Southern Ocean. Genetic and genomic studies have failed to detect any population structure for the species, suggesting a single panmictic population. However, the hyper-abundance of krill slows the rate of genetic differentiation, masking potential underlying structure. Here we use high-throughput sequencing of bacterial 16S rRNA genes to show that krill bacterial epibiont communities exhibit spatial structuring, driven mainly by distance rather than environmental factors, especially for strongly krill-associated bacteria. Estimating the ecological processes driving bacterial community turnover indicated this was driven by bacterial dispersal limitation increasing with geographic distance. Furthermore, divergent epibiont communities generated from a single krill swarm split between aquarium tanks under near identical conditions suggests physical isolation in itself can cause krill-associated bacterial communities to diverge. Our findings show that Antarctic krill-associated bacterial communities are geographically structured, in direct contrast with the lack of structure observed for krill genetic and genomic data.</p>
Data for "CryoDRGN: Reconstruction of heterogeneous cryo-EM structures using neural networks"
<p>Trained models and reconstructed density maps for:</p> <ul> <li>EMPIAR-10028: "Cryo-EM structure of a <em>Plasmodium falciparum</em> 80S ribosome bound to the anti-protozoan drug emetine" from Wong et al. (2014)</li> <li>EMPIAR-10049: "Molecular Mechanism of V(D)J Recombination from Synaptic RAG1-RAG2 Complex Structures" from Ru et al. (2015)</li> <li>EMPIAR-10076: "Modular assembly of the large bacterial ribosome" from Davis et al. (2016)</li> <li>EMPIAR-10180: "Structure of a pre-catalytic spliceosome" from Plaschka et al. (2017)</li> </ul> <p>Synthetic datasets with simulated heterogeneity and their ground truth density maps, poses, and labels:</p> <ul> <li>Uniform: 50k particle images (128x128, 6A/pix) uniformly sampled from 50 models along a 1-dimensional reaction coordinate</li> <li>Cooperative: 50k particle images (128x128, 6A/pix) sampled along the above reaction coordinate according to a 3-component Gaussian mixture model with overlapping components </li> <li>Noncontiguous: 50k particle images (128x128, 6A/pix) sampled along the above reaction coordinate according to a 3-component Gaussian mixture model without overlapping components</li> <li>Ribosomes: 50k particle images (128x128, 3A/pix) containing a mixture of 30S, 50S, 70S ribosomes simulating compositional heterogeneity</li> </ul>
Data from: New forms of structure in ecosystems revealed with the Kuramoto model
<p>This is the general Mathematica code for the article, "New forms of structure in ecosystems revealed with the Kuramoto model" by Vandermeer, Hajian-Forooshani, Medina and Perfecto. All results presented in the article can be obtained by running the code with appropriate parameter settings.</p>
Data from: Intraspecific genetic structure, divergence and high rates of clonality in an amphi-Atlantic starfish
Intraspecific genetic diversity and divergence have a large influence on the adaption and evolutionary potential of species. The widely distributed starfish, Coscinasterias tenuispina, combines sexual reproduction with asexual reproduction via fission. Here we analyse the phylogeography of this starfish to reveal historical and contemporary processes driving its intraspecific genetic divergence. We further consider whether asexual reproduction is the most important method of propagation throughout the distribution range of this species. Our study included 326 individuals from 16 populations, covering most of the species' distribution range. A total of 12 nuclear microsatellite loci and sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene were analysed. COI and microsatellites were clustered in two isolated lineages: one found along the south-western Atlantic and the other along the north-eastern Atlantic and Mediterranean Sea. This suggests the existence of two different evolutionary units. Marine barriers along the European coast would be responsible for population clustering: the Almeria-Oran Front that limits the entrance of migrants from the Atlantic to the Mediterranean, and the Siculo Tunisian strait that divides the two Mediterranean basins. The presence of identical genotypes was detected in all populations, although two monoclonal populations where found in two sites where annual mean temperatures and minimum values were the lowest. Our results based on microsatellite loci showed that intra-population genetic diversity was significantly affected by clonality whereas it had lower effect for the global phylogeography of the species, although still some impact on populations' genetic divergence could be observed between some populations.
