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California steelhead abundance and environmental conditions timeseries
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Data from Pliant pathogens: Estimating viral spread when confronted with new vector, host, and environmental conditions
To determine the effects of new conditions (host, vector, and nutrient) on pathogen spread rate, we introduced a vector-borne viral plant pathogen, Barley Yellow Dwarf Virus PAV (BYDV-PAV) into hosts, vectors, and host nutrient supplies that it had not encountered for thousands of viral generations. We quantified pathogen prevalence over the course of two serial inoculations under the new conditions.
Model-derived backbarrier marsh width from GEOMBEST+ simulations of barrier island-marsh coupled evolution for a range of environmental conditions.
Model-derived backbarrier marsh width from GEOMBEST+ simulations of barrier island-marsh coupled evolution for a range of environmental conditions. The input parameters were varied for a range of 10 different values for each of the flux of overwash (.2-2 m^3/yr), the rate of sea level rise (1-10mm/yr), and the flux of bay sediment (2-20 m^3/yr) Each simulation was for a one meter change in sea level, starting from one of three initial conditions, an empty backbarrier basin, starting with a narrow (400m wide) backbarrier marsh, and starting with a marsh-filled (2000m wide) backbarrier basin. With 10 variants of each parameter input and 3 initial conditions, this results in 3,000 total simulations run. Each row in the spreadsheet contains the input and output values for an individual simulation. The outputs reported are the final backbarrier marsh width, defined as the distance from the backside of the barrier island to the landward most marsh cell, the change in marsh width, and the rate of change in marsh width.
Data from: Last Glacial Maximum environmental conditions at Andøya, northern Norway; evidence for a northern ice-edge ecological "hotspot"
<p>Andøya on the NW coast of Norway is a key site for understanding the Last Glacial<br> Maximum (LGM) in northern Europe. Controversy has arisen concerning the local conditions,<br> especially about the timing and extent of local glacial cover, maximum July temperatures and<br> whether pine and/or spruce could have grown there. We reviewed all existing data and add<br> newly analysed ancient sedimentary DNA, pollen, macrofossils, geochemistry and stable<br> isotopes from three lake sediment cores from Øvre Æråsvatnet. A total of 23 new dates and<br> age-depth modelling suggests the lake has been ice-free since GI2 (<22.8 k cal. BP) and<br> possibly GS3 (<27.4 k cal. BP). <em>Pinus</em> and <em>Picea</em> sedimentary ancient DNA (<em>sed</em>aDNA) was<br> found in all three cores but at such low frequencies that it could not be distinguished from<br> background contamination. LGM samples have an exceptionally high organic matter content,<br> with isotopic values indicating that carbon and nitrogen derives from a marine source. Along<br> with finds of bones of the little auk (<em>Alle alle</em>), this indicates that the lake received guano from<br> an adjacent bird colony. DNA, pollen and macrofossil assemblages were dominated by<br> Poaceae, Brassicaceae and <em>Papaver</em>, but scattered occurrence of species currently restricted to<br> the Low Arctic Tundra Zone (July temperature of 8-9°C) such as Apiaceae (DNA, 8-9°C),<br> and <em>Alchemilla alpina</em> (macrofossil, 8-9°C) were also recorded. The review showed 94<br> recorded vascular plant taxa, of which 38% have a northern limit in Shrub Tundra or more<br> southern vegetation zones. This unusual assemblage likely stems from a combination of<br> proximity to ice-free water in summer, geographical isolation linked with stochastic long-<br> distance dispersal events, and the presence of bird-fertilized habitats. The environmental<br> reconstruction based on all records from the area does not preclude local growth of tree<br> species, as the local climate combined with high nutrient input may have led to periodically<br> suitable environmental 'hotspot' conditions.</p>
Milk production and environmental conditions of mountain-pastured Braunvieh cows between 2000 and 2015
