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9,882 results for “Scale”
Data from: Intercolony movement of pre-breeding seabirds over oceanic scales: implications of cryptic age-classes for conservation and metapopulation dynamics
Aim: Demographic linkage between subpopulations plays a critical role in population processes. Metapopulation dynamics, however, remains one of the most poorly understood aspects of population biology. This is especially true for small, pelagic seabirds because their discrete subpopulations are located on offshore islands, separated by vast areas of open ocean, making monitoring logistically challenging. Seabird populations often contain large numbers of immature pre-breeders that may be important for subpopulation connectivity and demography, but are poorly studied. Here we provide evidence for intercolony movement of pre-breeding Leach's storm-petrels Oceanodroma leucorhoa among three colonies spanning the North Atlantic Ocean. We discuss their influence on metapopulation dynamics and the extinction risk of a subpopulation under threat from extreme predation. Location: North Atlantic Ocean Islands (Scotland, Canada & Iceland). Methods: We use a novel application of Bayesian stable isotope mixing models to infer recent movement of pre-breeding birds between three major breeding populations in the North Atlantic. Carbon and nitrogen stable isotope values from breeding birds (central place foragers) sampled at each colony were used as model sources and pre-breeding birds as model mixtures. Results: Of 134 pre-breeding Leach's storm-petrels sampled at three colonies across the North Atlantic, five had isotope mixing model estimates dissimilar (< 25%) to their colony of capture and were instead isotopically similar to another breeding region. Nineteen further pre-breeders had highly mixed signatures (< 50% for the colony of capture), indicating possible recent movement between colonies. Main conclusions: Our findings provide evidence for interpopulation connectivity of pre-breeding Leach's storm-petrels among colonies spanning the North Atlantic. These results highlight the significance of cryptic young age-classes in metapopulation dynamics and the demographic processes. Moreover, they provide us with a better understanding of how one subpopulation remains extant, despite experiencing extreme predation rates.
Data from: Effects of spatial scale of sampling on food web structure
This study asks whether the spatial scale of sampling alters structural properties of food webs and whether any differences are attributable to changes in species richness and connectance with scale. Understanding how different aspects of sampling effort affect ecological network structure is important for both fundamental ecological knowledge and the application of network analysis in conservation and management. Using a highly resolved food web for the marine intertidal ecosystem of the Sanak Archipelago in the Eastern Aleutian Islands, Alaska, we assess how commonly studied properties of network structure differ for 281 versions of the food web sampled at five levels of spatial scale representing six orders of magnitude in area spread across the archipelago. Species (S) and link (L) richness both increased by approximately one order of magnitude across the five spatial scales. Links per species (L/S) more than doubled, while connectance (C) decreased by approximately two-thirds. Fourteen commonly studied properties of network structure varied systematically with spatial scale of sampling, some increasing and others decreasing. While ecological network properties varied systematically with sampling extent, analyses using the niche model and a power-law scaling relationship indicate that for many properties, this apparent sensitivity is attributable to the increasing S and decreasing C of webs with increasing spatial scale. As long as effects of S and C are accounted for, areal sampling bias does not have a special impact on our understanding of many aspects of network structure. However, attention does need be paid to some properties such as the fraction of species in loops, which increases more than expected with greater spatial scales of sampling.
Data from: Continental-scale patterns reveal potential for warming-induced shifts in cattle diet
In North America, it has been shown that cattle in warmer, drier grasslands have lower quality diets than those cattle grazing cooler, wetter grasslands, which suggests warming will increase nutritional stress and reduce weight gain. Yet, little is known about how the plant species that comprise cattle diets change across these gradients and whether these shifts in dietary quality coincide with shifts in dietary composition, i.e. the relative abundance of different plant species consumed by cattle. To quantify geographic patterns in dietary composition, we analyzed the dietary composition and dietary quality of unsupplemented cattle from 289 sites across the central US by sequence-based analyses of plant DNA isolated from cattle fecal samples. Overall, assuming that the percentage of reads for a species in a sample corresponds to the percentage of protein derived from the species, only 45% of the protein intake for cattle was derived from grasses. Within the Great Plains, northern cattle relied more on grasses than southern cattle, which derived a greater proportion of their protein from herbaceous and woody eudicots. Eastern cattle were also more likely to consume a unique assemblage of plant species than western cattle. High dietary protein was not strongly tied to consumption of any specific plant species, which suggests that efforts to promote individual plant species may not easily remedy protein deficiencies. A few plant species were consistently associated with lower quality diets. For example, the diets of cattle with high amounts of Elymus or Hesperostipa were more likely to have lower crude protein concentrations than diets with less of these grasses. Overall, our analyses suggest that climatic warming will increase the reliance of cattle on eudicots as protein concentrations of grasses decline. Monitoring cattle diet with this DNA-based sequencing approach can be an effective tool for quantifying cattle diet to better increase animal performance and guide mitigation strategies to changing climates.
