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3,655 results for “Structural data”
Data from: Evolution of population genetic structure of the British roe deer by natural and anthropogenic processes (Capreolus capreolus)
Human influence typically impacts on natural populations of conservation interest. These interactions are varied and sometimes complex, and may be negative and unintended or associated with conservation and management strategy. Understanding the details of how these interactions influence and are influenced by natural evolutionary processes is essential to the development of effective conservation strategies. In this study we investigate a species in Britain that has experienced both negative impact through over-hunting in historical times and management efforts through culls and translocations. At the same time, there are regional populations that have been less affected by human influence. We use mtDNA and nuclear microsatellite DNA markers to investigate patterns of connectivity and diversity and find multiple insular populations in Britain that likely evolved within the Holocene (when the habitat was free of ice). We identify three concurrent processes. First, surviving indigenous populations show highly provincial patterns of philopatry, maintaining and generating population structure on a small geographic scale. Second, founder populations into habitat extirpated of native populations have expanded but remained largely insular. Third, introductions into established populations generate some admixture. We discuss the implications for the evolution of diversity of the integration of natural processes with anthropogenic influences on population size and distribution.
Data from: Imperfect morphological convergence: variable changes in cranial structures underlie transitions to durophagy in moray eels
Convergence is central to the study of evolution because it demonstrates the power of natural selection to deterministically shape phenotypic diversity. However, the conditions under which a common morphology repeatedly evolves may be restrictive. Many factors—such as differing genetic and environmental backgrounds and many-to-one mapping of form to function—contribute to variability in responses to selection. Nevertheless, lineages may evolve similar, even if not identical, forms given a shared selective regime, providing opportunities to examine the relative importance of natural selection, constraint and contingency. Here, we show that following 10 transitions to durophagy in moray eels (Muraenidae), cranial morphology repeatedly evolved toward a novel region of morphological space indicative of enhanced feeding performance on hard prey. Disparity among the resulting 15 durophagous species, however, is greater than disparity among ancestors that fed on large evasive prey, contradicting the pattern expected under convergence. This elevated disparity is a consequence of lineage-specific responses to durophagy, in which independent transitions vary in the suites of traits exhibiting the largest changes. Our results reveal a pattern of imperfect convergence, which suggests shared selection may actually promote diversification because lineages often differ in their phenotypic responses to similar selective demands.
Data from: Evidence for interannual variation in genetic structure of Dungeness crab (Cancer magister) along the California Current System
Using a combination of population- and individual-based analytical approaches, we provide a comprehensive examination of genetic connectivity of Dungeness crab (Cancer magister) along ~1,200 km of the California Current System (CCS). We sampled individuals at 33 sites in 2012 to establish a baseline of genetic diversity and hierarchal population genetic structure, and then assessed inter-annual variability in our estimates by sampling again in 2014. Genetic diversity showed little variation among sites or across years. In 2012, we observed weak genetic differentiation among sites (FST range = -0.005 – 0.014) following a pattern of isolation by distance (IBD), and significantly high relatedness among individuals within nine sampling sites. In 2014, pairwise FST estimates were lower (FST range = -0.014 – 0.007), there was no spatial autocorrelation, and fewer sights had significant evidence of relatedness. Based on these findings, we propose that inter-annual variation in the physical oceanographic conditions of the CCS influence larval recruitment and thus gene flow, contributing to inter-annual variation in population genetic structure. Estimates of effective population size (Ne) were large in both 2012 and 2014. Together, our results suggest that Dungeness crab in the CCS may constitute a single evolutionary population, though geographically limited dispersal results in an ephemeral signal of isolation by distance. Furthermore, our findings demonstrate that populations of marine organisms may be susceptible to temporal changes in population genetic structure over short time periods, thus inter-annual variability in population genetic measures should be considered.