<p>This dataset is a subset of the dataset used in the associated article, linking environmental data to milk records of mountain-pastured cows between 2000 and 2015.</p> <p>In particular it contains information on the cow and lactation cycle (lactation number, date of calving, date of first record in the alp, average quantity of milk over 3 milk records taken in the alp) and environmental condition (temperature humidity index, cold stress index, averaged over 3 and 30 days before the milk records and precipitation during spring).</p> <p>This dataset does not allow the reproducibility of the associated article but enables the analysis of conjoint milk data and associated environmental conditions. It should be noted that the publication of the full dataset was not possible.</p>
Materials to study the phototropic response of different systematic groups of mesoplankton under adverse environmental conditions using the DHC
<p>“n_all” – number of all particles in a frame</p> <p>“n_z” – number of all particles in a frame moving towards the attracting light source</p> <p>“V_aver_all” – average particle speed</p> <p>“V_aver_z” – average particle speed towards the attracting light source</p> <p>Data in lines refer to the study hour, columns “1” – data in 30 sec without lighting, “2” – in 60 sec without lighting, “3” – in 90 sec without lighting, ..., “10” – data in 300 sec without lighting, “11” – data in 30 sec after the attracting light is turned on, “12” – data in 60 sec after the attracting light is turned on, ..., “20” – data in 300 sec after the attracting light is turned on.</p>
Data from: "Characterization of two Iberian freshwater fish transcriptomes, Squalius carolitertii and Squalius torgalensis, living in distinct environmental conditions" in Genomic Resources Notes Accepted 1 April 2015 to 31 May 2015
The advance of NGS technologies opened exciting research avenues, as for example expanding the study of the mechanisms underlying adaptation from model organisms to natural systems. We used NGS technologies to sequence 12 RNA-seq libraries, and provide the first transcriptomes of two endemic Iberian Cyprinids. The species Squalius carolitertii and S. torgalensis inhabit different regions of Portugal with distinct climate types, Atlantic in the North and Mediterranean in the South, respectively. While northern regions present mild temperatures, in southern regions fish are often under harsh temperatures and droughts. Herein, we sequenced the transcriptome from three tissues (skeletal muscle, liver and fins) in an Illumina HiSeq2000 of fish exposed to different temperatures: 18ºC (control) and 30ºC (test). Around 200 million raw reads were generated for each species, with similar number of reads per library (approximately 30 million), rendering de novo assemblies with a total of 145975 and 137303 contigs, for S. carolitertii and S. torgalensis, respectively. Gene ontology showed that around 60% of the annotated genes belonged to four biological processes and approximately 75% to two molecular functions. Besides, this study provides, for the first time, the transcriptome characterization of two endemic fish from Iberian freshwater basins, S. carolitertii and S. torgalensis, and constitutes a valuable resource for understanding environmental adaptations of Iberian Cyprinids.
Data from: Evolution of mating behaviour between two populations adapting to common environmental conditions
Populations from the same species may be differentiated across contrasting environments, potentially affecting reproductive isolation among them. When such populations meet in a novel common environment, this isolation may be modified by biotic or abiotic factors. Curiously, the latter have been overlooked. We filled this gap by performing experimental evolution of three replicates of two populations of Drosophila subobscura adapting to a common laboratorial environment, and simulated encounters at three time points during this process. Previous studies showed that these populations were highly differentiated for several life-history traits and chromosomal inversions. First, we show initial differentiation for some mating traits, such as assortative mating and male mating rate, but not others (e.g., female mating latency). Mating frequency increased during experimental evolution in both sets of populations. The assortative mating found in one population remained constant throughout the adaptation process, while disassortative mating of the other population diminished across generations. Additionally, differences in male mating rate were sustained across generations. This study shows that mating behavior evolves rapidly in response to adaptation to a common abiotic environment, although with a complex pattern that does not correspond to the quick convergence seen for life-history traits.
