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261 results for “hypothesis testing”
Data and Code: No support for the genetic hypothesis of the Black-white achievement gap using polygenic scores and tests for divergent selection
<p>Data and Code for article "No support for the genetic hypothesis of the Black-white achievement gap using polygenic scores and tests for divergent selection"</p>
Novel Tests of the Key Innovation Hypothesis: Adhesive Toepads in Arboreal Lizards
Abstract The evolution of key innovations—unique features that enable a lineage to interact with the environment in a novel way—may drive broad patterns of adaptive diversity. However, traditional tests of the key innovation hypothesis, those which attempt to identify the evolutionary effect of a purported key innovation by comparing patterns of diversity between lineages with and without the key trait, have been challenged on both conceptual and statistical grounds. Here, we explore alternative, untested hypotheses of the key innovation framework. In lizards, adhesive toepad structures increase grip strength on vertical and smooth surfaces such as tree trunks and leaves and have independently evolved multiple times. As such, toepads have been posited as a key innovation for the evolution of arboreality. Leveraging a habitat use dataset applied to a global phylogeny of 2692 lizard species, we estimated multiple origins of toepads in three major clades and more than 100 origins of arboreality widely across the phylogeny. Our results suggest that toepads arise adaptively in arboreal lineages and are subsequently rarely lost while maintaining arboreal ecologies. Padless lineages transition away from arboreality at a higher rate than those with toepads, and high rates of invasion of arboreal niches by non-arboreal padbearing lineages provides further evidence that toepads may be a key to unlocking evolutionary access to the arboreal zone. Our results and analytical framework provide novel insights to understand and evaluate the ecological and evolutionary consequences of key innovations.
Data from: Examining the microclimate hypothesis in Amazonian birds: indirect tests of the 'visual constraints' mechanism
Proposed mechanisms for the decline of terrestrial and understory insectivorous birds in the tropics include a related subset that together has been termed the "microclimate hypothesis." One prediction from this hypothesis is that sensitivity to bright light environments discourages birds of the dimly lit rainforest interior from using edges, gaps, or disturbed forest. Using a hierarchical Bayesian framework and capture data across time and space, we tested this by first determining vulnerability based on differences in within-species capture rates between disturbed and undisturbed forest for 64 bird species at the Biological Dynamics of Forest Fragments Project in central Amazonian Brazil. We found that 35 species (55%) were vulnerable to anthropogenic habitat degradation, whereas only four (6%) were more commonly captured in degraded forest. To infer visual sensitivity, we then examined two different characters: eye size (maximum pupil diameter) relative to body mass and the initiation time of dawn song, which presumably reflects a species' visual capacity under low light intensities. We predicted that species with large relative eye sizes and birds with earlier dawn songs would exhibit increased vulnerability in degraded habitats with bright light. Contrary to our predictions, however, vulnerability was positively correlated with the mean start time of dawn song. This indicates that species that wait to initiate dawn song are also more vulnerable to habitat degradation. After correcting for body size, there was no effect of eye size on vulnerability. Together, our results do not provide quantitative support for the light sensitivity mechanism of the microclimate hypothesis. More sensitive, experimental tests, such as behavioral assays with controlled light environments, especially in a comparative framework, are needed to rigorously evaluate the role of light sensitivity as an aspect of the microclimate hypothesis among Neotropical birds.
Data from: Employing hypothesis testing and data from multiple genomic compartments to resolve recalcitrant backbone nodes in Goodenia s.l. (Goodeniaceae)
Goodeniaceae is a primarily Australian flowering plant family with a complex taxonomy and evolutionary history. Previous phylogenetic analyses have successfully resolved the backbone topology of the largest clade in the family, Goodenia s.l., but have failed to clarify relationships within the species-rich and enigmatic Goodenia clade C, a prerequisite for taxonomic revision of the group. We used genome skimming to retrieve sequences for chloroplast, mitochondrial, and nuclear markers for 24 taxa representing Goodenia s.l., with a particular focus on Goodenia clade C. We performed extensive hypothesis tests to explore incongruence in clade C and evaluate statistical support for clades within this group, using datasets from all three genomic compartments. The mitochondrial dataset is comparable to the chloroplast dataset in providing resolution within Goodenia clade C, though backbone support values within this clade remain low. The hypothesis tests provided an additional, complementary means of evaluating support for clades. We propose that the major subclades of Goodenia clade C (C1–C3 + Verreauxia) are the result of a rapid radiation, and each represents a distinct lineage.
