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837 results for “associational effects”
Effects of maternal genotypic identity and genetic diversity of the red mangrove Rhizophora mangle on associated soil bacterial communities: a field-based experiment
<p>Loss of plant biodiversity can result in reduced abundance and diversity of associated species with implications for ecosystem functioning. In ecosystems low in plant species diversity, such as Neotropical mangrove forests, it is thought that genetic diversity within the dominant plant species could play an important role in shaping associated communities. Here, we used a manipulative field experiment to study the effects of maternal genotypic identity and genetic diversity of the red mangrove <i>Rhizophora mangle</i> on the composition and richness of associated soil bacterial communities. Using terminal restriction fragment length polymorphism (T-RFLP) community fingerprinting, we found that bacterial community composition differed among <i>R. mangle</i> maternal genotypes but not with genetic diversity. Bacterial taxa richness, total soil nitrogen, and total soil carbon were not significantly affected by maternal genotypic identity or genetic diversity of <i>R. mangle</i>. Our findings show that genotype selection in reforestation projects could influence soil bacterial community composition. Further research is needed to determine what impact these bacterial community differences might have on ecosystem processes, such as carbon and nitrogen cycling.</p>
Genetic mechanisms associated with floral initiation and the repressive effect of fruit on flowering in apple (Malus x domestica Borkh)
<p>Many apple cultivars are subject to biennial fluctuations in flowering and fruiting. It is believed that this phenomenon is caused by a repressive effect of developing fruit on the initiation of flowers in the apex of proximal bourse shoots. However, the genetic pathways of floral initiation are incompletely described in apple, and the biological nature of floral repession by fruit is currently unknown. In this study, we characterize the transcriptional landscape of bourse shoot apices in the biennial cultivar, 'Honeycrisp', during the period of floral initiation, in trees bearing a high fruit load and in trees without fruit. Trees with high fruit load produced almost exclusively vegetative growth in the subsequent year, whereas the trees without fruit produced flowers on the majority of the potential flowering nodes. Using RNA-based sequence data, we documented gene expression at high resolution, identifying >11,000 transcripts that had not been previously annotated, and characterized expression profiles associated with vegetative growth and flowering. We also conducted a census of genes related to known flowering genes, organized the phylogenetic and syntenic relationships of these genes, and compared expression among homologs. Several genes closely related to <em>AP1, FT, FUL, LFY, </em>and <em>SPLS </em>were more strongly expressed in apices from non-bearing, floral-determined trees, consistent with their presumed floral-promotive roles. In contast, a homolog of <em>TFL1 </em>exhibited strong and persistent up-regulation only in apices from bearing, vegetative-determined trees, suggesting a roles in floral repression. Additionally, we identified four <em>GIBBERELLIC ACID (GA) 2 OXIDASE </em>genes that were expressed to relatively high levels in apices from bearing trees. These results define the flowering-related transcriptional landscape in apple, and strongly support previous studies implicating both gibberellins and <em>TFL1 </em>as key components in repression of flowering by fruit. </p>
Data from: Effects of species diversity on fine root productivity increase with stand development and associated mechanisms in a boreal forest
There is a growing interest in understanding the relationship between diversity and below-ground productivity due to the critical contribution of below-ground systems to overall terrestrial productivity. Yet, the temporal (seasonal and developmental) changes in diversity effects on below-ground productivity and their underlying mechanisms remain unclear. We hypothesized that (i) diversity effects on fine root productivity increase with stand development, and (ii) increased diversity effects associated with stand development result from augmented horizontal soil space utilization, increased forest floor depth for rooting, enhanced effects in nutrient-poor soil layers and/or foraging towards high nutrient availability. We investigated the effects of tree species diversity on fine root productivity by sampling 18 stands dominated by single species and their mixtures in post-fire boreal forests of two stand ages (8 and 34 years following stand-replacing fire). Species evenness was significantly higher in species mixtures than in single-species-dominated stands at both age classes, while species richness did not differ across stand types and age classes. We found that the annual fine root production was higher in mixtures than the mean of single-species-dominated stands in both stand ages, with a significantly higher magnitude of effects in the 34-year-old than 8-year-old stands. Mixtures had higher horizontal soil volume filling than single-species-dominated stands with a more pronounced increase in the 34-year-old than 8-year-old stands. Compared with the 8-year-old stands, the 34-year-old stands had increased forest floor depth and greater overyielding with soil depth, and their fine root productivity was more responsive to the vertical variation in soil phosphorus concentrations among soil layers. Synthesis. Our results provide evidence for increasing positive diversity effects on fine root productivity with stand development in heterogeneous natural forests. Moreover, our results indicate that the increased positive diversity effects with stand development was the result of multiple mechanisms, including higher horizontal soil volume filling, a thicker forest floor layer for rooting, a higher magnitude of complementarity in nutrient-poor deep soil layers and stronger nutrient foraging towards soil layers with high nutrient concentrations in older than younger stands.