Data from: How environmental conditions shape the chemical signal design of lizards
1. The signals that animals use to communicate often differ considerably among species. Part of this variation in signal design may derive from differential natural selection on signal efficacy; the ability of the signal to travel efficiently through the environment and attract the receiver's attention. For the visual and acoustic modalities, the effect of the physical environment on signal efficacy is a well-studied selective force. Still, very little is known on its impact on the chemical signalling system. 2. Here, we take a broad, phylogenetic comparative approach to test for a relationship between animals' signal chemistry and properties of their natural environment. Our study focused on lizards from the Lacertidae family. 3. We sampled 64 species across three continents and determined the lipophilic composition of their glandular signalling secretions by using gas chromatography-mass spectrometry (GC-MS). For each species, an array of environmental variables of high temporal and spatial resolution was obtained from climate databases. 4. Species varied considerably in the overall richness (number of constituents) of their secretions, as well as in the relative contribution of the major chemical compound classes. Signal richness and the relative contribution of the respective compounds exhibited little evidence of phylogenetic relatedness, suggesting that chemical signals may change very rapidly. While neither insularity nor substrate use affected chemical signal composition, we found a strong statistical relationship between the chemistry of the lizards' secretions and aspects of the thermal and hydric environment they inhabit. 5. Species from 'xeric' milieus contained high proportions of stable fatty acid esters and high molecular weight alcohols in their glandular secretions, which likely increase the persistence of secretion scent-marks. In contrast, species inhabiting 'mesic' environments produced secretions of a high chemical richness comprising high levels of aldehydes and low molecular weight alcohols. This chemical mix probably creates a volatile-rich signal that can be used for long-distance airborne communication. 6. We argue that the observed variation in chemical signal design results from differential natural selection, optimizing signal efficacy under contrasting environmental conditions.
Data from: Disentangling the effects of environmental conditions on wintering and breeding grounds on age-specific survival rates in a trans-Saharan migratory raptor
Migratory species are subject to environmental variability occurring on breeding and wintering grounds. Estimating the relative contribution of environmental factors experienced sequentially during breeding and wintering, and their potential interaction, to the variation of survival is crucial to predict population viability of migratory species. Here we investigated this issue for the Montagu's harrier Circus pygargus, a trans-Saharan migrant. We analysed capture-recapture data from a 29-yr long monitoring of wing-tagged offspring and adults at two study sites in France (Rochefort-RO & Maine-et-Loire-ML). The study period covers a climatic shift occurring in the Sahel with increasing rainfall following a period of droughts (Sahel greening). We found that harriers' adult survival in RO (between 1988 and 2005) varied over time and was sensitive to the interaction between the amount of rainfall in the Sahel and the annual mean breeding success, two proxies of prey availability. The occurrence of adverse conditions on breeding and wintering grounds in the same year decreased survival from 0.70-0.77 to 0.48 ± 0.05. Juvenile survival in RO was slightly more sensitive to conditions in Europe than in the Sahel. Unexpectedly, lower survival rates were found in years with higher mean breeding success, suggesting compensatory density feedbacks may operate. By contrast, adult survival in ML, monitored between 1999 and 2017, was higher compared to RO (0.76 ± 0.03 vs. 0.66 ± 0.02), remained constant and unaffected by any proxy of prey availability. This difference seems consistent with the fact that harriers in ML experienced better and especially less variable environmental conditions during breeding and wintering seasons compared to RO. Overall, we showed that survival of a migratory bird is sensitive to the level of variability in environmental conditions and that adverse conditions on wintering grounds can amplify the negative effects of conditions during the previous breeding season on birds' survival.
Data from: Environmental conditions limit attractiveness of a complex sexual signal in the túngara frog
Animals choosing particular display sites often balance sexual and natural selection pressures. Here we assess how physical properties of display sites can alter this balance by influencing signal production and attractiveness of the túngara frog (Physalaemus pustulosus). Males that call from very shallow water bodies (few mm depth) benefit from reduced predation risk, but by manipulating water levels, we show that this comes at a cost of reduced attractiveness to females. Our data show that calling from shallower water reduces a male's ability to float, limits the inflation of his vocal sac, and consequently reduces signal conspicuousness in terms of amplitude and complexity. Our results demonstrate that display site properties can set limits on signal production and attractiveness and may hence influence signal evolution. Signallers may shift between sites or engineer their display location, which can play a crucial role in signal divergence and speciation, particularly in a rapidly changing world.