Data from: The effects of aging on neuropil structure in mouse somatosensory cortex—A 3D electron microscopy analysis of layer 1
This study has used dense reconstructions from serial EM images to compare the neuropil ultrastructure and connectivity of aged and adult mice. The analysis used models of axons, dendrites, and their synaptic connections, reconstructed from volumes of neuropil imaged in layer 1 of the somatosensory cortex. This shows the changes to neuropil structure that accompany a general loss of synapses in a well-defined brain region. The loss of excitatory synapses was balanced by an increase in their size such that the total amount of synaptic surface, per unit length of axon, and per unit volume of neuropil, stayed the same. There was also a greater reduction of inhibitory synapses than excitatory, particularly those found on dendritic spines, resulting in an increase in the excitatory/inhibitory balance. The close correlations, that exist in young and adult neurons, between spine volume, bouton volume, synaptic size, and docked vesicle numbers are all preserved during aging. These comparisons display features that indicate a reduced plasticity of cortical circuits, with fewer, more transient, connections, but nevertheless an enhancement of the remaining connectivity that compensates for a generalized synapse loss.
Data from: Nearly complete rRNA genes from 371 Animalia: updated structure-based alignment and phylogenetic analysis
This study presents a manually constructed alignment of nearly complete rRNA genes from most animal clades (371 taxa from ∼33 of the ∼36 metazoan phyla), expanded from the 197 sequences in a previous study. This thorough, taxon-rich alignment, available at http://www.wsu.edu/≃jmallatt/research/rRNAalignment.html and in the Dryad Repository (doi: http://dx.doi.org/10.5061/dryad.1v62kr3q), is based rigidly on the secondary structure of the SSU and LSU rRNA molecules, and is annotated in detail, including labeling of the erroneous sequences (contaminants). The alignment can be used for future studies of the molecular evolution of rRNA. Here, we use it to explore if the larger number of sequences produces an improved phylogenetic tree of animal relationships. Disappointingly, the resolution did not improve, neither when the standard maximum-likelihood method was used, nor with more sophisticated methods that partitioned the rRNA into paired and unpaired sites (stem, loop, bulge, junction), or accounted for the evolution of the paired sites. For example, no doublet model of paired-site substitutions (16-state, 16A and 16B, 7A–F, or 6A–C models) corrected the placement of any rogue taxa or increased resolution. The following findings are from the simplest, standard, ML analysis. The 371-taxon tree only imperfectly supported the bilaterian clades of Lophotrochozoa and Ecdysozoa, and this problem remained after 17 taxa with unstably positioned sequences were omitted from the analysis. The problem seems to stem from base-compositional heterogeneity across taxa and from an overrepresentation of highly divergent sequences among the newly added taxa (e.g., sequences from Cephalopoda, Rotifera, Acoela, and Myxozoa). The rogue taxa continue to concentrate in two locations in the rRNA tree: near the base of Arthropoda and of Bilateria. The approximately uncertain (AU) test refuted the monophyly of Mollusca and of Chordata, probably due to long-branch attraction of the highly divergent cephalopod and urochordate sequences out of those clades. Unlikely to be correct, these refutations show for the first time that rRNA phylogeny can support some 'wrong' clades. Along with its weaknesses, the rRNA tree has strengths: It recovers many clades that are supported by independent evidence (e.g., Metazoa, Bilateria, Hexapoda, Nonoculata, Ambulacraria, Syndermata, and Thecostraca with Malacostraca) and shows good resolution within certain groups (e.g., in Platyhelminthes, Insecta, Cnidaria). As another strength, the newly added rRNA sequences yielded the first rRNA-based support for Carnivora and Cetartiodactyla (dolphin + llama) in Mammalia, for basic subdivisions of Bryozoa ('Gymnolaemata + Stenolaemata' versus Phylactolaemata), and for Oligostraca (ostracods + branchiurans + pentastomids + mystacocarids). Future improvement could come from better sequence-evolution models that account for base-compositional heterogeneity, and from combining rRNA with protein-coding genes in phylogenetic reconstruction.
