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69 results for “trait shift”
Aligned bam files for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits"
<p>Aligned bam files used for analysis in "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits".</p> <p>This is an accompanying dataset to Datasets and code for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits" (https://zenodo.org/record/7442105).</p>
Resources for: Spatio-temporal integrated Bayesian species distribution models reveal lack of broad relationships between traits and range shifts
<p><strong>Aim</strong>: Climate change and habitat loss or degradation are some of the greatest threats that species face today, often resulting in range shifts. Species traits have been discussed as important predictors of range shifts, with the identification of general trends being of great interest for conservation efforts. However, studies reviewing relationships between traits and range shifts have questioned the existence of such generalized trends, due to mixed results and weak correlations, as well as analytical shortcomings. The aim of this study was to test this relationship empirically, using analytical approaches that account for common sources of bias when assessing range trends.<br><strong>Location</strong>: Tanzania, East Africa.<br><strong>Time period</strong>: 1980-1999 and 2000-2020.<br><strong>Major taxa studied</strong>: 57 savannah specialist birds found in Tanzania, belonging to 26 families and 11 orders.<br><strong>Methods</strong>: We applied recently developed integrated spatio-temporal species distribution models in R-INLA, combining citizen science and bird atlas data to estimate ranges of species, quantify range shifts, and test the predictive power of traditional trait groups, as well as exposure-related and sensitivity traits. We based our study on 40 years of bird observations in East African savannahs, a biome that has experienced increasing climatic and non-climatic pressures over recent decades. We correlated patterns of change with species traits.<br><strong>Results</strong>: We find indications of relationships identified by previous research, but low average explanatory power of traits from an ecological perspective, confirming the lack of meaningful general associations. However, our analysis finds compelling species-specific results.<br><strong>Main conclusions</strong>: We highlight the importance of individual assessments, while demonstrating the usefulness of our analytical approach for analyses of range shifts.</p>
Accounting for nonlinear responses to traits improves range shift predictions
<p>Accurately predicting species' range shifts in response to environmental change is paramount for understanding ecological processes and global change. In synthetic analyses, traits emerge as significant but weak predictors of species' range shifts across recent climate change. These studies assume linear responses to traits, while detailed empirical work often reveals trait responses that are unimodal and contain thresholds or other nonlinearities. We hypothesize that the use of linear modeling approaches fails to capture these nonlinearities and therefore may be under-powering traits to predict range shifts. We evaluate the predictive performance of approaches that can capture nonlinear relationships (ridge-regularized linear regression, support vector regression with linear and nonlinear kernels, and random forests). We apply our models using six multi-decadal range shift datasets for plants, moths, marine fish, birds, and small mammals. We show that nonlinear approaches can perform better than least-squares linear modeling in reproducing historical range shifts. Consistent with expectations, we identify dispersal and climatic niche traits as primary determinants of distribution shifts. Traits identified as important predictors and the direction of trait effects are generally consistent across models but there are notable exceptions. Among important predictors, there are more consistent responses to climatic niches than dispersal ability. Modest improvements in predictability when accounting for nonlinearities and interactions and the overall low amount of variance accounted for by trait predictors suggest limits to trait-based statistical predictive frameworks.</p>
Code and data for "Species traits associated with rapid shifts in elevational distributions of Swiss birds"
<p><strong>Abstract</strong><br> Global change in climate and land use have profound effects on species’ geographic and elevational distributions. In European birds, while species are predicted to track their climatic niches upslope, lowland agricultural intensification and high elevation land abandonment can drive elevational shifts. Species traits that can predict response to change in climate and land use can inform conservation, but thorough examination of their relationships with elevational shifts in European birds are lacking. We estimate change in the elevational distributions of 71 species from 1996 to 2016 in a region of the western Palearctic with wide elevational gradients (approximately 3,000 m) and large changes in temperature. We model the relationships between elevational shifts and species traits associated with resource preference and adaptive capacity at five reference points including the cool edge, warm edge, and the core of species’ elevational distributions. When intermediate reference points were removed changes to the results were negligible, indicating that three reference points are likely sufficient. We found significant upslope and downslope shifts in 56% and 23% of our study species, respectively. Asymmetric rates of shifts in the cool and warm edges caused significant contractions in elevational extent in 30% of our study species. The effect of elevational preference (i.e. midpoint elevation) was habitat dependent. Movement in alpine birds was unidirectionally upslope, with nearly half displaying significant or apparent elevational range contractions. In woodland birds, asymmetries of shifts in reference points led to expansions in extent in low elevation species and contractions in high elevation species. Generally, migrants, species with smaller mass, smaller relative brain size, smaller hand-wing index, and generalists in diet, habitat, and elevation had greater upslope shifts. While elevational shifts in European birds were heterogenous and species-specific, many were rapid, and species traits associated with resource preference and adaptive capacity were associated with common patterns of elevation.</p>