Data from: Cascading effects of thermally-induced anemone bleaching on associated anemonefish hormonal stress response and reproduction
Organisms can behaviorally, physiologically, and morphologically adjust to environmental variation via integrative hormonal mechanisms, ultimately allowing animals to cope with environmental change. The stress response to environmental and social changes commonly promotes survival at the expense of reproduction. However, despite climate change impacts on population declines and diversity loss, few studies have attributed hormonal stress responses, or their regulatory effects, to climate change in the wild. Here, we report hormonal and fitness responses of individual wild fish to a recent large-scale sea warming event that caused widespread bleaching on coral reefs. This 14-month monitoring study shows a strong correlation between anemone bleaching (zooxanthellae loss), anemonefish stress response, and reproductive hormones that decreased fecundity by 73%. These findings suggest that hormone stress responses play a crucial role in changes to population demography following climate change and plasticity in hormonal responsiveness may be a key mechanism enabling individual acclimation to climate change.
Data from: Effects of host genetics and environment on egg-associated microbiotas in brown trout (Salmo trutta)
Recent studies found fish egg-specific bacterial communities that changed over the course of embryogenesis, suggesting an interaction between the developing host and its microbiota. Indeed, single-strain infections demonstrated that the virulence of opportunistic bacteria is influenced by environmental factors and host immune genes. However, the interplay between a fish embryo host and its microbiota has not been studied yet at the community level. To test whether host genetics affects the assemblage of egg-associated bacteria, adult brown trout (Salmo trutta) were sampled from a natural population. Their gametes were used for full-factorial in vitro fertilizations to separate sire from dam effects. In total, 2520 embryos were singly raised under experimental conditions that differently support microbial growth. High-throughput 16S rRNA amplicon sequencing was applied to characterize bacterial communities on milt and fertilized eggs across treatments. Dam and sire identity influenced embryo mortality, time until hatching and composition of egg-associated microbiotas, but no link between bacterial communities on milt and on fertilized eggs could be found. Elevated resources increased embryo mortality and modified bacterial communities with a shift in their putative functional potential. Resource availability did not significantly affect any parental effects on embryo performance. Sire identity affected bacterial diversity that turned out to be a significant predictor of hatching time: embryos associated with high bacterial diversity hatched later. We conclude that both host genetics and the availability of resources define diversity and composition of egg-associated bacterial communities that then affect the life history of their hosts.
Data from: Effectiveness of managed gene flow in reducing genetic divergence associated with captive breeding
Captive breeding has the potential to rebuild depressed populations. However, associated genetic changes may decrease restoration success and negatively affect the adaptive potential of the entire population. Thus, approaches that minimize genetic risks should be tested in a comparative framework over multiple generations. Genetic diversity in two captive-reared lines of a species of conservation interest, Chinook salmon (Oncorhynchus tshawytscha), was surveyed across three generations using genome-wide approaches. Genetic divergence from the source population was minimal in an integrated line, which implemented managed gene flow by using only naturally-born adults as captive broodstock, but significant in a segregated line, which bred only captive-origin individuals. Estimates of effective number of breeders revealed that the rapid divergence observed in the latter was largely attributable to genetic drift. Three independent tests for signatures of adaptive divergence also identified temporal change within the segregated line, possibly indicating domestication selection. The results empirically demonstrate that using managed gene flow for propagating a captive-reared population reduces genetic divergence over the short term compared to one that relies solely on captive-origin parents. These findings complement existing studies of captive breeding, which typically focus on a single management strategy and examine the fitness of one or two generations.