Data from: Population structure and persistence of Pacific herring following the Great Tohoku earthquake
We evaluated the effect of the Great Tohoku earthquake, which occurred on March 11, 2011 in Japan, on the genetic diversity and population structure of Pacific herring (Clupea pallasii). Pacific herring (n = 4466) were collected between 2003 and 2014 through more than 20 sampling events during spawning periods at nine spawning sites throughout the Pacific herring distribution range in Japan. We measured them and genotyped 3784 fish at five microsatellite loci. Following the tsunami, the sea-spawning population at the center of the affected area was almost extirpated and was replaced by a genetically distinct lagoon-spawning population from an adjacent brackish lake. However, the pattern of gene flow was stable for populations, with unique admixture proportions in local populations despite the high gene flow (FST = 0.0184). Our results indicate that Pacific herring in Japan spawn in a range of salinities and exchange genes between local populations regardless of the spawning ecotypes. We hypothesize that the combination of constant gene flow between local populations from straying of spawners and spawning fidelity creates weak but significantly differentiated stable population structure. This process can allow restoration of the genetic characteristics of damaged populations over many generations and can thereby promote the long-term viability of marine fishes that have high gene flow.
Data from: Predator-induced collapse of niche structure and coexistence on islands
Biological invasions represent both a pressing environmental challenge and an opportunity to investigate fundamental ecological processes, such as the role of top predators in regulating species diversity and food-web structure. In whole-ecosystem manipulations of small Caribbean islands where brown anole lizards (Anolis sagrei) were the native top predator, we experimentally staged invasions by competitors (green anoles, A. smaragdinus) and/or novel top predators (curly-tailed lizards, Leiocephalus carinatus). We show that curly-tails destabilized coexistence of competing prey species, contrary to the classic idea of keystone predation. Fear-driven avoidance of predators collapsed the spatial and dietary niche structure that otherwise stabilized coexistence, intensifying interspecific competition within predator-free refuges and contributing to green-anole population extinctions. Moreover, whereas adding either green anoles or curly-tails lengthened food chains, adding both species reversed this effect, in part because apex predators were trophic omnivores. Our results underscore the importance of top-down control in community ecology, but show that its outcomes hinge on prey behavior, spatial structure, and omnivory. Diversity-enhancing effects of top predators cannot be assumed, and non-consumptive effects of predation risk may be a widespread constraint on species coexistence.
Data from: Multi-driver and multi-scale assessment of vine community structure and composition across a complex tropical environmental matrix
Ecological communities are structured by multiple processes operating at multiple scales yet understanding the scale-dependency of these processes remains an open challenge. This might be particularly true for parasites, for which biotic rather than abiotic processes may play a primary role in structuring communities. Focusing on vines, a group of structural parasites that gain access to the canopy using different climbing mechanisms, we examined the influence of abiotic factors in tandem with host-parasite and parasite-parasite interactions in the assembly of tropical vine communities. Two synthetic variables, namely Climate1 and landscape Variety, were consistently important in explaining variation in species richness and diversity, as well as species composition, but their importance varied with scale. Whereas Climate1 summarizes the largest variability among climatic variables, landscape Variety expresses landscape heterogeneity within a neighborhood. Significant patterns of species co-occurrences suggest that vine-vine interactions also contribute to vine community assembly. Our results may be critical to understand vine proliferation and help design management strategies for their control.