Data from: Spatial scales of genetic structure and gene flow in Calochortus albus (Liliaceae)
Calochortus (Liliaceae) displays high species richness, restriction of many individual taxa to narrow ranges, geographic coherence of individual clades, and parallel adaptive radiations in different regions. Here we test the first part of a hypothesis that all of these patterns may reflect gene flow at small geographic scales. We use amplified fragment length polymorphism variation to quantify the geographic scales of spatial genetic structure and apparent gene flow in Calochortus albus, a widespread member of the genus, at Henry Coe State Park in the Coast Ranges south of San Francisco Bay. Analyses of 254 mapped individuals spaced 0.001–14.4 km apart show a highly significant decline in genetic identity with ln distance, implying a root-mean-square distance of gene flow σ of 5–43 m. STRUCTURE analysis implies the existence of 2–4 clusters over the study area, with frequent reversals among clusters over short distances (<200 m) and a relatively high frequency of admixture within individuals at most sampling sites. While the intensity of spatial genetic structure in C. albus is weak, as measured by the Sp statistic, that appears to reflect low genetic identity of adjacent plants, which might reflect repeated colonizations at small spatial scales or density-dependent mortality of individual genotypes by natural enemies. Small spatial scales of gene flow and spatial genetic structure should permit, under a variety of conditions, genetic differentiation within species at such scales, setting the stage ultimately for speciation and adaptive radiation as such scales as well.
Data from: A porous convection model for small-scale grass patterns
Spatial ecological patterns are usually ascribed to Turing‐type reaction‐diffusion or scale‐dependent feedback processes, but morphologically indistinguishable patterns can be produced by instabilities in fluid flow. We present a new hypothesis that suggests that fluid convection and chill damage to plants could form vegetation patterns with wavelengths ≈1–2 times the plant height. Previous hypotheses for small‐scale vegetation pattern formation relied on a Turing process driven by competition for water, which is thought to occur in large vegetation patterns. Predictions of the new hypothesis were consistent with properties of natural grass patterns in North Carolina, contradicting the Turing hypothesis. These results indicate that similarities in pattern morphology should not be interpreted as implying similarities in the pattern‐forming processes, that small‐wavelength vegetation patterns may arise from mechanisms that are distinct from those generating long‐wavelength vegetation patterns, and that fluid instabilities should be recognized as a cause of ecological patterns.