Data from: Do environmental conditions experienced in early life affect recruitment age and performance at first breeding in common goldeneye females?
Environmental conditions experienced early in life may have long-term impacts on life history traits and reproductive performance. We investigated whether ambient temperature experienced during the first two to four weeks of life and weather severity during the first two winters affected recruitment age and relative timing of breeding in the year of recruitment in female common goldeneyes (Bucephala clangula). Our sample consisted of 141 female recruits hatched in a study population in central Finland between 1985 and 2013 and captured later as breeders. About 56% of the recruited females bred for the first time when 2 years old (range 2-6 years). Individuals facing colder ambient temperatures during the first two to four weeks posthatch or more severe winter conditions during the first two winters did not recruit at an older age. Nor did maternal characteristics, relative hatch date or nest site availability affect recruitment age. For females that recruited at 2 years old, the date of first breeding was usually late relative to the population mean that year (mean difference 6.9 days, range -7 to 21 days). Our results suggest developmental buffering enables female goldeneye ducklings to mitigate the impacts of adverse environmental conditions experienced during the first weeks of life, at least in terms of first breeding.
Data from: Natural selection on a measure of parasite resistance varies across ages and environmental conditions in a wild mammal
Parasites detrimentally affect host fitness, leading to expectations of positive selection on host parasite resistance. However, since immunity is costly, host fitness may be maximized at low, but non-zero, parasite infection intensities. These hypotheses are rarely tested on natural variation in free-living populations. We investigated selection on a measure of host parasite resistance in a naturally-regulated Soay sheep population using a longitudinal data set, and found negative correlations between parasite infection intensity and annual fitness in lambs, male yearlings, and adult females. However, having accounted for confounding effects of body weight, the effect was only significant in lambs. Associations between fitness and parasite resistance were environment-dependent, being strong during low-mortality winters, but negligible during harsher high-mortality winters. There was no evidence for stabilising selection. Our findings reveal processes that may shape variation in parasite resistance in natural populations, and illustrate the importance of accounting for correlated traits in selection analysis.
Data from: Migratory shorebird adheres to Bergmann's Rule by responding to environmental conditions through the annual lifecycle
The inverse relationship between body size and environmental temperature is a widespread ecogeographic pattern. However, the underlying forces that produce this pattern are unclear in many taxa. Expectations are particularly unclear for migratory species, as individuals may escape environmental extremes and reorient themselves along the environmental gradient. In addition, some aspects of body size are largely fixed while others are environmentally flexible and may vary seasonally. Here, we used a long‐term dataset that tracked multiple populations of the migratory piping plover Charadrius melodus across their breeding and non‐breeding ranges to investigate ecogeographic patterns of phenotypically flexible (body mass) and fixed (wing length) size traits in relation to latitude (Bergmann's Rule), environmental temperature (heat conservation hypothesis), and migratory distance. We found that body mass was correlated with both latitude and temperature across the breeding and non‐breeding ranges, which is consistent with predictions of Bergmann's Rule and heat conservation. However, wing length was correlated with latitude and temperature only on the breeding range. This discrepancy resulted from low migratory connectivity across seasons and the tendency for individuals with longer wings to migrate farther than those with shorter wings. Ultimately, these results suggest that wing length may be driven more by conditions experienced during the breeding season or trade‐offs related to migration, whereas body mass is modified by environmental conditions experienced throughout the annual lifecycle.
Data from: Genetic architecture of adaptation to novel environmental conditions in a predominantly selfing allopolyploid plant
Genetic architecture of adaptation is traditionally studied in the context of local adaptation, viz. spatially varying conditions experienced by the species. However, human made changes in the natural environment pose a new context to this issue, i.e. adaptation to an environment that is new for the species. In this study, we used crossbreeding to analyze genetic architecture of adaptation to conditions not currently experienced by the species but with high probability of encounter in the near future due to the global climate change. We performed targeted inter-population crossing using genotypes from two core and two peripheral Triticum dicoccoides populations and grew up the parents and three generations of hybrids in a greenhouse under simulated desert conditions to analyze the genetic architecture of adaptation to these conditions and an effect of gene flow from plants having different origin. The observed in allopolyploid T. dicoccoides low importance of epistatic gene interactions and low probability of hybrid breakdown appear to be the result of permanent fixation of heterozygosity and lack of inter-genomic recombination in this species. At the same time, predominant but not complete selfing combined with an advantage of bivalent pairing of homologous chromosomes appear to maintain high genetic variability in T. dicoccoides, greatly enhancing its adaptive ability.