Herbarium specimens reveal century-long trait shifts in poison ivy due to anthropogenic CO2 emissions
<p>Dataset for manuscript entitled "Herbarium specimens reveal century-long trait shifts in poison ivy due to anthropogenic CO<sub>2</sub> emissions." Contains one spreadsheet file ("Ng et al 2023 Poison Ivy trait data.xlsx"). Note that metadata can be found in first tab.</p>
Infauna shift trait-productivity relationships in submerged aquatic vegetation communities
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Resources for: Spatio-temporal integrated Bayesian species distribution models reveal lack of broad relationships between traits and range shifts
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Accounting for nonlinear responses to traits improves range shift predictions
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The evolutionary loss of paternal care is associated with shifts in female life history traits
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Data from: Aridity drives coordinated trait shifts but not decreased trait variance across the geographic range of eight Australian trees
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Learning from dynamic traits: Seasonal shifts yield insights into ecophysiological tradeoffs across scales from macroevolutionary to intra-individual
<p><strong>Premise of the Research.</strong> Phylogenetic comparative methods provide a powerful approach for exploring the macroevolution of plant functional traits. Such approaches can uncover trait-trait correlations through evolutionary time, as well as provide evidence of the role of traits in adaptation across environmental gradients. For continuous traits, most phylogenetic comparative approaches to date employ a single trait value per species, often a mean of sampled individuals, or alternatively incorporate intraspecific variation as a distribution around such a mean. It has been known for quite some time that many of the most physiologically and ecologically important plant traits are actually highly plastic, changing dynamically across a growing season, with whole-plant development, or in response to environmental conditions. Here we demonstrate one possible approach to assessing the evolution of such dynamic traits, the use of function-valued phylogenetic comparative methods.<br> <strong>Methodology.</strong> Leaf traits were sampled across 25 taxa in the genus <em>Cornus</em> at six time points throughout the growing season in a common garden context, followed by contrasting sets of alternative analyses to demonstrate the consequences of researcher decisions on study conclusions.<br> <strong>Pivotal Results. </strong>The vast majority of assessed traits exhibit substantial seasonal shifts. These shifts cause traditional macroevolutionary correlations assessed at different sampling dates to yield conflicting results. Function-valued approaches indicate that seasonal shifts in many traits are evolutionarily correlated, with implications for the origin of trait-trait tradeoffs. Seasonal trait plasticity is also evolutionarily correlated with native habitat environmental gradients across <em>Cornus</em>.<br> <strong>Conclusions.</strong> Because a very large number of plant functional traits are not fixed, but vary dynamically over time or with environmental conditions, stronger insights into the evolution of plant functional traits can emerge when this dynamism is explicitly incorporated into phylogenetic comparative approaches. We encourage the adoption of such approaches, as well as the development of better tools for doing so.</p>
Termite trait data from: Continental-scale shifts in termite diversity and nesting and feeding strategies
<p>Typically, termites are treated as a single guild, which ignores important internal diversity, including diverse feeding and nesting traits. These termite traits are crucial for both ecosystem-level fluxes and trophic webs, with implications for vertebrate species. Despite their ecological importance, the large-scale distribution of termite feeding and nesting traits and the relationship with termite diversity is largely unknown. We investigated whether functional diversity, species richness, and feeding (wood, litter, grass, dung) and nesting trait (aboveground mound, belowground nest, inside tree or outside tree nest) distributions of termites were climatically control. To address this gap, we assembled a continental-scale database of termite traits and occurrence in Australia and modelled termite nesting and feeding traits in response to macroclimate. Functional richness and evenness increased primarily with temperature. Australia showed multiple hotspots of termite diversity with each hotspot showing a distinct guild composition. The large-scale distribution of nesting traits showed that aboveground nesting species were the most common nesting guild in the dry and wet tropics while belowground nesting dominated in seasonally cold arid environments, demonstrating a strong climatic control on nesting strategy. Given their large biomass and many interactions with other species, the macro-ecology of termite traits may be especially important in predicting shifts in other species' distributions at continental and global scales.</p>
Directional selection shifts trait distributions of planted species in dryland restoration