Data from: Diet is the primary determinant of bacterial community structure in the guts of higher termites
The gut microbiota of termites plays critical roles in the symbiotic digestion of lignocellulose. While phylogenetically 'lower termites' are characterized by a unique association with cellulolytic flagellates, higher termites (family Termitidae) harbour exclusively prokaryotic communities in their dilated hindguts. Unlike the more primitive termite families, which primarily feed on wood, they have adapted to a variety of lignocellulosic food sources in different stages of humification, ranging from sound wood to soil organic matter. In this study, we comparatively analysed representatives of different taxonomic lineages and feeding groups of higher termites to identify the major drivers of bacterial community structure in the termite gut, using amplicon libraries of 16S rRNA genes from 18 species of higher termites. In all analyses, the wood-feeding species were clearly separated from humus and soil feeders, irrespective of their taxonomic affiliation, offering compelling evidence that diet is the primary determinant of bacterial community structure. Within each diet group, however, gut communities of termites from the same subfamily were more similar than those of distantly related species. A highly resolved classification using a curated reference database revealed only few genus-level taxa whose distribution patterns indicated specificity for certain host lineages, limiting any possible cospeciation between the gut microbiota and host to short evolutionary timescales. Rather, the observed patterns in the host-specific distribution of the bacterial lineages in termite guts are best explained by diet-related differences in the availability of microhabitats and functional niches.
Data from: Rearing group size determines social competence and brain structure in a cooperatively breeding cichlid
Social animals can greatly benefit from well-developed social skills. Because the frequency and diversity of social interactions often increase with the size of social groups, the benefits of advanced social skills can be expected to increase with group size. Variation in social skills often arises during ontogeny, depending on early social experience. Whether variation of social-group sizes affects development of social skills and related changes in brain structures remains unexplored. We investigated whether, in a cooperatively breeding cichlid, early group size (1) shapes social behavior and social skills and (2) induces lasting plastic changes in gross brain structures and (3) whether the development of social skills is confined to a sensitive ontogenetic period. Rearing-group size and the time juveniles spent in these groups interactively influenced the development of social skills and the relative sizes of four main brain regions. We did not detect a sensitive developmental period for the shaping of social behavior within the 2-month experience phase. Instead, our results suggest continuous plastic behavioral changes over time. We discuss how developmental effects on social behavior and brain architecture may adaptively tune phenotypes to their current or future environments.
Data from: The effect of variable frequency of sexual reproduction on the genetic structure of natural populations of a cyclical parthenogen
Cyclical parthenogens are a valuable system in which to empirically test theoretical predictions as to the genetic consequences of sexual reproduction in natural populations, particularly if the frequency of sexual relative to asexual reproduction can be quantified. In this study we utilized a series of lake populations of the cyclical parthenogen, Daphnia pulicaria, that vary consistently in their investment in sexual reproduction, to address the questions of whether the ecological variation in investment in sex is detectable at the genetic level, and if so, whether the genetic patterns seen are consistent with theoretical predictions. We show that there is variation in the genetic structure of these populations in a manner consistent with their investment in sexual reproduction. Populations engaging in a high frequency of sex were in Hardy-Weinberg and gametic phase equilibrium, and showed little genotypic differentiation across sampled years. In contrast, populations with a lower frequency of sex deviated widely from equilibrium, had reduced multi-locus clonal diversity, and showed significant temporal genotypic deviation.
Data from: Cytoskeleton structure and total methylation of mouse cardiac and lung tissue during space flight
The purpose of this work was to evaluate the protein and mRNA expression levels of multiple cytoskeletal proteins in the cardiac and lung tissue of mice that were euthanized onboard the United States Orbital Segment of the International Space Station 37 days after the start of the SpaceX-4 mission (September 2014, USA). The results showed no changes in the cytoskeletal protein content in the cardiac and lung tissue of the mice, but there were significant changes in the mRNA expression levels of the associated genes, which may be due to an increase in total genome methylation. The mRNA expression levels of DNA methylases, the cytosine demethylases Tet1 and Tet3, histone acetylase and histone deacetylase did not change, and the mRNA expression level of cytosine demethylase Tet2 was significantly decreased.