Data from: Effects of small-scale, shading-induced seagrass loss on blue carbon storage: Implications for management of degraded seagrass ecosystems
1. Seagrass meadows are important global 'blue carbon' sinks. Despite a 30% loss of seagrasses globally during the last century, there is limited empirical research investigating the effects of disturbance and loss of seagrass on blue carbon stocks. 2. In this study, we hypothesised that seagrass loss would reduce blue carbon stocks. Using shading cloth, we simulated small-scale die-offs of two subtropical seagrass species, Halodule wrightii and Thalassia testudinum, in a dynamic northern Gulf of Mexico lagoon. The change in quantity and quality of sediment organic matter and organic carbon were compared among kill, control and bare plots before the kill treatment, shortly after the kill treatment and 11 months after the kill treatment. 210 Pb age dating was performed on bare and Thalassia plots at 11 months to evaluate the impact of sediment erosion in the absence of vegetation. 3. The small-scale die-off led to a 50-65% organic matter (OM) loss in the sediment in the top 8 cm of Halodule plots. Thalassia plots lost significant portions OM (50%) and organic carbon (C; 21-47%) in only the top 1 cm of sediment. The 210 Pb profiles indicated Thalassia die-off reduced the C sequestration rate by 10%, in addition to a loss of ~1 years' worth of C stocks (~22 g m-2<). Furthermore, analyses on O Morg quality indicated a loss of labile OM/C and enhanced remineralisation by microbes. 4. Synthesis and applications: This study provides empirical evidence that small-scale shading-induced seagrass die-offs can reduce seagrass carbon sequestration capacity and trigger losses of blue carbon stocks. While the losses recorded here are modest, these losses in blue carbon storage capacity are notable due to the proximity of shading structures (for example, boat docks) to seagrass habitats. Thus, policies to avoid or protect seagrass habitats from common small-scale, shading disturbances are important for optimising both carbon sequestration capacity and coastline development and management.17-Nov-2017
Data from: Soil nutrients and dispersal limitation shape compositional variation in secondary tropical forests across multiple scales
1. Soil resource partitioning and dispersal limitation have been shown to shape the tree community structure of mature tropical forests, but are poorly studied in the context of forest succession. We examined the relative contributions of both ecological processes to the variation in the species composition of young tropical secondary forests at different spatial scales, and if the relative importance of these two ecological processes changed during succession. At the species level, we examined if the association between species abundances and soil fertility differed between early and late successional species and/or changed over the course of succession. 2. We used vegetation and soil data from 47 secondary forest sites with two plots each in a tropical agricultural landscape. A distance-based redundancy analysis and variation partition were employed to examine the relative importance of spatial distance (proxy for dispersal limitation) and heterogeneity in soil nutrients (proxy for soil nutrient partitioning) at the landscape scale, and a linear regression to test their effects at the local scale. We examined interspecific variation in species' responses to successional age and soil nutrients with a joint species distribution model. 3. Dispersal limitation and soil niche partitioning drove considerable variation in the composition of plant communities at local and landscape scales. The relative contribution of these two ecological processes changed with scale (local versus landscape), topography (lower slope versus upper slope plots). At the species level, significant abundance-soil fertility associations were mostly positive. Most species became less responsive to soil nutrients over the first few decades of tropical forest succession, probably because light became the main limiting resource in older forests. 4. Synthesis. Our key finding is that spatial heterogeneity in soil resources and spatial distance jointly drive compositional variation within and across early successional forests. Our results highlight that a network of forest fragments enhances the resilience of ecological processes and the potential of secondary forests to restore and preserve biodiversity in human-modified landscapes. To advance our understanding of ecological succession, we need to move beyond single-factor and local-scale studies and examine the effects of multiple variables on succession at multiple spatial scales.
Data from: Comparing cal3 and other a posteriori time-scaling approaches in a case study with the pterocephaliid trilobites
Reconstructing the tree of life involves more than identifying relationships among lineages; it also entails accurately estimating when lineages diverged. Paleontologists typically scale cladograms to time a posteriori by direct reference to first appearances of taxa in the stratigraphic record. Some approaches use probabilistic models of branching, extinction, and sampling processes to date samples of trees, such as the recently developed cal3 method, which stochastically draws divergence dates given a set of rates for those processes. However, these models require estimates of the rates of those processes, which may be hard to obtain, particularly for sampling. Here, we contrast the use of cal3 and other a posteriori time-scaling approaches by examining a previous study that documented a decelerating rate of morphological evolution in pterocephaliid trilobites. Although aspects of the data set make estimation of branching, extinction, and sampling rates difficult, we use a multifaceted approach to calculate and evaluate the rate estimates needed for applying cal3. In agreement with previous simulation studies, we find that the choice of phylogenetic dating method impacts downstream macroevolutionary conclusions. We also find contradictory evolutionary inferences between analyses on ancestor–descendant contrasts (based on ancestor trait reconstruction methods) and maximum-likelihood parameter estimates. Ancestral taxon inference in cal3 corroborates previously hypothesized ancestor–descendant sequences, but cal3 suggests greater support for budding cladogenesis than anagenesis. This case study demonstrates the potential and wide applicability of the cal3 method and the benefits afforded by choosing cal3 over simpler a posteriori time-scaling approaches.