Data from: A test of the seasonal availability of water hypothesis in a C3/C4 mixed grassland
<p>Understanding how cool-season C<sub>3</sub> and warm-season C<sub>4</sub> grasses will respond to climate change is critical for predicting future grassland functioning. With warming, C<sub>4</sub> grasses are expected to increase relative to C<sub>3</sub> grasses. But, alterations in the seasonal availability of water may also influence C<sub>3</sub>/C<sub>4</sub> dynamics because of their distinct seasons of growth. To better understand how shifts in the seasonal availability of water can affect ecosystem function in a northern mixed grass prairie in southeastern Wyoming, we reduced early season rainfall (April – June 2021) using rainout shelters and added the amount of excluded precipitation during the latter half of the growing season (July-September), effectively shifting spring rainfall to summer rainfall. As expected, this shift in precipitation seasonality influenced patterns of soil water availability, leading to increased soil respiration in the summer months and sustained canopy greenness throughout the growing season. Despite these responses, there were no significant differences in C<sub>3</sub> aboveground net primary production (ANPP) between the seasonally shifted treatment (SEAS) and the plots that received ambient (AMB) precipitation. This was likely due to the high levels of spring soil moisture present before rainout shelters were deployed that sustained C<sub>3</sub> grass growth. However, in plots with high C<sub>4</sub> grass cover, C<sub>4</sub> ANPP increased significantly in response to increased summer rainfall. Overall, we provide the first experimental evidence that shifts in the seasonality of precipitation, with no change in temperature, will differentially impact C<sub>3</sub> vs. C<sub>4</sub> species, altering the dynamics of carbon cycling and canopy albedo in this extensive semi-arid grassland.</p>
Function of a multimodal signal: a multiple hypothesis test using a robot frog
<p>1. Multimodal communication may evolve because different signals may convey information about the signaller (content-based selection), increase efficacy of signal processing or transmission through the environment (efficacy-based selection), or modify the production of a signal or the receiver's response to it (inter-signal interaction selection).</p> <p>2. To understand the function of a multimodal signal (aggressive calls + toe flags) emitted by males of the frog Crossodactylus schmidti during territorial contests, we tested two hypotheses related to content-based selection (quality and redundant signal), one related to efficacy-based selection (efficacy backup), and one related to inter-signal interaction selection (context). For each hypothesis we derived unique predictions based on the biology of the study species.</p> <p>3. In a natural setting, we exposed resident males to a robot frog simulating aggressive calls (acoustic stimulus) and toe flags (visual stimulus), combined and in isolation, and measured quality-related traits from males and local levels of background noise and light intensity.</p> <p>4. Our results provide support to the context hypothesis, as toe flags (the context signal) are insufficient to elicit a receiver's response on their own. However, when toe flags are emitted together with aggressive calls, they evoke in the receiver qualitatively and quantitatively different responses from that evoked by aggressive calls alone. In contrast, we found no evidence that toe flags and aggressive calls provide complementary or redundant information about male quality, which are key predictions of the quality and redundant signal hypotheses, respectively. Finally, the multimodal signal did not increase the receiver's response across natural gradients of light and background noise, a key prediction of the efficacy backup hypothesis.</p> <p>5. Toe flags accompanying aggressive calls seem to provide contextual information that modify the receiver's response in territorial contests. We suggest this contextual information is increased motivation to escalate the contest, and discuss the benefits to the signallers and receivers of adding a contextual signal to the aggressive display. Examples of context-dependent multimodal signals are rare in the literature, probably because most studies focus on single hypotheses assuming content- or efficacy-based selection. Our study highlights the importance of considering multiple selective pressures when testing multimodal signal function. </p>
Out of the temperate zone: a phylogenomic test of the biogeographical conservatism hypothesis in a contrarian clade of ants (Hymenoptera: Formicidae: Stenammini)
<p><strong>Aim: </strong>The standard latitudinal diversity gradient (LDG), in which species richness decreases from equator to pole, is a pervasive pattern observed in most organisms. Some lineages, however, exhibit inverse LDGs. Seemingly problematic, documenting and studying contrarian groups can advance understanding of LDGs generally. Here, we identify the ant tribe Stenammini as a contrarian clade and use a historical approach to evaluate alternative hypotheses that might explain the group's atypical diversity pattern. We focus on the biogeographical conservatism hypothesis (BCH) and the diversification rate hypothesis (DRH).</p> <p><strong>Location:</strong> Global.</p> <p><strong>Taxon:</strong> Ants.</p> <p><strong>Methods: </strong>We examined the shape of the LDG in Stenammini by plotting latitudinal midpoints for all described, extant species. We then inferred a genome-scale phylogeny and used the tree to estimate divergence dates and ancestral areas. We also examined diversification rate heterogeneity across the tree and tested for a correlation between rate and latitude.