Data from: A computational model of flow between the microscale respiratory structures of fish gills
The gills of most teleost fishes are covered by plate-like structures, the secondary lamellae, that provide the bulk of the respiratory surface area. Water passing over the secondary lamellae exchanges gases with blood passing through the secondary lamellae, forming a system that has served as a classic model of counter-current exchange. In this study, a computational model of flow around the secondary lamellae is used to examine the hydrodynamic consequences of changes to the lamellar morphology. Consistent with previous studies, the interlamellar distance is found to strongly affect the hydrodynamic resistance of the gills. However, the presence of a small gap between the tips of the secondary lamellae is found to have a similar strong effect on the hydrodynamic resistance and flow patterns within the gills. The results from this model have been generally formulated, allowing the calculation of the hydrodynamic resistance for measured morphometric parameters. These results provide a new basis for comparing theoretical predictions of the gill resistance with measured values, and provide a general model for examining the diversity gill morphologies observed in teleost fishes.
Data from: The effects of spatial structure, frequency dependence and resistance evolution on the dynamics of toxin-mediated microbial invasions
Recent evidence suggests that interference competition between bacteria shapes the distribution of the opportunistic pathogen Staphylococcus aureus in the lower nasal airway of humans, either by preventing colonization or by driving displacement. This competition within the nasal microbial community would add to known host factors that affect colonization. We tested the role of toxin-mediated interference competition in both structured and unstructured environments, by culturing S. aureus with toxin-producing or nonproducing Staphylococcus epidermidis nasal isolates. Toxin-producing S. epidermidis invaded S. aureus populations more successfully than nonproducers, and invasion was promoted by spatial structure. Complete displacement of S. aureus was prevented by the evolution of toxin resistance. Conversely, toxin-producing S. epidermidis restricted S. aureus invasion. Invasion of toxin-producing S. epidermidis populations by S. aureus resulted from the evolution of toxin resistance, which was favoured by high initial frequency and low spatial structure. Enhanced toxin production also evolved in some invading populations of S. epidermidis. Toxin production therefore promoted invasion by, and constrained invasion into, populations of producers. Spatial structure enhanced both of these invasion effects. Our findings suggest that manipulation of the nasal microbial community could be used to limit colonization by S. aureus, which might limit transmission and infection rates.
Data from: Structural mouthpart interaction evolved already in the earliest lineages of insects
In butterflies, bees, flies and true bugs specific mouthparts are in close contact or even fused to enable piercing, sucking or sponging of particular food sources. The common phenomenon behind these mouthpart types is a complex composed of several consecutive mouthparts which structurally interact during food uptake. The single mouthparts are thus only functional in conjunction with other adjacent mouthparts, which is fundamentally different to biting–chewing. It is, however, unclear when structural mouthpart interaction (SMI) evolved since this principle obviously occurred multiple times independently in several extant and extinct winged insect groups. Here, we report a new type of SMI in two of the earliest wingless hexapod lineages—Diplura and Collembola. We found that the mandible and maxilla interact with each other via an articulatory stud at the dorsal side of the maxillary stipes, and they are furthermore supported by structures of the hypopharynx and head capsule. These interactions are crucial stabilizing elements during food uptake. The presence of SMI in these ancestrally wingless insects, and its absence in those crustacean groups probably ancestral to insects, indicates that SMI is a groundplan apomorphy of insects. Our results thus contradict the currently established view of insect mouthpart evolution that biting–chewing mouthparts without any form of SMI are the ancestral configuration. Furthermore, SMIs occur in the earliest insects in a high anatomical variety. SMIs in stemgroup representatives of insects may have triggered efficient exploitation and fast adaptation to new terrestrial food sources much earlier than previously supposed.