Data from: Genetic diversity is largely unpredictable but scales with museum occurrences in a species-rich clade of Australian lizards
Genetic diversity is a fundamental characteristic of species and is affected by many factors, including mutation rate, population size, life history and demography. To better understand the processes that influence levels of genetic diversity across taxa, we collected genome-wide restriction-associated DNA data from more than 500 individuals spanning 76 nominal species of Australian scincid lizards in the genus Ctenotus. To avoid potential biases associated with variation in taxonomic practice across the group, we used coalescent-based species delimitation to delineate 83 species-level lineages within the genus for downstream analyses. We then used these genetic data to infer levels of within-population genetic diversity. Using a phylogenetically informed approach, we tested whether variation in genetic diversity could be explained by population size, environmental heterogeneity or historical demography. We find that the strongest predictor of genetic diversity is a novel proxy for census population size: the number of vouchered occurrences in museum databases. However, museum occurrences only explain a limited proportion of the variance in genetic diversity, suggesting that genetic diversity might be difficult to predict at shallower phylogenetic scales.
Data from: A generalizable energetics-based model of avian migration to facilitate continental-scale waterbird conservation
Conserving migratory birds is made especially difficult because of movement among spatially disparate locations across the annual cycle. In light of challenges presented by the scale and ecology of migratory birds, successful conservation requires integrating objectives, management, and monitoring across scales, from local management units to ecoregional and flyway administrative boundaries. We present an integrated approach using a spatially explicit energetic-based mechanistic bird migration model useful to conservation decision-making across disparate scales and locations. This model moves a Mallard-like bird (Anas platyrhynchos), through spring and fall migration as a function of caloric gains and losses across a continental-scale energy landscape. We predicted with this model that fall migration, where birds moved from breeding to wintering habitat, took a mean of 27.5 d of flight with a mean seasonal survivorship of 90.5% (95% CI = 89.2%, 91.9%), whereas spring migration took a mean of 23.5 d of flight with mean seasonal survivorship of 93.6% (95% CI = 92.5%, 94.7%). Sensitivity analyses suggested that survival during migration was sensitive to flight speed, flight cost, the amount of energy the animal could carry, and the spatial pattern of energy availability, but generally insensitive to total energy availability per se. Nevertheless, continental patterns in the bird-use days occurred principally in relation to wetland cover and agricultural habitat in the fall. Bird-use days were highest in both spring and fall in the Mississippi Alluvial Valley and along the coast and near-shore environments of South Carolina. Spatial sensitivity analyses suggested that locations nearer to migratory endpoints were less important to survivorship; for instance, removing energy from a 1036 km2 stopover site at a time from the Atlantic Flyway suggested coastal areas between New Jersey and North Carolina, including the Chesapeake Bay and the North Carolina piedmont, are essential locations for efficient migration and increasing survivorship during spring migration but not locations in Ontario and Massachusetts. This sort of spatially explicit information may allow decision-makers to prioritize their conservation actions toward locations most influential to migratory success. Thus, this mechanistic model of avian migration provides a decision-analytic medium integrating the potential consequences of local actions to flyway-scale phenomena.
Data from: Rapid adaptation in large populations with very rare sex: scalings and spontaneous oscillations
Genetic exchange in microbes and other facultative sexuals can be rare enough that evolution is almost entirely asexual and populations almost clonal. But the benefits of genetic exchange depend crucially on the diversity of genotypes in a population. How very rare recombination together with the accumulation of new mutations shapes the diversity of large populations and gives rise to faster adaptation is still poorly understood. This paper analyzes a particularly simple model: organisms with two asexual chromosomes that can reassort during rare matings that occur at a rate r. The speed of adaptation for large population sizes, N, is found to depend on the ratio ∼ log(Nr)/log(N). For larger populations, the r needed to yield the same speed deceases as a power of N. Remarkably, the population undergoes spontaneous oscillations alternating between phases when the fittest individuals are created by mutation and when they are created by reassortment, which—in contrast to conventional regimes—decreases the diversity. Between the two phases, the mean fitness jumps rapidly. The oscillatory dynamics and the strong fluctuations this induces have implications for the diversity and coalescent statistics. The results are potentially applicable to large microbial populations, especially viruses that have a small number of chromosomes. Some of the key features may be more broadly applicable for large populations with other types of rare genetic exchange.