<p>1. The match between species trait values and local abiotic filters can restrict community membership. An often-implicit assumption of this relationship is that abiotic filters select for a single locally optimal strategy, though difficulty in isolating effects of the abiotic environment from those of dispersal limitation and biotic interactions has resulted in few empirical tests of this assumption. Similar constraints have made it difficult to assess whether the type and intensity of abiotic filters shift along gradients of environmental harshness, as predicted by the stress dominance hypothesis.</p> <p>2. We planted 9,216 plants of perennial grass and forb species that had a range of functional trait values and were assigned to a warm, intermediate, or cool temperature tolerance pools across eight sites on the Colorado Plateau. We compared the distributions of traits of surviving individuals to null distributions to evaluate whether there were shifts in trait means and variation. Borrowing from phenotypic selection concepts in evolutionary biology, we assessed support for stabilizing, directional, and disruptive abiotic filtering of trait distributions and whether these types of filtering varied with initial species pool.</p> <p>3. Functional composition was significantly different from null distributions for nearly all traits at all sites, with trait variation more restricted in harsher abiotic conditions, supporting the stress-dominance hypothesis. Contrary to expectations, we primarily found evidence for directional selection, which increased in frequency in warm species pools while disruptive selection was found more often in cool and intermediate species pools.</p> <p>4. Synthesis: This study provides a controlled experimental approach to test the effect of the abiotic environment on plant trait filtering. We found that opportunistic strategies allowing for rapid water acquisition during favorable periods improved survival at warmer sites. Species with these strategies may be expected to benefit from increasing aridity and may be selected for active management efforts. More generally, the prevalence of directional selection may have important implications for dynamic vegetation models that rely on trait distributions for translating environmental variation into ecosystem processes.</p>
Species-level CWM values mask contrasting intra- vs interspecific trait shifts at subtropical forest edges
<p>Altered microclimatic conditions and higher disturbance at forest edges create environmental stress and modify resource gradients from edge to interior, changing the selection pressures acting on individuals. Although community-weighted trait-mean (CWM) shifts along edge gradients have been widely documented at the species level, it is unclear how edge effects act at the individual level, and whether the direction of intraspecific trait shifts mirrors that of CWM shifts in response to edge effects. On 20 islands in the Thousand Island Lake, China, we established 484 plots (2×2 m) in a stratified random design across distances of 0 – 128 m from the forest edge. Within each plot, we sampled leaves (n=34,768) from within and among all 2,993 individuals of 68 species and measured five leaf traits (leaf area, LA; specific leaf area, SLA; leaf dry matter content, LDMC; thickness, LT; chlorophyll content, LCC). Using generalized linear mixed models, we found that different leaf traits exhibited contrasting shifts in inter- vs. intraspecific trait variation in response to edge effects. For SLA, LT, and LCC, negative covariance between inter- and intraspecific trait shifts resulted in dampening of community-wide trends compared to CWM response to edge effects. In contrast, the community-wide trend for LDMC was reinforced due to positive covariance between inter- and intraspecific trait shifts, while for LA the direction of covariance shifted from negative to positive on small vs. large islands. Together, edge effects alter selection regimes in reassembling plant communities. Predicting the community-wide consequences depends on the degree to which there is negative vs. positive covariance between species sorting and within-species adaptation. The widely-used CWM approach can mask contrasting trait selection pressures acting on individuals within local populations. Individual-level trait variation can improve understanding of community re-assembly trajectories in response to global environmental change.</p>
Functional traits and their plasticity shift from tolerant to avoidant under extreme drought
<p>Under climate change, extreme droughts will limit water availability for plants. However, the species-specific responses make it difficult to draw general conclusions. We hypothesized that changes in species' abundance in response to extreme drought can be best explained by a set of water economic traits under ambient conditions in combination with the ability to adjust these traits towards higher drought resistance. We conducted a four-year field experiment in temperate grasslands using rainout shelters with 30% and 50% rainfall reduction. We quantified the response as the change in species abundance between ambient conditions and the rainfall reduction. Abundance response to extreme drought was best explained by a combination of traits in ambient conditions and their functional adjustment, most likely reflecting plasticity. Smaller leaved species decreased less in abundance under drought. With increasing drought intensity, we observed a shift from drought tolerance, i.e. an increase leaf dry matter content, to avoidance, i.e. a less negative turgor loss point (TLP) in ambient conditions and a constancy in TLP under drought. We stress the importance of using a multidimensional approach of variation in multiple traits and the importance of considering a range of drought intensities to improve predictions of species' response to climate change.</p>
Trait shifts in bird communities from primary forest to human settlements in Mexican seasonal forests: Are there ruderal birds?
