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1,034 results for “Empirical”
Long-term empirical evidence, early warning signals, and multiple drivers of regime shifts in a lake ecosystem
<p>1. Catastrophic regime shifts in various ecosystems are increasing with the intensification of anthropogenic pressures. Understanding and predicting critical transitions are thus a key challenge in ecology. Previous studies have mainly focused on single environmental drivers (e.g., eutrophication) and early warning signals (EWSs) prior to population collapse. However, how multiple environmental stressors interact to shape ecological behaviour and whether EWSs were detectable prior to the recovery process in lake ecosystems are largely unknown.</p> <p>2. We present long-term empirical evidence of the critical transition and hysteresis with the combined pressures of climate warming, eutrophication and trophic cascade effects by fish stocking in a subtropical Chinese lake in the Yangtze floodplain. The catastrophic regime shifts are cross-validated by 64-year multi-trophic level monitoring data and paleo-diatom records.</p> <p>3. We show that EWSs are detectable in both the collapse and recovery trajectories and that including body size information in composite EWSs requires shorter time series data and can improve the predictive ability of regime shifts. Although full recovery has not yet been observed, EWSs prior to recovery provide us with the opportunity to take measures for a clear-water regime.</p> <p>4. Climate warming and top-down cascade effects have a negative influence on water clarity by altering lower trophic level abundance and body size, which in turn have a negative effect on macrophyte abundance. Furthermore, we identify a shift in the dominant driving forces from bottom-up to top-down after regime shifts, decoupling the relationships between nutrients and biological components and thus decreasing the efficiency of nutrient reduction.</p> <p>5. Synthesis This study provides new insights into ecological hysteresis under multiple external stressors and improves our understanding of trait-based EWSs in both the collapse and recovery processes in natural freshwater ecosystems. For management practice, our work suggests that slowing down climate warming and weakening the fish predation pressure on food webs are necessary to increase the effectiveness of nutrient reduction in the restoration of lakes.</p>
Empirical investigations on quantifier scope ambiguities in German
<p>The paper presents the results of a novel experimental study on inverse scope readings in German, which are considered to be possible only under highly constrained conditions in prior literature (Frey 1993; Pafel, 2005; Bobaljik & Wurmbrand, 2012). We show that inverse scope readings are in fact possible in canonical main clauses with an ∃ -subject QP preceding and c-commanding an ∀-object QP under verum focus, with the potential of object-scrambling over the subject. The existing literature on quantifier scope in German is unanimous in claiming that inverse scope is impossible in this configuration. Our findings are line with previous experiments on German that found inverse readings to be available in other syntactic configurations (e.g. Bott & Radó, 2007; Radó & Bott 2011; Bott & Schlotterbeck, 2015). Moreover, the availability of inverse readings is boosted when the context biases towards them, a finding which is compatible with previous evidence suggesting that context plays an important role in scope ambiguity resolution (Kurtzman & MacDonald, 1993; Saba & Corriveau, 2001; Villalta, 2003; Reinhart, 2006). Our results also suggest that inverse readings are not banned from relative clauses, a result that is incompatible with the assumptions that relative clauses are islands, and that inverse scope interpretations are obtained via the covert movement operation QR in syntax. Finally, we show that scope interpretation strategies differ drastically between speakers of the same language, in line with introspective judgments.</p>
Empirical evidence of disturbance interactions: examples from Australian ecosystems