Data from: Genetic assessment of population structure and connectivity in the threatened Mediterranean coral Astroides calycularis (Scleractinia, Dendrophylliidae) at different spatial scales
Understanding dispersal patterns, population structure and connectivity among populations is helpful in the management and conservation of threatened species. Molecular markers are useful tools as indirect estimators of these characteristics. In this study we assess the population genetic structure of the endemic Mediterranean coral Astroides calycularis in the Alboran Sea at local and regional scales, and at three localities outside of this basin. Bayesian clustering methods, traditional F-statistics and Dest statistics were used to determine the patterns of genetic structure. Likelihood and coalescence approaches were used to infer migration patterns and effective population sizes. The results obtained reveal a high level of connectivity among localities separated by as much as one kilometer and moderate levels of genetic differentiation among more distant localities, somewhat corresponding with a stepping-stone model of gene flow and connectivity. These data suggest that connectivity among populations of this coral is mainly driven by the biology of the species, with low dispersal abilities; in addition, hydrodynamic processes, oceanographic fronts and the distribution of rocky substrate along the coastline may influence larval dispersal.
Data from: Fire influences the structure of plant-bee networks
1. Fire represents a frequent disturbance in many ecosystems, which can affect plant-pollinator assemblages and hence the services they provide. Furthermore, fire events could affect the architecture of plant-pollinator interaction networks, modifying the structure and function of communities. 2. Some pollinators, such as wood-nesting bees, may be particularly affected by fire events due to damage to nesting material and its long regeneration time. However, it remains unclear whether fire influences the structure of bee plant interactions. 3. Here, we used quantitative plant-wood nesting bee interaction networks sampled across four different post-fire age categories (from freshly-burnt to unburnt sites) in an arid ecosystem to test whether the abundance of wood-nesting bees, the breadth of resource use and the plant-bee community structure change along a post-fire age gradient. 4. We demonstrate that freshly-burnt sites present higher abundances of generalist than specialist wood-nesting bees and this translates into lower network modularity than that of sites with greater post-fire ages. Bees do not seem to change their feeding behaviour across the post-fire age gradient despite changes in floral resource availability. 5. Despite the effects of fire on plant-bee interaction network structure, these mutualistic networks seem to be able to recover a few years after the fire event. This result suggests that these interactions might be highly resilient to this type of disturbance.
Data from: Genetic structure across broad spatial and temporal scales: Rocky Mountain tailed frogs (Ascaphus montanus; Anura: Ascaphidae) in the inland temperate rainforest
Contemporary and historical processes interact to structure genetic variation, however discerning between these can be difficult. Here, we analyze range-wide variation at 13 microsatellite loci in 2098 Rocky Mountain tailed frogs, Ascaphus montanus, collected from 117 streams across the species distribution in the Inland Northwest (INW) and interpret that variation in light of historical phylogeography, contemporary landscape genetics, and the reconstructed paleodistribution of the species. Further, we project species distribution models (SDMs) to predict future changes in the range as a function of changing climate. Genetic structure has a strong spatial signature that is precisely congruent with a deep (~1.8 MY) phylogeographic split in mtDNA when we partition populations into 2 clusters (K = 2), and is congruent with refugia areas inferred from our paleorange reconstructions. There is a hierarchical pattern of geographic structure as we permit additional clusters, with populations clustering following mountain ranges. Nevertheless, genetic diversity is the highest in populations at the center of the range and is attenuated in populations closer to the range edges. Similarly, geographic distance is the single best predictor of pairwise genetic differentiation, but connectivity also is an important predictor. At intermediate and local geographic scales, deviations from isolation-by-distance are more apparent, at least in the northern portion of the distribution. These results indicate that both historical and landscape factors are contributing to the genetic structure and diversity of tailed frogs in the Inland Northwest.