<p><span><span><span><span>Agriculture, cattle grazing, and human settlements negatively affect bird biodiversity, driving the loss of ecologically specialized species and favoring the dominance of generalists. Because ecological pressures define organisms' success by acting on their intrinsic traits, biodiversity loss due to anthropization might cause directional trait shifts. Here, we use a trait-based approach to find empirical evidence of trait-shifts in bird communities across an anthropization gradient in seasonal forests in central Mexico. We performed point-count bird surveys within a region of tropical deciduous and seasonal oak forests considering three degrees of anthropization: primary forest, secondary growth, and human settlements. A multivariate analysis (PCA) showed similar trait-covariation patterns for both forest types; in the anthropized habitat the bird communities exhibited shorter life-cycles, higher fecundity, and broader ecological niches (diet, foraging habitat, and nesting resources) than those in the primary forests. Our finding of directional trait shifts resembles Evolutionary Ecological Strategies Theory (EES) predictions for successful organisms within highly disturbed anthropized habitats, which are known as a "ruderal adaptative strategy" in the EES framework. The use of trait-based approaches could improve ecological generalizations in bird communities, leading to a better understanding of avian biodiversity's responses to anthropization.</span></span></span></span></p>
Data from: Ecological release and insular shifts in avian morphological traits in the Caribbean
<p>We compared support for 3 hypotheses that might explain observed morphological variation among islands of 4 1.70 species of Caribbean land birds: ecological release from competition and predation pressure, predation pressure from 1 novel predator species (small Indian mongoose, <em>Herpestes auropunctatus</em>), and climate. We measured wing chord, tarsus length, bill length, and mass of Bananaquits (<em>Coereba flaveola</em>), Black-faced Grassquits (<em>Tiaris bicolor</em>), Lesser Antillean Bullfinches (<em>Loxigilla noctis</em>), and Common Ground Doves (<em>Columbina passerina</em>) in Grenada, 2015–2017, and combined these measures with data from 23 other Caribbean islands collated from academic papers and researchers, for a total sample size of 6,518 individuals. We found the strongest support for the ecological release hypothesis, but each of our hypotheses received some support, suggesting that ecological release from competition, predation pressure from mongoose, and climate may all interact to influence morphological adaptations of birds to local conditions in the Caribbean.</p>
Decoupling pioneering traits from latitudinal patterns in a North American bird experiencing a southward range shift
<ol> <li>Eco-geographic rules describe spatial patterns in biological trait variation and shed light on the drivers of such variation. In animals, a consensus is emerging that 'pioneering' traits may facilitate range shifts via a set of bold, aggressive, and stress-resilient traits. Many of these same traits are associated with more northern latitudes, and most range shifts in the northern hemisphere indicate northward movement. As a consequence, it is unclear whether pioneering traits are simply corollaries of existing latitudinal variation, or whether they override other well-trodden latitudinal patterning as a unique eco-geographic rule of phenotypic variation.</li> <li>The tree swallow (<em>Tachycineta</em> <em>bicolor</em>) is a songbird undergoing a <em>southward</em> range shift in the eastern United States, in direct opposition of the poleward movement seen in most other native species' range shifts. Because this organic range shift countervails the typical direction of movement, this case study provides for unique ecological insights on organisms and their ability to thrive in our changing world.</li> <li>We sampled female birds across seven populations, quantifying behavioral, physiological, and morphological traits. We also used GIS and field data to quantify a core set of ecological factors with strong ties to these traits as well as female performance.</li> <li>Females at more southern expansion sites displayed higher maternal aggression, higher baseline corticosterone, and more pronounced elevation of corticosterone following a standardized stressor, contrary to otherwise largely conserved latitudinal patterning in these traits. Microhabitat variation explained some quantitative phenotypic variation, but the expansion and historic ranges did not differ in openness, distance to water, or breeding density.</li> <li>This countervailing range shift therefore suggests that pioneering traits are not simply corollaries of existing latitudinal variation, but rather, they may override other well-trodden latitudinal patterning as a unique eco-geographic rule of phenotypic variation.</li> </ol>