<ol> <li>Ecosystems are shaped by a range of drivers including natural and human disturbances. Many natural disturbances such as fire, insect attack and windstorms are increasing in frequency and severity. At the same time, human disturbances like logging, land clearing and plantation establishment are expanding. Co-occurring disturbances can interact with far-reaching consequences, including altered ecological processes and losses of biodiversity. Whilst the importance of interacting disturbances is increasingly recognized, the majority of empirical studies focus only on a single driver of change.</li> <li>We evaluate evidence for interacting drivers of change, including natural and human disturbances, in 57 empirical studies completed within two markedly different ecosystems in southern Australia that had been subject to large-scale, long-term research programs. These programs have documented the ecological effects of fire, native forest logging, post-fire (salvage) logging, browsing by native herbivores, and invasive species control.</li> <li>We found effects of interactions among disturbances on every vertebrate class that we examined (mammals, birds, reptiles and amphibians), as well as on vegetation and ecosystem processes (e.g. tree germination and tree mortality). Interactions between disturbances were often statistically significant when tested for. Similarly, where tested, environmental context often significantly modified disturbance effects. Finally, we found evidence of one disturbance affecting the likelihood or intensity of a subsequent disturbance (<i>viz</i>: an interaction chain or linked disturbances), and of the order in which disturbances occurred altering biotic responses.</li> <li> <a> <b>Synthesis and applications</b></a>. Interactions between disturbances warrant more attention in empirical studies because they can be common and have substantial impacts over large spatial scales, and prolonged timeframes. Approaches to limit adverse impacts of interacting disturbances include eliminating some drivers if possible (particularly where interaction chains are present), reducing the spatial overlap of disturbances (e.g. by protecting key refugia), reducing the potential for temporal overlap of multiple disturbances, and identifying key leverage points where actions are most effective.</li> </ol>
Data for: Gene tree estimation error with ultraconserved elements: An empirical study on Pseudapis bees
<p>Summarizing individual gene trees to species phylogenies using two-step coalescent methods is now a standard strategy in the field of phylogenomics. However, practical implementations of summary methods suffer from gene tree estimation error, which is caused by various biological and analytical factors. Greatly understudied is the choice of gene tree inference method and downstream effects on species tree estimation for empirical data sets. To better understand the impact of this method choice on gene and species tree accuracy, we compare gene trees estimated through four widely used programs under different model-selection criteria: PhyloBayes, MrBayes, IQ-Tree and RAxML. We study their performance in the phylogenomic framework of > 800 ultraconserved elements from the bee subfamily Nomiinae (Halictidae). Our taxon sampling focuses on the genus <i>Pseudapis</i>, a distinct lineage with diverse morphological features, but contentious morphology-based taxonomic classifications and no molecular phylogenetic guidance. We approximate topological accuracy of gene trees by assessing their ability to recover two uncontroversial, monophyletic groups, and compare branch lengths of individual trees using the stemminess metric (the relative length of internal branches). We further examine different strategies of removing uninformative loci and the collapsing of weakly supported nodes into polytomies. We then summarize gene trees with ASTRAL and compare resulting species phylogenies, including comparisons to concatenation-based estimates. Gene trees obtained with the reversible jump model search in MrBayes were most concordant on average and all Bayesian methods yielded gene trees with better stemminess values. The only gene tree estimation approach whose ASTRAL summary trees consistently produced the most likely correct topology, however, was IQ-Tree with automated model designation (MFP). We discuss these findings and provide practical advice on gene tree estimation for summary methods. Lastly, we establish the first phylogeny-informed classification for <i>Pseudapis</i> s. l. and map the distribution of distinct morphological features of the group.</p>
The geometry of resource constraint: an empirical study of the golden snub-nosed monkey