Data from: Novel bird responses to successive large-scale, landscape transformations
Transformation of intact vegetation into new kinds and configurations of human-modified habitats is a well established driver of biodiversity loss. Following initial conversion, many human-dominated landscapes are then subject to further large-scale changes in land use. The impacts on biodiversity of repeated changes in land use remain poorly known, particularly how changes in the matrix interact with initial patterns of vegetation clearing. We used an 18-year study of birds in remnant patches of endangered temperate woodland in south-eastern Australia to quantify the spatial and temporal effects of successive land use transformation in the surrounding landscape. We examined bird response to: (1) initial patterns of landscape modification (creating semi-cleared grazing land dominated by pastures that surrounded remnant woodland patches), (2) subsequent establishment and maturation of exotic tree plantations on the pastures surrounding woodland patches, and (3) additive and interactive effects of both types of landscape transformation. The majority of the 57 bird species modelled responded to conversion of grazing land to exotic plantations, either independently from initial patterns of landscape transformation (20 species), or interactively (18 species) or additively (15 species) with initial landscape transformation. The occurrence of only one species (the Common Bronzewing) was related to patterns of initial transformation but not subsequent transformation due to plantation establishment. Thus, despite many characteristics of the woodland patches within the plantation remaining largely unaltered throughout our 18 year investigation, the matrix had a profound effect on the kinds of species inhabiting them, with such impacts often magnified over time as the matrix continued to change. Plantation establishment triggered new regional-level spatial processes with effects on birds detected in woodland patches up to 2 km away from the plantation. Matrix conversion selected for species with different traits (size, diet and movement patterns) compared to the initial transformation, suggesting it is acting as a different filter on the bird community. New kinds of landscape transformation (such as plantation establishment on previously cleared land) can radically affect the species that have persisted for many decades in previously modified landscapes. This highlights the challenges, but also opportunities, for conserving taxa in ever changing human-dominated environments.
Data from: Scale insect host ranges are broader in the tropics
The specificity of the interactions between plants and their consumers varies considerably. The evolutionary and ecological factors underlying this variation are unclear. Several potential explanatory factors vary with latitude, for example plant species richness and the intensity of herbivory. Here, we use comparative phylogenetic methods to test the effect of latitude on host range in scale insects. We find that, on average, scale insects that occur in lower latitudes are more polyphagous. This result is at odds with the general pattern of greater host-plant specificity of insects in the tropics. We propose that this disparity reflects a high cost for host specificity in scale insects, stemming from unusual aspects of scale insect life history, for example, passive wind-driven dispersal. More broadly, the strong evidence for pervasive effects of geography on host range across insect groups stands in stark contrast to the weak evidence for constraints on host range due to genetic trade-offs.
Data from: Choice of resolution by functional trait or taxonomy affects allometric scaling in soil food webs
Belowground organisms often display a shift in their mass-abundance scaling relationships due to environmental factors such as soil chemistry and atmospheric deposition. Here we present new empirical data that show strong differences in allometric scaling according to whether the resolution at the local scale is based on a taxonomic or a functional classification, while only slight differences arise according to soil environmental conditions. For the first time, isometry (an inverse 1∶1 proportion) is recognized in mass-abundance relationships, providing a functional signal for constant biomass distribution in soil biota regardless of discrete trophic levels. Our findings are in contrast to those from aquatic ecosystems, in that higher trophic levels in soil biota are not a direct function of increasing body mass.