Plant functional traits predict heterogeneous distributional shifts in response to climate change
<p>Climate change is causing the rapid redistribution of vegetation as plant species move to track their climatic optima. Despite a global trend of upward movement in latitude and elevation, there is extensive heterogeneity among species and locations, with few emerging generalizations. Greater generalization may be achieved by considering multidimensional changes in species' distributions as well as incorporating ecologically relevant functional traits into studies of range shifts.</p> <p>To better understand how recent changes in climate are influencing the elevational distribution of plant species and how species' functional traits mediate distributional changes, we resampled a 2,438-meter elevation transect spanning a distance of 16 kilometers which encompasses desert scrub, pinyon-juniper woodland, chaparral, and coniferous forest plant communities.</p> <p>Over the last 42 years, total perennial cover and species' average cover increased at lower elevations and decreased at higher elevations while the average elevational leading-edge increased 116 m and the elevational rear edge decreased 84 m. Notably, these changes were mediated by species' functional traits, where species exhibiting more conservative traits (lower SLA, greater δ13C, larger seed mass) and taller height shifted upward in their leading-edge range limit, average elevation, and trailing edge range limit, while declining in abundance at the median and trailing edge of their range. Species possessing more acquisitive traits (higher SLA, lower δ13C, smaller seed mass) and shorter height shifted downward and increased in abundance at their trailing edge, with increases in their total range size.</p> <p>Our results provide clear evidence that heterogeneous range dynamics under recent climate change can be generalized by considering ecologically relevant plant functional traits, and how they respond to localized climate exposure. Further, by documenting changes across a steep ecological gradient comprising a large aridity gradient, we show divergent patterns for plants occupying contrasting positions along the global spectrum of plant form and function, which provides critical insight into how trait-mediated changes under increasing aridity will impact ecosystem functioning.</p>
Winter range shifts and their associations with species traits are heterogeneous in eastern North American birds
<p>Many species' distributions are shifting in response to climate change. Many distributional shifts are predictably poleward or higher in elevation, but heterogeneity in the rate and direction of shifts both within and between species appears to be common. We found high heterogeneity in the trajectory of winter range shifts for 65 species of birds across eastern North America and in the different traits and trait interactions associated with these shifts across the spatial scales we examined. We used data from the Christmas Bird Count to quantify the trajectory of winter latitudinal center of abundance range shifts over four decades (1980–2019) for 65 species of songbirds and woodpeckers in North America, both across eastern North America (ENA) as a whole and for the Atlantic (ATL) and Mississippi (MISS) flyways separately. We then used linear models and AICc model selection to test whether species traits could explain variation in range shifts or flyway discrepancies. Across ENA, most species showed northward latitudinal range shifts, but some showed no latitudinal shift while others shifted southwards. Amongst ATL and MISS, we documented both within- and between-species differences in the rate and direction of latitudinal shifts, complicating the results from across ENA. No single trait emerged as a dominant driver of range shift differences at the ENA and flyway scales. Migration strategy interacted with insectivory to explain variation at the largest spatial scale (ENA), whereas frugivory and mean winter latitude explained much of the variation in ATL and MISS, respectively. Exploring heterogeneity in range shifts within and between species, and in the associations between range shifts and life history traits, will help us better understand the mechanisms that mediate differing responses to environmental change and predict which species will be better able to adapt to those changes. </p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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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.