<p>1. Apposite conceptualization and measurement of resource variation is critical for understanding many issues in ecology, including ecological niches, persistence and distribution of populations, the structure of communities, and population resilience to perturbations.</p> <p>2. We apply the nutritional geometry framework to conceptualise and quantify the responses of a temperate-living primate, the golden snub-nosed monkey (<i>R</i><i>hinopithecus</i><i> roxellana</i>) to variation in resource quality and quantity and in nutrient requirements associated with seasonal environments.</p> <p>3. We present a geometric model distinguishing qualitative constraint, quantitative constraint, and "pseudo-constraint" whereby nutrient intakes resemble response to qualitative resource constraint but are in fact driven by variation in nutrient requirements. The model is applied to analyse nutrient intakes recorded in 164 full day observations of monkeys from two populations, one wild and the other captive, across seasons. Additionally, we recorded the diet of a single animal over 32 consecutive days in the wild.</p> <p>4. Despite considerable differences in available resources, the captive and wild populations showed marked similarities in nutrient intakes, including indistinguishable amounts and ratios of ingested macronutrients during summer and autumn and strong year-round maintenance of protein compared to seasonally variable fat and carbohydrate intakes. These similarities suggest homeostatically regulated nutritional targets and provide reference points to identify factors driving population differences in macronutrient intake in winter and spring.</p> <p>5. Our framework enabled us to distinguish examples of quantitative, qualitative, and "pseudo-constraint". We suggest that this approach can increase the resolution at which resource constraint is conceptualised and measured in ecological studies.</p>
Computational code for CCV metrics and two empirical datasets (D. dichotoma and S. viridis)
<p>The zipped file contains: 1) the self-explained R script for conducting multi-scale grid sampling and calculating various CCV metrics presented in the paper, 2) the users' guide for the R code, 3) abundance of <em>D. dichotoma</em> in sampling quadrats of the Changjiang water reservoir in Zhongshan City of the Guangdong Province of China, and 4) <em>S. viridis</em> in sampling quadrats of the highland barley cropland Rikaze City of Tibet, China.</p>
Empirical data for project: Mining user reviews of COVID contact-tracing apps
<p>Empirical data for project: Mining user reviews of COVID contact-tracing apps</p>
Empirical evidence of different egg morphs that match host eggs in the brush cuckoo (Cacomantis variolosus)
<p>One of the most efficient defences against obligate brood parasitism in birds is egg ejection, where a host recognises and removes the parasitic egg from the nest. This defence often selects for egg mimicry in parasitic species to reduce the likelihood of egg ejection. If a parasite uses multiple host species with distinctive egg types, this could lead to the evolution of egg gentes (host-specific egg types) in the parasite. There is observational evidence that the brood parasitic Brush Cuckoo (Cacomantis variolosus) might exhibit egg gentes, but there has been no objective study conducted to determine how closely eggs of this cuckoo species resemble those of its hosts from a bird's visual perspective. Using objective measurements to quantify egg appearance, we found that Brush Cuckoos exhibit at least two egg morphs that closely match the eggs of two of its primary hosts in colour, luminance and volume. While the determination of actual egg gentes in the Brush Cuckoo was beyond the scope of our study, our results are a first and necessary step in determining whether egg gentes might exist in this species. We suggest at least a third egg morph matching another primary host (or at least the genus of that host) might exist, but more data would be necessary to confirm this. Additionally, we provide a mechanism researchers can use to help distinguish between Brush Cuckoo eggs that are closely matched to their host eggs for future studies in this system.</p>
Lost in Zero Space -- An Empirical Comparison of 0.y.z Releases in Four Software Package Distributions
<pre>The notebooks in "notebooks/" require the dependencies specified in "requirements.txt" to be installed. They rely on data files in "data/". These data can be obtained by running the "convert.py" scripts in that folder. The script requires data files from "data-raw/". These files can be generated by running "extract.py" in that folder. This script requires the libraries.io data dump, as explained in the README file contained in this folder. If you don't have these data, or if you don't want to download them, you can ask for the required data/*.csv.gz files by email.</pre>
Replication package of the paper titled "Mining the ROS ecosystem for Green Architectural Tactics in Robotics and an Empirical Evaluation".