Data from: Large-scale natural disturbance alters genetic population structure of the sailfin molly, Poecilia latipinna
Many inferences about contemporary rates of gene flow are based on the assumption that the observed genetic structure among populations is stable. Recent studies have uncovered several cases in which this assumption is tenuous. Most of those studies have focused on the effects that regular environmental fluctuations can have on genetic structure and gene flow patterns. Occasional catastrophic disturbances could also alter either the distribution of habitat or the spatial distribution of organisms in a way that affects population structure. However, evidence of such effects is sparse in the literature because it is difficult to obtain. Hurricanes, in particular, have the potential to exert dramatic effects on population structure of organisms found on islands or coral reefs or in near shore and coastal habitats. Here we draw on a historic genetic data set and new data to suggest that the genetic structure of sailfin molly (Poecilia latipinna) populations in north Florida was altered dramatically by an unusually large and uncommon type of storm surge associated with Hurricane Dennis in 2005. We compare the spatial pattern of genetic variation in these populations after Hurricane Dennis to the patterns described in an earlier study in this same area. We use comparable genetic data from another region of Florida, collected in the same two periods, to estimate the amount of change expected from typical temporal variation in population structure. The comparative natural history of sailfin mollies in these two regions indicates that the change in population structure produced by the storm surge is not the result of many local extinctions with recolonization from a few refugia but emerged from a pattern of mixing and redistribution.
Data from: Effects of mis-alignment between dispersal traits and landscape structure on dispersal success in fragmented landscapes
Dispersal is fundamental to population dynamics and hence extinction risk. The dispersal success of animals depends on the biophysical structure of their environments and their biological traits; however, comparatively little is known about how evolutionary trade-offs among suites of biological traits affect dispersal potential. We developed a spatially explicit agent-based simulation model to evaluate the influence of trade-offs among a suite of biological traits on the dispersal success of vagile animals in fragmented landscapes. We specifically chose traits known to influence dispersal success: speed of movement, perceptual range, risk of predation, need to forage during dispersal, and amount of suitable habitat required for successful settlement in a patch. Using the metric of relative dispersal success rate, we assessed how the costs and benefits of evolutionary investment in these biological traits varied with landscape structure. In heterogeneous environments with low habitat availability and scattered habitat patches, individuals with more equal allocation across the trait spectrum dispersed most successfully. Our analyses suggest that the dispersal success of animals in heterogeneous environments is highly dependent on hierarchical interactions between trait trade-offs and the geometric configurations of the habitat patches in the landscapes through which they disperse. In an applied sense, our results indicate potential for ecological mis-alignment between species' evolved suites of dispersal-related traits and altered environmental conditions as a result of rapid global change. In many cases identifying the processes that shape patterns of animal dispersal, and the consequences of abiotic changes for these processes, will require consideration of complex relationships among a range of organism-specific and environmental factors.
Data from: Reproductive isolation with a learned trait in a structured population
Assortative mating displays and/or preferences can be affected by learning across a wide range of animal taxa, but the specifics of how this learning affects speciation with gene flow are not well understood. We use population genetic models with trait learning to investigate how the identity of the tutor affects the divergence of a self-referent phenotype-matching trait. We find that oblique learning (learning from unrelated individual of the previous generation) and maternal learning mask sexual selection and therefore do not allow the maintenance of divergence. In contrast, by enhancing positive frequency-dependent sexual selection, paternal learning can maintain more divergence than genetic inheritance, but leads to the loss of polymorphism more easily. Furthermore, paternal learning inhibits the invasion of a novel self-referent phenotype-matching trait, especially in a large population.
Data from: Patients with primary biliary cholangitis and fatigue present with depressive symptoms and selected cognitive deficits, but with normal attention performance and brain structure
Background: In primary biliary cholangitis (PBC) fatigue is a major clinical challenge of unknown etiology. By demonstrating that fatigue in PBC is associated with an impaired cognitive performance, previous studies have pointed out the possibility of brain abnormalities underlying fatigue in PBC. Whether structural brain changes are present in PBC patients with fatigue, however, is unclear. To evaluate the role of structural brain abnormalities in PBC patients severely affected from fatigue we, therefore, performed a case-control cerebral magnetic resonance imaging (cMRI) study and correlated changes of white and grey brain matter with the cognitive and attention performance. Methods: 20 female patients with PBC and 20 female age-matched controls were examined in this study. The assessment of fatigue, psychological symptoms, cognitive and attention performance included clinical questionnaires, established cognition tests and a computerized test battery of attention performance. T1-weighted cMRI and diffusion tensor imaging (DTI) scans were acquired with a 3 Tesla scanner. Structural brain alterations were investigated with voxel-based morphometry (VBM) and DTI analyses. Results were correlated to the cognitive and attention performance. Results: Compared to healthy controls, PBC patients had significantly higher levels of fatigue and associated psychological symptoms. Except for an impairment of verbal fluency, no cognitive or attention deficits were found in the PBC cohort. The VBM and DTI analyses revealed neither major structural brain abnormalities in the PBC cohort nor correlations with the cognitive and attention performance. Conclusions: Despite the high burden of fatigue and selected cognitive deficits, the attention performance of PBC patients appears to be comparable to healthy people. As structural brain alterations do not seem to be present in PBC patients with fatigue, fatigue in PBC must be regarded as purely functional. Future studies should evaluate, whether functional brain changes underlie fatigue in PBC.