Data from: Parasitism in early life: environmental conditions shape intra-brood variation in responses to infection
Parasites play key ecological and evolutionary roles through the costs they impose on their host. In wild populations, the effect of parasitism is likely to vary considerably with environmental conditions, which may affect the availability of resources to hosts for defense. However, the interaction between parasitism and prevailing conditions is rarely quantified. In addition to environmental variation acting on hosts, individuals are likely to vary in their response to parasitism, and the combined effect of both may increase heterogeneity in host responses. Offspring hierarchies, established by parents in response to uncertain rearing conditions, may be an important source of variation between individuals. Here, we use experimental antiparasite treatment across 5 years of variable conditions to test how annual population productivity (a proxy for environmental conditions) and parasitism interact to affect growth and survival of different brood members in juvenile European shags (Phalacrocorax aristotelis). In control broods, last-hatched chicks had more plastic growth rates, growing faster in more productive years. Older siblings grew at a similar rate in all years. Treatment removed the effect of environment on last-hatched chicks, such that all siblings in treated broods grew at a similar rate across environmental conditions. There were no differences in nematode burden between years or siblings, suggesting that variation in responses arose from intrinsic differences between chicks. Whole-brood growth rate was not affected by treatment, indicating that within-brood differences were driven by a change in resource allocation between siblings rather than a change in overall parental provisioning. We show that gastrointestinal parasites can be a key component of offspring's developmental environment. Our results also demonstrate the value of considering prevailing conditions for our understanding of parasite effects on host life-history traits. Establishing how environmental conditions shape responses to parasitism is important as environmental variability is predicted to increase.
Data from: Importance of antecedent environmental conditions in modeling species distributions
Although species distributions can change in an unexpectedly short period of time, most species distribution models (SDMs) use only long-term averaged environmental conditions to explain species distributions. We aimed to demonstrate the importance of incorporating antecedent environmental conditions into SDMs in comparison to long-term averaged environmental conditions. We modeled the presence/absence of 18 fish species captured across 108 sampling events along a 50-km length of the Sagami River in Japan throughout the 1990s (one to four times per site at 45 sites). We constructed and compared the two types of SDMs: (1) a conventional model that uses only long-term averaged (10-year) environmental conditions; and (2) a proposed model that incorporates environmental conditions 2 years prior to a sampling event (antecedent conditions) together with long-term averages linked to life-history stages. These models both included geomorphological, hydrological, and sampling conditions as predictors. A random forest algorithm was applied for modeling and quantifying the relative importance of the predictors. For seven species, antecedent hydrological conditions were more important than the long-term averaged hydrological conditions. Furthermore, the distributions of two species with low prevalence could not be predicted using long-term averaged hydrological conditions but only using antecedent hydrological conditions. In conclusion, incorporating antecedent environmental factors linked with life-history stages at appropriate time scales can better explain changes in species distribution through time.