<p>This is the replication package of the paper titled "Mining the ROS ecosystem for Green Architectural Tactics in Robotics and an Empirical Evaluation".</p> <p>The replication package is structured according to the research questions of the study (RQ1 and RQ2) and it is composed of the following elements:</p> <ul> <li><strong>Supplementary Material (RQ1).pdf</strong>: a 93-pages technical report providing the details about our mining activities and application of thematic analysis for identifying green architectural tactics for robotics software.</li> <li><strong>Supplementary Material (RQ2).pdf</strong>: a 75-pages technical report detailing the design, conduction, and results of the empirical assessment of the identified green tactics.</li> <li><strong>RQ1_data_software.zip</strong>: the raw data and mining source code related to all the activities we carried out for answering RQ1.</li> <li><strong>RQ2_data.zip</strong>: the raw data related to all the activities we carried out for answering RQ2.</li> <li><strong>RQ2_ros_implementation.zip</strong>: the source code of the ROS-based system we implemented for performing the experiment in RQ2.</li> </ul>
Data from: The challenges of resolving a rapid, recent radiation: empirical and simulated phylogenomics of Philippine shrews
Phylogenetic relationships in recent, rapid radiations can be difficult to resolve due to incomplete lineage sorting and reliance on genetic markers that evolve slowly relative to the rate of speciation. By incorporating hundreds to thousands of unlinked loci, phylogenomic analyses have the potential to mitigate these difficulties. Here, we attempt to resolve phylogenetic relationships among eight shrew species (genus Crocidura) from the Philippines, a phylogenetic problem that has proven intractable with small (< 10 loci) data sets. We sequenced hundreds of ultraconserved elements and whole mitochondrial genomes in these species and estimated phylogenies using concatenation, summary coalescent, and hierarchical coalescent methods. The concatenated approach recovered a maximally supported and fully resolved tree. In contrast, the coalescent-based approaches produced similar topologies, but each had several poorly supported nodes. Using simulations, we demonstrate that the concatenated tree could be positively misleading. Our simulations also show that the tree shape we tend to infer, which involves a series of short internal branches, is difficult to resolve, even if substitution models are known and multiple individuals per species are sampled. As such, the low support we obtained for backbone relationships in our coalescent-based inferences reflects a real and appropriate lack of certainty. Our results illuminate the challenges of estimating a bifurcating tree in a rapid and recent radiation, providing a rare empirical example of a nearly simultaneous series of speciation events in a terrestrial animal lineage as it spreads across an oceanic archipelago.
Data from: Empirical evidence that large marine predator foraging behavior is consistent with area-restricted search theory
When prey is patchily distributed, predators are expected to spend more time searching for food in proximity of recent prey captures before searching in other areas. This behavior, known as area-restricted search, results in predators remaining localized in areas where prey had been detected previously because of the higher probability of encountering additional prey. However, few studies have tested these predictions on marine species because of the difficulties of observing feeding behavior. In this study, we utilized passive acoustic detections of echolocating dolphins to identify foraging behavior. C-PODs (click train detectors) were deployed for two years with an acoustic recorder attached to the same mooring during the second year. The time series of feeding buzzes, indicative of foraging behavior, revealed that both bottlenose (Tursiops truncatus) and common dolphins (Delphinus delphis) were more likely to stay in the area longer when foraging activity was high at the beginning of the encounter. The probability of foraging was also higher following previous foraging activity. This suggests that dolphins were feeding on spatially patchy prey and previous foraging experience influenced their movement behavior. This is consistent with the predictions of area-restricted search behavior, a nonrandom foraging strategy.
Data from: An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population
Because of their high variability, microsatellites are still considered the marker of choice for studies on parentage and kinship in wild populations. Nevertheless, single nucleotide polymorphisms (SNPs) are becoming increasing popular in many areas of molecular ecology, owing to their high-throughput, easy transferability between laboratories and low genotyping error. An ongoing discussion concerns the relative power of SNPs compared to microsatellites – that is, how many SNP loci are needed to replace a panel of microsatellites? Here, we evaluate the assignment power of 80 SNPs (HE=0.30, 80 independent alleles) and 11 microsatellites (HE =0.85, 194 independent alleles) in a wild population of about 400 sockeye salmon with two commonly used software packages (Cervus3, Colony2) and, for SNPs only, a newly developed software (SNPPIT). Assignment success was higher for SNPs than for microsatellites, especially for parent pairs, irrespective of the method used. Colony2 assigned a larger proportion of offspring to at least one parent than the other methods, though Cervus and SNPPIT detected more parent pairs. Identification of full sib groups without parental information from relatedness measures was possible using both marker systems, though explicit reconstruction of such groups in Colony2 was impossible for SNPs because of computation time. Our results confirm the applicability of SNPs for parentage analyses and refute the predictability of assignment success from the number of independent alleles.
