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43 results for “animal history”
Improving estimations of life history parameters of small animals in mesocosm experiments: A case study on mosquitoes
<p>We used an experimental setup with 48 aquatic mesocosms, each with twenty first instar mosquito (<em>Culex pipiens</em>) larvae and under one of twelve treatments with varying temperatures and nutrient concentrations. We took daily subsamples of the aquatic life stages as well as counting the emerging adults. We developed a method to estimate the survival and development probabilities at each life stage, based on optimising a matrix population model. We used two different approaches, one calculating the difference between predictions and observations based on a normal distribution, and the other using a combination of a normal and a multinomial distribution. For each approach, the resulting optimisation problem had around 100 parameters, making conventional gradient descent ineffective with our limited number of data points. We solved this by computing the formal derivatives of our matrix model.</p>
Data and code for: Diversity-dependent diversification in the history of marine animals
<p>By comparing detrended estimates of diversity (taxonomic richness) and rates of origination, extinction, and net diversification, I show that, at the global scale over the course of the Phanerozoic Eon, rates of diversification and origination are negatively correlated with diversity. By contrast, extinction rates are only weakly correlated with diversity for the most part. These results hold for both genus- and species-level data and for many alternative analytical protocols. The asymmetry between extinction on the one hand and origination and net diversification, on the other hand, supports a model whereby extinction is largely driven by abiotic perturbations, with subsequent origination filling the void left by depleted diversity. Diversity-dependence is somewhat weaker, but still evident, if the initial Ordovician radiation or rebounds from major mass extinctions are omitted from analysis; thus, diversity-dependence is influenced, but not dominated, by these special intervals of Earth history. In the transition from Paleozoic to post-Paleozoic time, diversity-dependence of origination weakens while that of extinction strengthens; however, diversity-dependence of net diversification barely changes in strength. Despite nuances, individual clades largely yield results consistent with those for the aggregate data on all animals. On the whole, diversity-dependent diversification appears to be a pervasive factor in the macroevolution of marine animal life.</p>
Data and code for: Diversity-dependent diversification in the history of marine animals
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Improving estimations of life history parameters of small animals in mesocosm experiments: A case study on mosquitoes
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Data from: Can interbreeding of wild and artificially propagated animals be prevented by using broodstock selected for a divergent life history?
Two strategies have been proposed to avoid negative genetic effects of artificially propagated individuals on wild populations: (i) integration of wild and captive populations to minimize domestication selection, and (ii) segregation of released individuals from the wild population to minimize interbreeding. We tested the efficacy of the strategy of segregation by divergent life history in a steelhead trout, Oncorhynchus mykiss system, where hatchery fish were selected to spawn months earlier than the indigenous wild population. Up to 80% of the naturally produced steelhead in any given year were hatchery-wild hybrids. The proportion of wild ancestry smolts and adults declined by 10 to 20% over the three generations since the beginning of the program, due to an increase in hybrids. Regression model selection analysis suggested that proportions of hybrid smolts and adults were positively correlated with the number of naturally spawning hatchery-produced adults. Furthermore, the proportion of smolt hybrids was higher in years with high stream discharge allowing hatchery fish to bypass the weir protecting wild spawning habitat. Divergent life history failed to prevent interbreeding when physical isolation was compromised following changes in environmental conditions, an inadequacy of the segregation strategy that is likely to prevail in many other situations.
Data from: Interactive life-history traits predict sensitivity of plants and animals to temporal autocorrelation
Temporal autocorrelation in demographic processes is an important aspect of population dynamics, but a comprehensive examination of its effects on different life-history strategies is lacking. We use matrix populations models from 454 plant and animal populations to simulate stochastic population growth rates (log λs) under different temporal autocorrelations in demographic rates, using simulated and observed covariation among rates. We then test for differences in sensitivities, or changes, of log λs to changes in autocorrelation among two major axes of life-history strategies, obtained from phylogenetically-informed principal component analysis: the fast-slow and semelparous-iteroparous continua. Fast life histories exhibit highest sensitivities to simulated autocorrelation in demographic rates across reproductive strategies. Slow life histories are less sensitive to temporal autocorrelation, but their sensitivities increase among highly iteroparous species. We provide cross-taxonomic evidence that changes in the autocorrelation of environmental variation may affect a wide range of species, depending on complex interactions of life-history strategies.