Data from: Strong but opposing effects of associational resistance and susceptibility on defense phenotype in an African savanna plant
The susceptibility of plants to herbivores can be strongly influenced by the identity, morphology, and palatability of neighboring plants. While the defensive traits of neighbors often determine the mechanism and strength of associational resistance and susceptibility, the effect of neighbors on plant defense phenotype remains poorly understood. We used field surveys and a prickle‐removal experiment in a semi‐arid Kenyan savanna to evaluate the efficacy of physical defenses against large mammalian herbivores in a common understory plant, Solanum campylacanthum. We then quantified the respective effects of spinescent Acacia trees and short‐statured grasses on browsing damage and prickle density in S. campylacanthum. We paired measurements of prickle density beneath and outside tree canopies with long‐term herbivore‐exclusion experiments to evaluate whether associational resistance reduced defense investment by decreasing browsing damage. Likewise, we compared defense phenotype within and outside pre‐existing and experimentally created clearings to determine whether grass neighbors increased defense investment via associational susceptibility. Removing prickles increased the frequency of browsing by ~25%, and surveys of herbivory damage on defended leaves suggested that herbivores tended to avoid prickles. As predicted, associational resistance and susceptibility had opposing effects on plant phenotype: individuals growing beneath Acacia canopies (or, analogously, within large‐herbivore exclosures) had a significantly lower proportion of their leaves browsed and produced ca 70–80% fewer prickles than those outside refuges, whereas plants in grass‐dominated clearings were more heavily browsed and produced nearly twice as many prickles as plants outside clearings. Our results demonstrate that associational resistance and susceptibility have strong, but opposing, effects on plant defense phenotype, and that variable herbivore damage is a major source of intraspecific variation in defense phenotype in this system.
Data from: Sex-specific fitness effects of unpredictable early life conditions are associated with DNA methylation in the avian glucocorticoid receptor
Organisms can adapt to variable environments by using environmental cues to modulate developmental gene expression. In principle, maternal influences can adaptively adjust offspring phenotype when early life and adult environments match, but they may be maladaptive when future environments are not predictable. One of the best-studied 'maternal effects' is through modification of the offspring's hypothalamic–pituitary–adrenal (HPA) axis, the neuroendocrine system that controls responses to stress. In addition to the direct transfer of glucocorticoids from mother to offspring, offspring HPA function and other phenotypes can also be affected by epigenetic modifications like DNA methylation of the glucocorticoid receptor promoter. Here we examine how among-year variation in rainfall is related to DNA methylation during development and fitness in adulthood in the superb starling (Lamprotornis superbus), which lives in a climatically unpredictable environment where early life and adult environments are unlikely to match. We found that DNA methylation in the putative promoter of the glucocorticoid receptor gene is reduced in chicks – particularly in males – born following drier prebreeding periods. Additionally, DNA methylation is lower in males that become breeders than those that never breed. However, there is no relationship in females between DNA methylation and the likelihood of dispersing from the natal group to breed elsewhere. These results suggest that early life conditions may positively affect fitness in a sex-specific manner through chemical modification of an HPA-associated gene. This study is the first to show that epigenetic modifications during early life may influence the fitness of free-living organisms adapted to unpredictable environments.