Data from: Generation time, net reproductive rate, and growth in stage-age structured populations
Major insights into the relationship between life-history features and fitness have come from Lotka's proof that population growth rate is determined by the level (expected amount) of reproduction and the average timing of reproduction of an individual. But this classical result is limited to age-structured populations. Here we generalize this result to populations structured by stage and age by providing a new, unique measure of reproductive timing (Tc) that, along with net reproductive rate (R0), has a direct mathematical relationship to and approximates growth rate (r). We use simple examples to show how reproductive timing Tc and level R0 are shaped by stage dynamics (individual trait changes), selection on the trait, and parent-offspring phenotypic correlation. We also show how population structure can affect dispersion in reproduction among ages and stages. These macroscopic features of the life history determine population growth rate r and reveal a complex interplay of trait dynamics, timing, and level of reproduction. Our results contribute to a new framework of population and evolutionary dynamics in stage-and-age-structured populations.
Data from: More than meets the eye: detecting cryptic microgeographic population structure in a parasite with a complex life cycle
Nonrandom recruitment of parasites among hosts can lead to genetic differentiation among hosts and mating dynamics that promote inbreeding. It has been hypothesized that strictly aquatic parasites with intermediate hosts will behave as panmictic populations among hosts because ample opportunity exists for random mixing of unrelated individuals during transmission to the definitive host. A previous allozyme study on the marine trematode Lecithochirium fusiforme did not support this hypothesis in that there was genetic differentiation among, and significant heterozygote deficiencies within, definitive hosts. We revisit this system and use microsatellites to obtain multilocus genotypes. Our goal was to determine if cryptic subgroups and/or the presence of clones could account for the apparent deviation from 'panmixia'. We find strong evidence for cryptic subdivision (three genetic clusters) that causes the Wahlund effect and differentiation among definitive hosts. After accounting for these cryptic groups, we see panmictic genetic structure among definitive hosts that is consistent with the "high mixing in aquatic habitats" hypothesis. We see evidence for co-transmission of clones in all three clusters, but this level of clonal structure did not have a major impact in causing deviations from Hardy-Weinberg equilibrium, and only affected genetic differentiation among hosts in one cluster. A cursory examination of the data may have led to incorrect conclusions about non-random transmission. However, it is obvious in this system that there is more than meets the eye in relation to the actual makeup of parasite populations. In general, the methods we employ will be useful for elucidating hidden patterns in other organisms where cryptic structure may be common (e.g., those with limited morphology or complex life histories).
Data from: Identification and validation of single nucleotide polymorphisms as tools to detect hybridization and population structure in freshwater stingrays
Single nucleotide polymorphism (SNP) markers were identified and validated for two stingrays species, Potamotrygon motoro and Potamotrygon falkneri, using double digest restriction-site associated DNA (ddRAD) reads using 454-Roche technology. A total of 226 774 reads (65.5 Mb) were obtained (mean read length 289 ± 183 bp) detecting a total of 5399 contigs (mean contig length: 396 ± 91 bp). Mining this data set, a panel of 143 in silico SNPs was selected. Eighty-two of these SNPs were successfully validated and 61 were polymorphic: 14 in P. falkneri, 21 in P. motoro, 3 in both species and 26 fixed for alternative variants in both species, thus being useful for population analyses and hybrid detection.