Data from: A redescription of the leggiest animal, the millipede Illacme plenipes, with notes on its natural history and biogeography (Diplopoda, Siphonophorida, Siphonorhinidae)
With up to 750 legs, the millipede Illacme plenipes Cook and Loomis, 1928 is the leggiest animal known on Earth. It is endemic to the northwestern foothills of the Gabilan Range in San Benito County, California, where it is the only known species of the family Siphonorhinidae in the Western Hemisphere. Illacme plenipes is only known from 3 localities in a 4.5 km2 area; the 1926 holotype locality is uncertain. Individuals of the species are strictly associated with large arkose sandstone boulders, and are extremely rare, with only 18 specimens known to exist in natural history collections. In contrast with its small size and unassuming outward appearance, the microanatomy of the species is strikingly complex. Here we provide a detailed redescription of the species, natural history notes, DNA barcodes for I. plenipes and similar-looking species, and a predictive occurrence map of the species inferred using niche based distribution modeling. Based on functional morphology of related species, the extreme number of legs is hypothesized to be associated with a life spent burrowing deep underground, and clinging to the surface of sandstone boulders.
The relative influence of history, climate, topography and vegetation structure on local animal richness varies among taxa and spatial grains
<p>Understanding the spatial scales at which environmental factors drive species richness patterns is a major challenge in ecology. Due to the trade-off between spatial grain and extent, studies tend to focus on a single spatial scale, and the effects of multiple environmental variables operating across spatial scales on the pattern of local species richness have rarely been investigated.</p> <p>Here, we related variation in local species richness of ground beetles, landbirds, and small mammals to variation in vegetation structure and topography, regional climate, biome diversity, and glaciation history for 27 sites across the USA at two different spatial grains.</p> <p>We studied the relative influence of broad-scale (landscape) environmental conditions using variables estimated at the site level (climate, productivity, biome diversity, and glacial era ice cover) and fine-scale (local) environmental conditions using variables estimated at the plot level (topography and vegetation structure) to explain local species richness. We also examined whether plot-level factors scale up to drive continental scale richness patterns. We used Bayesian hierarchical models and quantified the amount of variance in observed richness that was explained by environmental factors at different spatial scales.</p> <p>For all three animal groups, our models explained much of the variation in local species richness (85-89%), but site-level variables explained a greater proportion of richness variance than plot-level variables. Temperature was the most important site-level predictor for explaining variance in landbirds and ground beetles richness. Some aspects of vegetation structure were the main plot-level predictors of landbird richness. Environmental predictors generally had poor explanatory power for small mammal richness, while glacial era ice cover was the most important site-level predictor.</p> <p>Relationships between plot-level factors and richness varied greatly among geographical regions and spatial grains, and most relationships did not hold when predictors were scaled up to continental scale. Our results suggest that the factors that determine richness may be highly dependent on spatial grain, geography, and animal group. We demonstrate that instead of artificially manipulating the resolution to study multi-scale effects, a hierarchical approach that uses fine grain data at broad extents could help solve the issue of scale selection in environment-richness studies. </p>
FIGURE 10. Calibration diagram for mammals, excluding Archonta. Euarchontoglires continued into Figure 11 in Constraints on the timescale of animal evolutionary history
FIGURE 10. Calibration diagram for mammals, excluding Archonta. Euarchontoglires continued into Figure 11.
FIGURE 11 in Constraints on the timescale of animal evolutionary history
FIGURE 11. Calibration diagam for Archonta, including Primates. Other mammals continued in Figure 10.
Data from: Can interbreeding of wild and artificially propagated animals be prevented by using broodstock selected for a divergent life history?