Cost-effectiveness of preventative care for perinatal anxiety and associated disorders: A rapid review
<p><strong>Objectives: </strong>Perinatal mental health (PMH) problems affect one in five women and cost the United Kingdom (UK) £8.1 billion for every year of births, with 72% of this cost due to the long-term impact on the child. We conducted a rapid review of health economic evaluations of preventative care for perinatal anxiety and associated disorders.</p> <p><strong>Design: </strong>This study adopted a rapid review approach, using principles of the standard systematic review process to generate quality evidence. This methodology features a systematic database search, PRISMA diagram, screening of evidence, data extraction, critical appraisal, and narrative synthesis.</p> <p><strong>Data Sources: </strong>PubMed, Cumulative Index to Nursing and Allied Health Literature (CINAHL), Cochrane Library, <em>Applied Social Sciences Index and Abstracts</em> (ASSIA), PsycINFO and MEDLINE.</p> <p><strong>Eligibility criteria for selecting studies: </strong>Studies that evaluated the costs and cost-effectiveness of preventative care for perinatal anxiety and associated disorders carried out within the National Health Service (NHS) and similar healthcare systems.</p> <p><strong>Data extraction and synthesis:</strong> A minimum of two independent reviewers used standardised methods to search, screen, critically appraise and synthesise included studies.</p> <p><strong>Results: </strong>The results indicate a lack of economic evaluation specifically for perinatal anxiety, with most studies focussing on postnatal depression (PND). Interventions to prevent postnatal mental health problems are cost-effective. Modelling studies have also been conducted, which suggest that treating PND with counselling would be cost-effective.</p> <p><strong>Conclusion:</strong> The costs of not intervening in maternal mental health outweigh the costs of preventative interventions. Preventative measures such as screening and counselling for maternal mental health are shown to be cost-effective interventions to improve outcomes for women and children.</p> <p><strong>PROSPERO registration number: </strong>CRD42022347859</p>
FIGURE 1 in Effectiveness of multigene analysis for associating dimorphic partners in flat wasps (Hymenoptera, Bethylidae, Dissomphalus)
FIGURE 1: Bayesian phylogram of Dissomphalus using COI and 28S genes. Posterior probabilities are drawn near the nodes.
FIGURE 3 in Effectiveness of multigene analysis for associating dimorphic partners in flat wasps (Hymenoptera, Bethylidae, Dissomphalus)
FIGURE 3: Dissomphalus verus, female.A. Head, dorsal view; B. Head, frontal view; C. Mesosoma, dorsal view; D. Mesosoma, lateral view. Scale bars = 200 µm.
FIGURE 2 in Effectiveness of multigene analysis for associating dimorphic partners in flat wasps (Hymenoptera, Bethylidae, Dissomphalus)
FIGURE 2: Bayesian phylogram of Dissomphalus using ITS2. Posterior probabilities are drawn near the nodes.
Effects of the fungicide penconazole on the leaf litter associated aquatic mycobiome in artificial stream channel and flask experiments
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Data from: Genomic region associated with run-timing has similar haplotypes and phenotypic effects across three lineages of Chinook salmon
<p><span><span><span><span><span><span><span><span><span><span><span>Conserving life history variation is a stated goal of many management programs, but the most effective means by which to accomplish this are often far from clear. Early, premature migrating and late, mature migrating forms of Chinook salmon face unequal pressure from natural and anthropogenic forces. These forces may result in the diminishment of migration variation in some stocks because migration timing is known to be highly heritable. Genomic regions of chromosome 28 are known to be strongly associated with migration variation in adult Chinook salmon, but it remains unclear whether there is consistent association among the diverse populations of Chinook salmon. Therefore, application of this association for management may be premature. We examined the association of genetic variation in 28 markers on chromosome 28 surveyed with high-throughout genotyping (GT-seq) with individual run timing characteristics gleaned from passive integrated transponder recordings of over 5,000 Chinook salmon from the three phylogeographic lineages that inhabit the Columbia River Basin. Despite the strong genetic differences among them, the three lineages exhibited very similar genetic variants in the chromosome 28 region and moderate to strong association of these variants and run timing phenotypes. This is particularly notable for the interior stream-type lineage, which exhibits an earlier and more constrained migration of fish than the other lineages and which are exclusively premature when they enter freshwater. In both interior stream-type and interior-ocean type Chinook salmon, heterozygotes of the most strongly associated linkage groups are largely intermediate to homozygotes in migration timing, and while we make no robust conclusions about dominance, results indicate codominance or marginal partial dominance of the early migrating allele. Our results lend support to the cautious utilization of chromosome 28 variation in tracking and predicting run timing in these Chinook salmon.</span></span></span></span></span></span></span></span></span></span></span></p>