Data from: Empirical evaluation of neutral interactions in host-parasite networks
While niche-based processes have been invoked extensively to explain the structure of interaction networks, recent studies propose that neutrality could also be of great importance. Under the neutral hypothesis, network structure would simply emerge from random encounters between individuals and thus would be directly linked to species abundance. We investigated the impact of species abundance distributions on qualitative and quantitative metrics of 113 host-parasite networks. We analysed the concordance between neutral expectations and empirical observations at interaction, species and network levels. We found that species abundance accurately predicts network metrics at all levels. Despite host-parasite systems being constrained by physiology and immunology, our results suggest that neutrality could also explain, at least partially, their structure. We hypothesize that trait-matching would determine potential interactions between species, while abundance would determine their realization.
Data from: Empirical tests of harvest-induced body-size evolution along a geographic gradient in Australian macropods
1. Life-history theory predicts the progressive dwarfing of animal populations that are subjected to chronic mortality stress but the evolutionary impact of harvesting terrestrial herbivores has seldom been tested. In Australia, marsupials of the genus Macropus (kangaroos and wallabies) are subjected to size-selective commercial harvesting. Mathematical modelling suggests that harvest quotas (ca. 10–20 % of population estimates annually) could be driving body-size evolution in these species. 2. We tested this hypothesis for three harvested macropod species with continental-scale distributions. To do so, we measured more than 2 000 macropod skulls sourced from wildlife collections spanning the last 130 years. We analysed these data using spatial Bayesian models that controlled for the age and sex of specimens as well as environmental drivers and island effects. 3. We found no evidence for the hypothesized decline in body size for any species; rather, models that fit trend terms supported minor body size increases over time. This apparently counterintuitive result is consistent with reduced mortality due to a depauperate predator guild and increased primary productivity of grassland vegetation following European settlement in Australia. 4. Spatial patterns in macropod body size supported the heat dissipation limit and productivity hypotheses proposed to explain geographic body-size variation (i.e., skull size increased with decreasing summer maximum temperature and increasing rainfall, respectively). 5. There is no empirical evidence that size-selective harvesting has driven the evolution of smaller body size in Australian macropods. Bayesian models are appropriate for investigating the long-term impact of human harvesting because they can impute missing data, fit non-linear growth models and account for non-random spatial sampling inherent in wildlife collections.
Data from: Sex-specific arrival times on the breeding grounds: hybridizing migratory skuas provide empirical support for the role of sex ratios
In migratory animals, protandry (earlier arrival of males on the breeding grounds) prevails over protogyny (females preceding males). In theory, sex differences in timing of arrival should be driven by the operational sex ratio, shifting toward protogyny in female-biased populations. However, empirical support for this hypothesis is, to date, lacking. To test this hypothesis, we analyzed arrival data from three populations of the long-distance migratory south polar skua (Catharacta maccormicki). These populations differed in their operational sex ratio caused by the unidirectional hybridization of male south polar skuas with female brown skuas (Catharacta antarctica lonnbergi). We found that arrival times were protandrous in allopatry, shifting toward protogyny in female-biased populations when breeding in sympatry. This unique observation is consistent with theoretical predictions that sex-specific arrival times should be influenced by sex ratio and that protogyny should be observed in populations with female-biased operational sex ratio.