</p> <p><strong>Results: </strong>Stenammini has a skewed inverse LDG with a richness peak in the northern temperate zone. Phylogenomic analyses revealed five major clades and several instances of non-monophyly among genera (<em>Goniomma, Aphaenogaster</em>). Stenammini and all its major lineages arose in the northern temperate zone. The tribe originated ~51 Ma during a climatic optimum and then diversified and dispersed southward as global climate cooled. Stenammini invaded the tropics at least seven times, but these events occurred more recently and were not linked with increased diversification. There is evidence for a diversification rate increase in Holarctic <em>Aphaenogaster</em> + <em>Messor</em>, but we found no significant correlation between latitude and diversification rate generally.</p> <p><strong>Main Conclusions:</strong> Our results largely support the BCH as an explanation for the inverse latitudinal gradient in Stenammini. The clade originated in the Holarctic and likely became more diverse there due to the combined effects of center-of-origin, time-for-speciation, and niche conservatism, rather than latitudinal differences in diversification rate.</p>
Datasets and Code for "Hypothesis Tests with Functional Data for Surface Quality Change Detection in Surface Finishing Processes"
<p>This is the set of data and computer code used for reproducing the results in Jin, Tuo, Tiwari, Bukkapatnam, Aracne-Ruddle, Lighty, Hamza, and Ding, 2022, “Hypothesis tests with functional data for surface quality change detection in surface finishing processes,” <em>IISE Transactions</em>, in press.</p>
Data and models in Support of "Joint and Constrained Inversion as Hypothesis Testing Tools"
<p>The model and data files as well as the plotting and run scripts to reproduce the examples in "Joint and Constrained Inversion as Hypothesis Testing Tools".</p>
Tracks for Egyptian fruit bats included in the field manipulation for testing the use of the communal roost as an information center hypothesis
<p>According to the Information Centre Hypothesis (ICH), colonial species use social information in roosts to locate ephemeral resources. Validating the ICH necessitates showing that uninformed individuals follow informed ones to the new resource. However, the following behavior may not be essential when not all resources are ephemeral. For instance, Egyptian fruit bats forage on spatially predictable trees, but some bear fruit at unpredictable times. These circumstances suggest an alternative ICH pathway in which bats learn when fruits emerge from social cues in the roost but then use spatial memory to locate them without following conspecifics. Here, using a unique field manipulation and high-frequency tracking data, we test for this alternative pathway: We introduced bats smeared with the fruit odor of the unpredictably fruiting <em>Ficus sycomorus </em>trees to the roost, when they bore no fruits, and then tracked the movement of conspecifics exposed to the manipulated social cue. As predicted, bats visited the <em>F. sycomorus</em> trees with significantly higher probabilities than during routine foraging trips (of >200 bats). Our results show how the integration of spatial memory and social cues leads to efficient resource tracking and highlight the value of using large movement datasets and field experiments in behavioral ecology.</p>
Fungi and deadwood diversity: A test of the area-heterogeneity trade-off hypothesis
<p>Environmental heterogeneity is one of the most fundamental drivers of species diversity. For decades, ecologists have suggested that heterogeneity-diversity relationships are generally positive. But today, a greater variety of heterogeneity-diversity relationships is discussed. In this study, we contrasted two hypotheses for wood-inhabiting fungi: The classical heterogeneity-diversity hypothesis, that predicts positive relationships due to an increase in niche dimensionality with increasing heterogeneity. And the more recently stated area-heterogeneity trade-off hypothesis, that predicts a unimodal pattern due to an inherent trade-off between the number of occupied niches and the effective area per species. It allows positive and negative relationships only as special cases.</p> <p>We sampled 3,715 deadwood objects on 135 plots along a forest structure gradient in the Black Forest, Germany, and recorded 284 wood-inhabiting fungal species. To assess heterogeneity of deadwood structures, we calculated two multidimensional structural diversity indices: Structural richness was used as a measure of available niche space, and structural divergence as a measure of multivariate variance within that niche space. Those indices were then related to species richness estimates for rare, common, and dominant species, using the framework of Hill numbers.</p> <p>We found a linear, positive effect of structural richness and a unimodal effect for structural divergence on estimated species diversity. Structural richness, but not structural divergence was strongly correlated with the number of sampled deadwood objects. No clear differences between the responses of rare, common, and dominant species to the two heterogeneity gradients were found. We also estimated the mean abundance as proxy for mean population size, which decreased significantly with structural richness, but was non-significantly related to structural divergence.</p> <p><em>Synthesis: </em>In general, the results of this study suggest a unimodal heterogeneity-diversity relationship for deadwood-inhabiting fungi, and are thereby in line with the area-heterogeneity trade-off hypothesis. Thus, the negative effect of heterogeneity should lead to lower species richness and higher risk of stochastic extinctions at high levels of heterogeneity. However, as deadwood amount and deadwood diversity are often strongly correlated, we argue that the positive effect of resource availability on species richness may mask the negative effect of structural heterogeneity in some cases.</p>