Effects of cold or warm ischemia and ex-vivo lung perfusion on the release of damage associated molecular patterns and inflammatory cytokines in experimental lung transplantation
<p>Lung transplantation (LTx) is associated with sterile inflammation, possibly related to the release of damage associated molecular patterns (DAMPs) by injured allograft cells. We have measured cellular damage and the release of DAMPs and cytokines in an experimental model of LTx after cold or warm ischemia and examined the effect of pretreatment with ex-vivo lung perfusion (EVLP).</p>
Observational evidence of herbivore-specific associational effects between neighboring conspecifics in natural, dimorphic populations of Datura wrightii
Associational effects – in which the vulnerability of a plant to herbivores is influenced by its neighbors – have been widely implicated in mediating plant-herbivore interactions. Studies of associational effects typically focus on interspecific interactions or pest-crop dynamics. However, associational effects may also be important for species with intraspecific variation in defensive traits. In this study, we observed hundreds of Datura wrightii – which exhibits dimorphism in its trichome phenotype – from over 30 dimorphic populations across California. Our aim was to determine whether a relationship existed between the trichome phenotype of neighboring conspecifics and the likelihood of being damaged by four species of herbivorous insects. We visited plants at three timepoints to assess how these effects vary both within and between growing seasons. We hypothesized that the pattern of associational effects would provide rare-morphs (i.e. focal plants that are a different morph than their neighbors) with an advantage in the form of reduced herbivory, thereby contributing to the negative frequency-dependent selection previously documented in this system. We found the best predictor of herbivory/herbivore presence on focal plants was the phenotype of the focal plant. However, we also found some important neighborhood effects. The total number of plants near a focal individual predicted the likelihood and/or magnitude of herbivory by Tupiochoris notatus, Lema daturaphila, and Manduca sexta. We also found that velvety focal plants with primarily sticky neighbors are more susceptible to infestation by Tupiochoris notatus and Lema daturaphila. This does not align with the hypothesis that associational effects at the near-neighbor scale contribute to a rare-morph advantage in this system. Overall the results of our study show that the number and trichome-morph composition of neighboring conspecifics impact interactions between D. wrightii and insect herbivores.
Fish habitat associations in shoal habitats and implications for climate change effects on species conservation
<p>The dataset and examples of R script used in our analysis.</p>
Some neighbors are better than others: variation in associational effects among plants in an old field community
<p>Consumer-resource interactions are often influenced by other species in the community, such as when neighboring plants increase or reduce herbivory to a focal plant species (known as associational effects). The many studies on associational effects between a focal plant and some neighbor have shown that these effects can vary greatly in strength and direction. But because almost all of these studies measure associational effects from only one or two neighbor species, we know little about the actual range of associational effects that a plant species might encounter in a natural setting. This makes it difficult to determine how important effects of neighbors are in real field settings, and how associational effects might interact with competition and other processes to influence plant community composition. </p> <p>In this study, we used a field experiment with a focal species, <em>Solanum carolinense</em>, and 11 common neighbor species to investigate how associational effects vary among many co-occurring neighbor species and to test whether factors such as neighbor plant apparency, phylogenetic proximity to the focal species, or effects on focal plant defense traits help to explain interspecific variation in associational effect strength. </p> <p>We found that some neighbor species affected <em>S. carolinense</em> damage and attack by specialist herbivores, but associational effects of most neighbors were weak. Associational effects increased herbivore attack on average earlier in the season (associational susceptibility) and reduced herbivore attack on average later in the season (associational resistance) relative to <em>S. carolinense</em> in monoculture. </p> <p>We found some evidence that a neighbor's associational effect was related to its biomass and phylogenetic proximity to the focal species. While neighbor species differed in their effects on physical leaf traits of focal plants (trichome density, specific leaf area, leaf toughness), these traits did not appear to mediate the effects of neighbors on focal plant herbivory. </p> <p><em>Synthesis</em>: Our results suggest that the distribution of associational effect strengths in natural communities are similar to those observed for other interaction types, and that multiple mechanisms are likely acting simultaneously to shape associational effects of different neighbor species.</p>
Crop Diversification Effects on Soil Aggregation and Aggregate-Associated Carbon and Nitrogen in Short-Term Rainfed Olive Groves under SemiaridMediterranean Conditions
<p>Soil particle aggregation and their associated carbon (C) and nitrogen (N) content can<br> provide valuable diagnostic indicators of changes in soil properties in response to the implementation<br> of different agricultural management practices. In this sense, there is limited knowledge regarding the<br> impact of intercropping on soil organic carbon (SOC) and total nitrogen (TN) pools in aggregates. This<br> study aimed to evaluate the short-term effect (4 years) of three crop diversifications in rainfed olive<br> orchards on soil aggregation, SOC and TN concentration and SOC stocks (SOC-S) under semi-arid<br> Mediterranean conditions. Olive orchards were diversified with Crocus sativus (D-S), Vicia sativa and<br> Avena sativa in rotation (D-O) and Lavandula x intermedia (D-L) and compared with monocropping<br> system (CT). Soil samples were collected at two depths (0–10 and 10–30 cm) and analysed for soil<br> aggregate mass, SOC and TN content in aggregate-size fractions obtained by the wet-sieving method.<br> Changes caused by crop diversifications on SOC-S were also determined. Overall, after 4 years,<br> a reduction in aggregation values was observed. However, D-S increased the macroaggregates<br> (>250 m) percentage, Mean Weigh Diameter values, and Geometric Mean Value in the 0–10 cm.<br> Across treatments, aggregate-associated C in 0–10 cm was higher in the D-S treatment, while in<br> the 10–30 cm soil layer, the greatest values were found in CT. Regarding the SOC-S, after 4 years,<br> significant losses were recorded under CT management in 0–10 cm (1.21 Mg ha1) and 10–30 cm<br> (0.84 Mg ha1), while D-O and D-L showed similar values to those obtained at the beginning of the<br> study. The highest increases in SOC-S were found in D-S, with an increase of 5.88% in the 0–10 cm<br> and 14.47% in the 10–30 cm. Our results showed the high potential of the diversified cropping system<br> to increase soil stability and SOC sequestration.</p>
Data from: Backfire effects after correcting misinformation are strongly associated with reliability
<p>The backfire effect is when a correction increases belief in the very misconception it is attempting to correct, and it is often used as a reason not to correct misinformation. The current study aimed to test whether correcting misinformation increases belief more than a no-correction control. Furthermore, we aimed to examine whether item-level differences in backfire rates were associated with test-retest reliability or theoretically meaningful factors. These factors included worldview-related attributes, namely perceived importance and strength of pre-correction belief, and familiarity-related attributes, namely perceived novelty and the illusory truth effect. In two nearly identical experiments, we conducted a longitudinal pre/post design with N = 388 and 532 participants. Participants rated 21 misinformation items and were assigned to a correction condition or test-retest control. We found that no items backfired more in the correction condition compared to test-retest control or initial belief ratings. Item backfire rates were strongly negatively correlated with item reliability (⍴ = -.61 / -.73) and did not correlate with worldview-related attributes. Familiarity-related attributes were significantly correlated with backfire rate, though they did not consistently account for unique variance beyond reliability. While there have been previous papers highlighting the non-replicable nature of backfire effects, the current findings provide a potential mechanism for this poor replicability. It is crucial for future research into backfire effects to use reliable measures, report the reliability of their measures, and take reliability into account in analyses. Furthermore, fact-checkers and communicators should not avoid giving corrective information due to backfire concerns.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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.