Data from: Trophy hunting mediates sex-specific associations between early-life environmental conditions and adult mortality in bighorn sheep
1. Environmental conditions during early development, from conception to sexual maturity, can have lasting consequences on fitness components. Although adult lifespan often accounts for much of the variation in fitness in long-lived animals, we know little about how early environment affects adult lifespan in the wild, and even less about whether these effects differ between the sexes. 2. Using data collected over 45 years from wild bighorn sheep (Ovis canadensis), we investigated the effects of early environment on adult mortality in both sexes, distinguishing between natural and anthropogenic sources of mortality. 3. We used the average body mass of yearlings (at about 15 months of age) as a yearly index of environmental quality. We first examined sex differences in natural mortality responses to early environment by censoring harvested males in the year they were shot. We then investigated sex differences in the effects of early environment on overall mortality (natural and hunting mortality combined). Finally, we used path analysis to separate the direct influence of early environment from indirect influences, mediated by age at first reproduction, adult mass and horn length. 4. As early environmental conditions improved, natural adult mortality decreased in both sexes, although for males the effect was not statistically supported. Sex differences in the effects of early environment on adult mortality were detected only when natural and hunting mortality were pooled. Males that experienced favorable early environment had longer horns as adults and died earlier because of trophy hunting, which does not mimic natural mortality. Females that experienced favorable early environment started to reproduce earlier and early primiparity was associated with reduced mortality, suggesting a silver-spoon effect. 5. Our results show that early conditions affect males and females differently because of trophy hunting. These findings highlight the importance of considering natural and anthropogenic environmental factors across different life stages to understand sex differences in mortality.
Data from: Environmental conditions shape the temporal pattern of investment in reproduction and survival
The relationship between environmental stress exposure and ageing is likely to vary with stressor severity, life history stage, and the time scale over which effects are measured. Such factors could influence whether stress exposure accelerates or slows the ageing process, but their interactions have not previously been experimentally investigated. We found that experimental exposure of zebra finches to mildly challenging environmental circumstances from young to old adulthood, which increased exposure to stress hormones, reduced breeding performance during early adulthood, but had positive effects when individuals were bred in old adulthood. This difference was not due to selective mortality, since the effects were evident within individuals, and no evidence of habituation in the response to the stressor was found. The more stressful environment had no effects on survival during young or old adulthood, but substantially improved survival during middle age. Changes in the effects at different ages could be due to the duration and nature of the challenging exposure, or to variation in coping capacity or strategy with age. These results show that living under challenging environmental circumstances can influence ageing trajectories in terms of both reproductive performance and longevity. Our results provide experimental support for the emerging idea that stress exposure needs to be optimised rather than minimised to obtain the best health outcomes.
Data from: Environmental conditions and biotic interactions acting together promote phylogenetic randomness in semi-arid plant communities: new methods help to avoid misleading conclusions
QUESTIONS: Molecular phylogenies are increasingly used to better understand the mechanisms structuring natural communities. The prevalent theory is that environmental factors and biotic interactions promote the phylogenetic clustering and over-dispersion of plant communities, respectively. However, both environmental filtering and biotic interactions are very likely to interact in most natural communities, jointly affecting community phylogenetic structure. How do environmental filters and biotic interactions jointly affect the phylogenetic structure of plant communities across environmental gradients? LOCATION: Eleven Stipa tenacissima L. grasslands located along an environmental gradient from central to southeast Spain, covering the core of the distribution area of this vegetation type in Europe. METHODS: We jointly evaluated the effects of environmental conditions and plant–plant interactions on the phylogenetic structure – measured with the mean phylogenetic distance index of the studied communities. As an indicator of environmental conditions, we used a PCA ordination including eight climatic variables. Different metrics were used to measure the following processes: (1) competition/facilitation shifts at the entire community level (species combination index), and (2) the effect of microclimatic amelioration provided by the two most important nurse plants on neighbour composition (similarity indices and comparison of the phylogenetic pattern between canopy patches and bare ground areas). RESULTS: Biotic interactions and, to a less extent, environmental conditions affected the phylogenetic pattern of the studied communities. While positive plant–plant interactions (both at community level and the scale of individual nurse plants) increased phylogenetic overdispersion, higher rainfall increased phylogenetic clustering. The opposing effects of environmental conditions and biotic interactions could be the main cause of the overall random phylogenetic structure found inmost of these communities. CONCLUSIONS: Our results illustrate, for the first time, how an overall random phylogenetic pattern may not only be promoted by the lack of influence of either environmental filtering or biotic interactions, but rather by their joint and opposing effects. They caution about making inferences on the underlying mechanisms shaping plant communities from the sole use of their phylogenetic pattern. We also provide a comprehensive set of easy-to-measure tools to avoid misleading conclusions when interpreting phylogenetic structure data obtained from observational studies.
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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.
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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.
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