Data from: Spatial and temporal genetic structure of Symbiodinium populations within a common reef-building coral on the central Great Barrier Reef
The dinoflagellate photosymbiont Symbiodinium plays a fundamental role in defining the physiological tolerances of coral holobionts, but little is known about the dynamics of these endosymbiotic populations on coral reefs. Sparse data indicate that Symbiodinium populations show limited spatial connectivity; however, no studies have investigated temporal dynamics for in hospite Symbiodinium populations following significant mortality and recruitment events in coral populations. We investigated the combined influences of spatial isolation and disturbance on the population dynamics of the generalist Symbiodinium type C2 (ITS1 rDNA) hosted by the scleractinian coral Acropora millepora in the central Great Barrier Reef. Using eight microsatellite markers, we genotyped Symbiodinium in a total of 401 coral colonies, which were sampled from seven sites across a 12-year period including during flood plume–induced coral bleaching. Genetic differentiation of Symbiodinium was greatest within sites, explaining 70–86% of the total genetic variation. An additional 9–27% of variation was explained by significant differentiation of populations among sites separated by 0.4–13 km, which is consistent with low levels of dispersal via water movement and historical disturbance regimes. Sampling year accounted for 6–7% of total genetic variation and was related to significant coral mortality following severe bleaching in 1998 and a cyclone in 2006. Only 3% of the total genetic variation was related to coral bleaching status, reflecting generally small (8%) reductions in allelic diversity within bleached corals. This reduction probably reflected a loss of genotypes in hospite during bleaching, although no site-wide changes in genetic diversity were observed. Combined, our results indicate the importance of disturbance regimes acting together with limited oceanographic transport to determine the genetic composition of Symbiodinium types within reefs.
Data from: Secondary contact and changes in coastal hydrology influence the nonequilibrium population structure of a salmonid (Oncorhynchus keta)
Numerous empirical studies have reported lack of migration–drift equilibrium in wild populations. Determining the causes of nonequilibrium population structure is challenging because different evolutionary processes acting at a variety of spatiotemporal scales can produce similar patterns. Studies of contemporary populations in northern latitudes suggest that nonequilibrium population structure is probably caused by recent colonization of the region after the last Pleistocene ice age ended ~13 000 years ago. The chum salmon's (Oncorhynchus keta) range was fragmented by dramatic environmental changes during the Pleistocene. We investigated the population structure of chum salmon on the North Alaska Peninsula (NAP) and, using both empirical data and simulations, evaluated the effects of colonization timing and founder population heterogeneity on patterns of genetic differentiation. We screened 161 single nucleotide polymorphisms and found evidence of nonequilibrium population structure when the slope of the isolation-by-distance relationship was examined at incremental spatial scales. In addition, simulations suggested that this pattern closely matched models of recent colonization of the NAP by secondary contact. Our results agree with geological and archaeological data indicating that the NAP was a dynamic landscape that may have been more recently colonized than during the last deglaciation because of dramatic changes in coastal hydrology over the last several thousand years.
Data from: Geographical parthenogenesis and population genetic structure in the alpine species Ranunculus kuepferi (Ranunculaceae)
Geographical parthenogenesis describes the enigmatic phenomenon that asexual organisms have larger distribution areas than their sexual relatives, especially in previously glaciated areas. Classical models suggest temporary advantages to asexuality in colonization scenarios because of uniparental reproduction and clonality. We analyzed population genetic structure and self-fertility of the plant species Ranunculus kuepferi on 59 populations from the whole distribution area (European Alps, Apennines and Corsica). Amplified fragment length polymorphisms (AFLPs) and five microsatellite loci revealed individual genotypes for all populations and mostly insignificant differences between diploid sexuals and tetraploid apomicts in all measures of genetic diversity. Low frequencies of private AFLP fragments/simple sequence repeat alleles, and character incompatibility analyses suggest that facultative recombination explains best the unexpectedly high genotypic diversity of apomicts. STRUCTURE analyses using AFLPs revealed a higher number of partitions and a stronger geographical subdivision for diploids than for tetraploids, which contradicts expectations of standard gene flow models, but indicates a reduction of genetic structure in asexuals. Apomictic populations exhibited high admixture near the sexual area, but appeared rather uniform in remote areas. Bagging experiments and analyses of pollen tube growth confirmed self-fertility for pollen-dependent apomicts, but self-sterility for diploid sexuals. Facultative apomixis combines advantages of both modes of reproduction: uniparental reproduction allows for rapid colonization of remote areas, whereas facultative sexuality and polyploidy maintains genetic diversity within apomictic populations. The density dependence of outcrossing limits range expansions of sexual populations.