Data from: Spatially structured statistical network models for landscape genetics
A basic understanding of how the landscape impedes, or creates resistance to, the dispersal of organisms and hence gene flow is paramount for successful conservation science and management. Spatially structured ecological networks are often used to represent spatial landscape-genetic relationships, where nodes represent individuals or populations and resistance to movement is represented using non-binary edge weights. Weights are typically assigned or estimated by the user, rather than observed, and validating such weights is challenging. We provide a synthesis of current methods used to estimate edge weights and an overview of common model types, stressing the advantages and disadvantages of each approach and their ability to model landscape-genetic data. We further explore a set of spatial-statistical methods that provide ecologists with alternative approaches for modeling spatially explicit processes that may affect genetic structure. This includes an overview of spatial autoregressive models, with a particular focus on how correlation and partial correlation are used to represent neighborhood structure with the inverse of the covariance matrix (i.e., precision matrix). We then demonstrate how to model resistance by specifying an appropriate statistical model on the nodes, conditioned on the edge weights, through the precision matrix. This integration of network ecology and spatial statistics provides a practical analytical framework for landscape-genetic studies. The results can be used to make statistical inferences about the relative importance of individual landscape characteristics, such as the vegetative cover, hillslope, or the presence of roads or rivers, on gene flow. In addition, the R code we include allows readers to explore landscape-genetic structure in their own datasets, which will potentially provide new insights into the evolutionary processes that generated ecological networks, as well as valuable information about the optimal characteristics of conservation corridors.
Data from: Rapid prey evolution can alter the structure of predator-prey communities
Although microevolution has been shown to play an important role in pairwise antagonistic species interactions, its importance in more complex communities has received little attention. Here, we used two Pseudomonas fluorescens prey bacterial strains (SBW25 and F113) and Tetrahymena thermophila protist predator to study how rapid evolution affects the structuring of predator–prey communities. Both bacterial strains coexisted in the absence of predation, and F113 was competitively excluded in the presence of both SBW25 and predator during the 24-day experiment, an initially surprising result given that F113 was originally poorer at growing, but more resistant to predation. However, this can be explained by SBW25 evolving greater antipredatory defence with a lower growth cost than F113. These results show that rapid prey evolution can alter the structure of predator–prey communities, having different effects depending on the initial composition of the evolving community. From a more applied perspective, our results suggest that the effectiveness of biocontrol bacteria, such as F113, could be weaker in communities characterized by intense bacterial competition and protist predation.
Data from: The geographical variation of network structure is scale dependent: understanding the biotic specialization of host-parasitoid networks
Research on the structure of ecological networks suggests that a number of universal patterns exist. Historically, biotic specialization has been thought to increase towards the Equator. Yet, recent studies have challenged this view showing non-conclusive results. Most studies analysing the geographical variation in biotic specialization focus, however, only on the local scale. Little is known about how the geographical variation of network structure depends on the spatial scale of observation (i.e., from local to regional spatial scales). This should be remedied, as network structure changes as the spatial scale of observation changes, and the magnitude and shape of these changes can elucidate the mechanisms behind the geographical variation in biotic specialization. Here we analyse four facets of biotic specialization in host-parasitoid networks along gradients of climatic constancy, classifying the networks according to their spatial extension (local or regional). Namely, we analyse network connectance, consumer diet overlap, consumer diet breadth, and resource vulnerability at both local and regional scales along the gradients of both current climatic constancy and historical climatic change. While at the regional scale none of the climatic variables are associated to biotic specialization, at the local scale, network connectance, consumer diet overlap, and resource vulnerability decrease with current climatic constancy, whereas consumer generalism increases (i.e., broader diet breadths in tropical areas). Similar patterns are observed along the gradient of historical climatic change. We provide an explanation based on different beta-diversity for consumers and resources across the geographical gradients. Our results show that the geographical gradient of biotic specialization is not universal. It depends on both the facet of biotic specialization and the spatial scale of observation.
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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.