Data from: A test of the competitive ability – cold tolerance trade-off hypothesis in seasonally breeding beetles
<p><span>Closely related species that use similar resources often differ in their seasonal patterns of activity, but the factors that limit their distributions across seasons are unknown for most species. One hypothesis to explain seasonal variation in the distributions of species involves a trade-off between competitive ability and cold tolerance, where tolerance to the cold compromises competitive ability in warmer (benign) temperatures, either at the level of the individual or population.</span></p> <p><span>We tested both individual-level and population-level mechanisms of this hypothesis in two co-occurring species of temperate burying beetles (Silphidae: <em>Nicrophorus sayi</em>, <em>N. orbicollis</em>) that differ in their seasonal patterns of activity.</span></p> <p><span>We measured cold tolerance, breeding activity as a function of temperature, and competitive ability as a function of temperature and season.</span></p> <p><span>Consistent with our hypothesis, the mid-season <em>N. orbicollis</em> was less able to function at the cold temperatures that characterize early spring, when the early-season <em>N. sayi</em> is most active. The larger beetle, however, always won one-on-one competitive trials at warm temperatures, regardless of species, inconsistent with an individual-level trade-off. <em>N. orbicollis</em> was usually larger and successful when competing for the same carrion later in the season, mostly because of its larger population size, consistent with a trade-off between competitive ability and cold tolerance acting at the population level.</span></p> <p><span>Our findings suggest that cold temperatures limit the mid-season <em>N. orbicollis</em> from earlier spring emergence, while competitive pressure from the more abundant, larger <em>N. orbicollis</em> constrains the early-season <em>N. sayi</em> from remaining active through the summer.</span></p>
Trans-eQTL effects on risk of type 1 diabetes: a test of the sparse effector (omnigenic) hypothesis of complex trait genetics (supplementary data)
<p>This repository contains summary-level data generated by performing <a href="https://github.com/molepi-precmed/trans-qtls">Genomewide aggregated trans- effects (GATE) analysis</a> in case-control study of Type 1 Diabetes (T1D).</p>
Data from: A test of the green wave hypothesis in omnivorous brown bears across North America
<p>Herbivorous animals tend to seek out plants at intermediate phenological states to improve energy intake while minimizing consumption of fibrous material. In some ecosystems, the timing of green-up is heterogeneous and propagates across space in a wave-like pattern, known as the green wave. Tracking the green wave allows individuals to prolong access to higher-quality forage. While there is a plethora of empirical support for such behavior in herbivorous taxa, the green wave hypothesis (GWH) is nuanced based on factors such as body morphometrics and digestive capacity. Furthermore, little is known about whether other taxa, such as omnivores, track the green wave. Our objective was to assess whether the GWH can be extended to explain the movements of omnivores. Using GPS collar data from seven populations (n = 127 individuals) of brown bears (<em>Ursus</em> <em>arctos</em>) across their entire North American range, we first tested whether bears tracked the green wave. Using conditional resource selection functions, we found that variation in proxies of vegetative forage quality better-explained movement and habitat selection than proxies of forage biomass in over half of the bears in our study, providing evidence of green wave tracking. Second, we assess factors that explained variation in green wave tracking using linear mixed-effects models. Green wave tracking in brown bears was explained by the variation in availability of green-up within spring home ranges, and how green-up transitioned across those home ranges. Our results demonstrate that the GWH can partially explain movement of a non-migratory omnivorous species, extending the generality of the GWH as a broad predictor of animal space use. The green wave is another resource wave brown bears track, and our findings help predict brown bear space use, which can be used to guide conservation and habitat restoration efforts.</p>
Fungi and deadwood diversity: A test of the area-heterogeneity trade-off hypothesis
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Rainfall seasonality shapes belowground root trait dynamics in an Amazonian tropical rainforest: A test of the stress-dominance hypothesis
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Out of the temperate zone: a phylogenomic test of the biogeographical conservatism hypothesis in a contrarian clade of ants (Hymenoptera: Formicidae: Stenammini)
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Data from: Testing the adaptive hypothesis of Batesian mimicry among hybridizing North American admiral butterflies
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Function of a multimodal signal: a multiple hypothesis test using a robot frog
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Data from: A test of the green wave hypothesis in omnivorous brown bears across North America
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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.