Data from: Temporal population-genetic structure of eastern mosquitofish in a dynamic aquatic landscape
We analyzed the effect of periodic drying in the Florida Everglades on spatio-temporal population genetic structure of eastern mosquitofish (Gambusia holbrooki). Severe periodic drying events force individuals from disparate sources to mix in dry-season relatively deep-water refuges. In 1996 (a wet year) and 1999 (a dry year), we sampled mosquitofish at 20 dry-season refuges distributed in three water-management regions and characterized genetic variation for 10 allozyme and 3 microsatellite loci. In 1996, most of the ecosystem did not dry, while in 1999, many of our sampling locations were isolated by expanses of dried marsh surface. In 1996, most spatial genetic variation was attributed to heterogeneity within regions. In 1999, spatial genetic variation within regions was not significant. In both years, a small but significant amount of variation (less than 1% of the total variation) was partitioned among regions. Variance was consistently greater than zero among long-hydroperiod sites within a region, but not among short-hydroperiod sites within a region, where hydroperiod was measured as time since last marsh surface dry-down forcing fishes into local refuges. In 1996, all sites were in Hardy-Weinberg equilibrium. In 1999, we observed fewer heterozygotes than expected for most loci and sites suggesting a Wahlund effect arising from fish leaving areas that dried and mixing in deep-water refuges.
Data from: Real-time quantification of damage in structural materials during mechanical testing
A novel methodology is introduced for quantifying the severity and morphology of damage created during testing in composite components. The method utilises digital image correlation combined with image processing techniques to monitor the rate at which the strain field changes during mechanical tests. The methodology is demonstrated using two distinct experimental datasets, a ceramic matrix composite specimen loaded in tension at high temperature and nine polymer matrix composite specimens containing fibre-waviness defects loaded in bending. The changes in the strain field due to damage creation are shown to be a more effective indicator that the specimen has reached its proportional limit than using load-extension diagrams. The technique also introduces a new approach to using experimental data for creating maps showing the spatio-temporal distribution of damage in a component. These maps indicate where damage occurs in a component, its morphology and the time of occurrence. This presentation format is both easier and faster to interpret than the raw data which, for some tests, can consist of tens of thousands of images. This methodology has the potential to reduce the time taken to interpret large material test datasets whilst increasing the amount of knowledge that can be extracted from each test.
Data from: Low genetic diversity and strong population structure shaped by anthropogenic habitat fragmentation in a critically endangered primate, Trachypithecus leucocephalus
Habitat fragmentation may strongly impact population genetic structure and reduce the genetic diversity and viability of small and isolated populations. The white-headed langur (Trachypithecus leucocephalus) is a critically endangered primate species living in a highly fragmented and human-modified habitat in southern China. We examined the population genetic structure and genetic diversity of the species and investigated the environmental and anthropogenic factors that may have shaped its population structure. We used 214 unique multi-locus genotypes from 41 social groups across the main distribution area of T. leucocephalus, and found strong genetic structure and significant genetic differentiation among local populations. Our landscape genetic analyses using a causal modelling framework suggest that a large habitat gap and geographical distance represent the primary landscape elements shaping genetic structure, yet high levels of genetic differentiation also exist between patches separated by a small habitat gap or road. This is the first comprehensive study that has evaluated the population genetic structure and diversity of T. leucocephalus using nuclear markers. Our results indicate strong negative impacts of anthropogenic land modifications and habitat fragmentation on primate genetic connectivity between forest patches. Our analyses suggest that two management units of the species could be defined, and indicate that habitat continuity should be enforced and restored to reduce genetic isolation and enhance population viability.
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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.