Data from: Nonlinear thermal gradients shape broad-scale patterns in geographic range size and can reverse Rapoport's rule
Aim: Species living at latitudes that have greater annual temperature variations are expected to achieve broader geographic ranges than species living at latitudes that have smaller annual temperature variations, generating a positive relationship between range size and latitude (Rapoport's rule). However, this prediction fails to take into account the greater latitudinal extent of tropical temperatures relative to those at higher latitudes. Here we model the contributions of the broader latitudinal extent of equal-temperature habitats at low latitudes and the greater annual temperature variation at high latitudes to the range size–latitude relationship, and test whether the latitudinal variation in geographic range size in marine bivalves can be explained by models that account for both annual temperature variation and the steepness of latitudinal thermal gradients. Location: Western Pacific, eastern Pacific and western Atlantic. Methods: We use a null model where geographic ranges are placed on the ocean surface independently of thermal gradients, and a range-expansion model where the minimum and maximum temperatures encompassed by the geographic range of a species (macroecological thermal ranges) are positively related to annual temperature minima and maxima at the location where the species originated. We compare results with a database containing 40,820 occurrences of 4760 marine bivalve species. Result: Models incorporating temperature-limited range expansion along realistic thermal gradients predict an inverse relationship between range size and latitude, in opposition to Rapoport's rule. The distribution patterns of marine bivalves match this prediction. Main conclusions: The poleward trend in latitudinal range size is determined by the nonlinearity of the latitudinal gradient of temperature minima and maxima and less by the latitudinal gradient of the local seasonal range in temperatures. Although tropical species do have narrower macroecological thermal ranges than high-latitude species, the nearly constant temperatures over wide areas of the tropics allow tropical species to achieve broad latitudinal ranges.
Data from: Genomic signatures of fine‐scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis, and immune defence‐related genes
Elucidating the genetic basis of adaptation to the local environment can improve our understanding of how the diversity of life has evolved. In this study we used a dense SNP array to identify candidate loci potentially underlying fine-scale local adaptation within a large Atlantic salmon (Salmo salar) population. By combining outlier, gene–environment association, and haplotype homozygosity analyses, we identified multiple regions of the genome with strong evidence for diversifying selection. Several of these candidate regions had previously been identified in other studies, demonstrating that the same loci could be adaptively important in Atlantic salmon at sub-drainage, regional and continental scales. Notably, we identified signals consistent with local selection around genes associated with variation in sexual maturation, energy homeostasis, and immune defence. These included the large-effect age-at-maturity gene vgll3, the known obesity gene mc4r, and major histocompatibility complex II. Most strikingly, we confirmed a genomic region on Ssa09 that was extremely differentiated among subpopulations, and that is also a candidate for local selection over the global range of Atlantic salmon. This region co-localized with a haplotype strongly associated with spawning ecotype in sockeye salmon (Oncorhynchus nerka), with circumstantial evidence that the same gene (six6) may be the selective target in both cases. The phenotypic effect of this region in Atlantic salmon remains cryptic, although allelic variation is related to upstream catchment area and co-varies with timing of the return spawning migration. Our results further inform management of Atlantic salmon and open multiple avenues for future research.
Data from: Scale-dependent variation in nitrogen cycling and soil fungal communities along gradients of forest composition and age in regenerating tropical dry forests
Rates of ecosystem nitrogen (N) cycling may be mediated by the presence of ectomycorrhizal fungi, which compete directly with free‐living microbes for N. In the regenerating tropical dry forests of Central America, the distribution of ectomycorrhizal trees is affected by succession and soil parent material, both of which may exert independent influence over soil N fluxes. In order to quantify these interacting controls, we used a scale‐explicit sampling strategy to examine soil N cycling at scales ranging from the microsite to ecosystem level. We measured fungal community composition, total and inorganic N pools, gross proteolytic rate, net N mineralization and microbial extracellular enzyme activity at multiple locations within 18 permanent plots that span dramatic gradients of soil N concentration, stand age and forest composition. The ratio of inorganic to organic N cycling was correlated with variation in fungal community structure, consistent with a strong influence of ectomycorrhiza on ecosystem‐scale N cycling. However, on average, > 61% of the variation in soil biogeochemistry occurred within plots, and the effects of forest composition were mediated by this local‐scale heterogeneity in total soil N concentrations. These cross‐scale interactions demonstrate the importance of a spatially explicit approach towards an understanding of controls on element cycling.