Data from: Crossing fitness valleys: empirical estimation of adaptive landscape associated with polymorphic mimicry
Characterising the fitness landscapes associated with polymorphic adaptive traits enables the investigation of the mechanisms allowing transitions between fitness peaks. Here, we explore how natural selection can promote genetic mechanisms preventing heterozygous phenotypes from falling into non-adaptive valleys. Polymorphic mimicry is an ideal system to investigate such fitness landscapes, because the direction of selection acting on complex mimetic colour patterns can be predicted by the local mimetic community composition. Using more than 5,000 artificial butterflies displaying colour patterns exhibited by the polymorphic Müllerian mimic Heliconius numata, we directly tested the role of wild predators in shaping fitness landscapes. We compared predation rates on mimetic phenotypes (homozygotes at the supergene controlling colour pattern), intermediate phenotypes (heterozygotes), exotic morphs (absent from the local community) and palatable cryptic phenotypes. Exotic morphs were significantly more attacked than local morphs, highlighting predators' discriminatory capacities. Overall, intermediates were attacked twice as much as local homozygotes, suggesting the existence of deep fitness valleys promoting strict dominance and reduced recombination between supergene alleles. By including information on predators' colour perception, we also showed that protection on intermediates strongly depends on their phenotypic similarity to homozygous phenotypes and that ridges exist between similar phenotypes, which may facilitate divergence in colour patterns.
Data from: EuMIXFOR empirical forest mensuration and ring width data from pure and mixed stands of Scots pine (Pinus sylvestris L.) and European beech (Fagus sylvatica L.) through Europe
This data set provides unique empirical data from triplets of Scots pine (Pinus sylvestris L.) and European beech (Fagus sylvatica L.) across Europe. Dendrometric variables are provided for 32 triplets, 96 plots, 7555 trees and 4695 core samples. These data contribute to our understanding of mixed stand dynamics.
Data from: Do respiratory limitations affect metabolism of insect larvae before moulting: an empirical test at the individual level
Recent data suggest that oxygen limitation may induce moulting in larval insects. This oxygen dependent induction of moulting (ODIM) hypothesis stems from the fact that the tracheal respiratory system of insects grows primarily at moults, whereas tissue mass increases massively between moults. This may result in a mismatch between oxygen supply and demand at the end of each larval instar because oxygen demand of growing tissues exceeds the relatively fixed supply capacity of the respiratory system. The ODIM hypothesis predicts that, within larval instars, respiration and metabolic rates of an individual larva first increase with increasing body mass but eventually level off once the supply capacity of the tracheal system starts to constrain metabolism. Here, we provide the first individual-level test of this key prediction of the ODIM hypothesis. We use a novel methodology where we repeatedly measure respiration and metabolic rates throughout the penultimate- and final-instar larvae in the butterfly Pieris napi. In the penultimate instar, respiration and metabolic rates gradually decelerated along with growth, supporting the ODIM hypothesis. However, respiration and metabolic rates increased linearly during growth in the final instar, contradicting the prediction. Moreover, our data suggest considerable variation among individuals in the association between respiration rate and mass in the final instar. Overall, the results provide partial support for the ODIM hypothesis and suggest that oxygen limitation may emerge gradually within a larval instar. The results also suggest that there may be different moult induction mechanisms in larva-to-larva moults compared to the final metamorphic moult.
Data from: Does human-induced hybridization have long-term genetic effects? Empirical testing with domesticated, wild and hybridized fish populations
Current conservation practices exclude human-generated hybridized populations from protection, as the genetic effects of hybridization in the wild have been observed to be long-lasting based on neutral genetic markers and are considered potentially irreversible. Theory, however, predicts otherwise for genes under selection. We transplanted combinations of wild, domesticated and hybridized populations of a fish species to new environments. We then compared survival, phenotypic variation and plasticity to determine whether hybridization affects adaptive potential after multiple generations of selection in the wild. Although the fitness of our hybridized populations at the onset of hybridization cannot be assessed, our results suggest that within five to eleven generations, selection can remove introduced foreign genes from wild populations that have hybridized with domesticated conspecifics. The end result is hybridized populations that, in terms of survival, phenotypic plasticity, mean trait expression and overall general responses to environmental change, closely resemble neighbouring wild populations. These results have important implications for considering the potential conservation value of hybridized populations and illustrate the effectiveness of selection in a local environment.
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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.