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Data from: A redescription of the leggiest animal, the millipede Illacme plenipes, with notes on its natural history and biogeography (Diplopoda, Siphonophorida, Siphonorhinidae)
Open the record for dataset details and reuse information.
Data from: Interactive life-history traits predict sensitivity of plants and animals to temporal autocorrelation
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The relative influence of history, climate, topography and vegetation structure on local animal richness varies among taxa and spatial grains
Open the record for dataset details and reuse information.
Decoupling the effects of food and density on life history plasticity of wild animals using field experiments: Insights from the steward who sits in the shadow of its tail, the North American red squirrel
<p>Long-term studies of wild animals provide the opportunity to investigate how phenotypic plasticity is used to cope with environmental fluctuations, and how the relationships between phenotypes and fitness can be dependent upon the ecological context.</p> <p>Most previous studies have only investigated life history plasticity in response to changes in temperature, yet wild animals often experience multiple environmental fluctuations simultaneously. This requires field experiments to decouple which ecological factor induces plasticity in fitness-relevant traits to better understand their population-level responses to those environmental fluctuations.</p> <p>For the past 32 years, we have conducted a long-term integrative study of individually marked North American red squirrels (<i>Tamiasciurus hudsonicus </i>Erxleben) in the Yukon, Canada. We have used multi-year field experiments to examine the physiological and life history responses of individual red squirrels to fluctuations in food abundance and conspecific density.</p> <p>Our long-term observational study and field experiments show that squirrels can anticipate increases in food availability and density, thereby decoupling the usual pattern where animals respond to, rather than anticipate, an ecological change.</p> <p>As in many other study systems, ecological factors that can induce plasticity (such as food and density) co-vary. However, our field experiments that manipulate food availability and social cues of density (frequency of territorial vocalizations) indicate that increases in social (acoustic) cues of density in the absence of additional food can induce similar life history plasticity, as does experimental food supplementation.</p> <p>Changes in the levels of metabolic hormones (glucocorticoids) in response to variation in food and density are one mechanism that seems to induce this adaptive life history plasticity. </p> <p>Although we have not yet investigated the energetic response of squirrels to elevated density or its association with life history plasticity, energetics research in red squirrels has overturned several standard pillars of knowledge in physiological ecology.</p> <p>We show how a tractable model species combined with integrative studies can reveal how animals cope with resource fluctuations through life history plasticity.</p>
Data from: Molecular paleobiology of early-branching animals integrating DNA and fossils elucidates the evolutionary history of hexactinellid sponges
Reconciliation of paleontological and molecular phylogenetic evidence holds great promise for a better understanding of the temporal succession of cladogenesis and character evolution, especially for taxa with a fragmentary fossil record and uncertain classification. In zoology, studies of this kind have largely been restricted to Bilateria. Hexactinellids (glass sponges) readily lend themselves to test such an approach for early-branching (non-bilaterian) animals: they have a long and rich fossil record, but for certain taxa paleontological evidence is still scarce or ambiguous. Furthermore, there is a lack of consensus for taxonomic interpretations, and discrepancies exist between neontological and paleontological classification systems. Using conservative fossil calibration constraints and the largest molecular phylogenetic data set assembled for this group, we infer divergence times of crown-group Hexactinellida in a Bayesian relaxed molecular clock framework. With some notable exceptions, our results are largely congruent with interpretations of the hexactinellid fossil record, but also indicate long periods of undocumented evolution for several groups. This study illustrates the potential of an integrated molecular/paleobiological approach to reconstructing the evolution of challenging groups of organisms.
FIGURE 5 in Constraints on the timescale of animal evolutionary history
FIGURE 5. Calibration diagram for actinopterygians (basal teleosts and Clupeocephala).
FIGURE 6 in Constraints on the timescale of animal evolutionary history
FIGURE 6. Calibration diagram for actinopterygians (Acanthomorpha).
FIGURE 3 in Constraints on the timescale of animal evolutionary history
FIGURE 3. Calibration diagram for gnathostomes.
FIGURE 8 in Constraints on the timescale of animal evolutionary history
FIGURE 8. Calibration diagram for amniotes.
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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
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.