Data from: Canopy leaf area index at its higher end: dissection of structural controls from leaf to canopy scales in bryophytes
There is evidence that mosses with miniature foliage elements have extremely large leaf area indices (LAI), but it is unclear what canopy traits are responsible for these high LAI values in architecturally divergent mosses, and how the inherent tradeoffs limiting maximum LAI in vascular plants can be overcome in mosses. To determine the quantitative significance of different traits in determining LAI, we developed a method to dissect LAI into underlying functionally dependent constituent traits at leaf, shoot and canopy scales. The suites of structural traits were studied altogether for 43 moss canopies from 11 species with contrasting light and water requirements along gap-understory gradients to obtain as large a range of variation in moss architecture as possible and evaluate the differentiation in moss LAI in relation to species ecology. Extensive variation in moss structural traits, 11- (shoot length) to 77-fold (shoot number per area, NS), was observed at all structural scales from leaf to canopy. However, LAI only varied 9-fold, as the result of two key tradeoffs, leaf size vs. number tradeoff and shoot leaf area vs. shoot density tradeoff. Due to these negative relationships, and greater variability in NS, LAI primarily scaled with NS. and LAI increased with site light availability, and LAI was greater in open and dry habitat species. The current study highlights a huge structural diversity among moss canopies, but indicates that canopies converge to a much narrower range of LAI due to trait tradeoffs such that, counterintuitively, minute leaf size and densely leafed stems are not necessarily responsible for high LAI in mosses.
Identification of hidden population structure in time-scaled phylogenies
Population structure influences genealogical patterns, however data pertaining to how populations are structured are often unavailable or not directly observable. Inference of population structure is highly important in molecular epidemiology where pathogen phylogenetics is increasingly used to infer transmission patterns and detect outbreaks. Discrepancies between observed and idealised genealogies, such as those generated by the coalescent process, can be quantified, and where significant differences occur, may reveal the action of natural selection, host population structure, or other demographic and epidemiological heterogeneities. We have developed a fast non-parametric statistical test for detection of cryptic population structure in time-scaled phylogenetic trees. The test is based on contrasting estimated phylogenies with the theoretically expected phylodynamic ordering of common ancestors in two clades within a coalescent framework. These statistical tests have also motivated the development of algorithms which can be used to quickly screen a phylogenetic tree for clades which are likely to share a distinct demographic or epidemiological history. Epidemiological applications include identification of outbreaks in vulnerable host populations or rapid expansion of genotypes with a fitness advantage. To demonstrate the utility of these methods for outbreak detection, we applied the new methods to large phylogenies reconstructed from thousands of HIV-1 partial pol sequences. This revealed the presence of clades which had grown rapidly in the recent past, and was significantly concentrated in young men, suggesting recent and rapid transmission in that group. Furthermore, to demonstrate the utility of these methods for the study of antimicrobial resistance, we applied the new methods to a large phylogeny reconstructed from whole genome <i>Neisseria gonorrhoeae</i> sequences. We find that population structure detected using these methods closely overlaps with the appearance and expansion of mutations conferring antimicrobial resistance.
Data from: Male clasping ability, female polymorphism and sexual conflict: fine-scale elytral morphology as a sexually antagonistic adaptation in female diving beetles
During sexual conflict, males and females are expected to evolve traits and behaviours with a sexually antagonistic function. Recently, sexually antagonistic coevolution was proposed to occur between male and female diving beetles (Dytiscidae). Male diving beetles possess numerous suction cups on their forelegs whereas females commonly have rough structures on their elytra. These rough structures have been suggested to obstruct adhesion from male suction cups during mating attempts. However, some diving beetle species are dimorphic, where one female morph has a rough elytra and the other has a smooth elytra. Here, we used biomechanics to study the adhesive performance of male suction cups on the female morphs in two diving beetle species: Dytiscus lapponicus and Graphoderus zonatus. We compared adhesion on the rough and the smooth female morphs to infer the function of the rough elytral modifications. We found that the adhesive force on the rough structures was much lower than on other surfaces. These findings support the suggestion of sexual conflict in diving beetles and a sexually antagonistic function of the rough female structures. In addition, males differed in their adhesive capacity on different female surfaces, indicating a male trade-off between adhering to smooth and rough female morphs.
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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.