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359 results for “trait associations”
Data from: Integrating Bayesian genomic cline analyses and association mapping of morphological and ecological traits to dissect reproductive isolation and introgression in a Louisiana Iris hybrid zone
Hybrid zones provide unique opportunities to examine reproductive isolation and introgression in nature. We utilized 45,384 Single Nucleotide Polymorphism (SNP) loci to perform association mapping of 14 floral, vegetative, and ecological traits that differ between Iris hexagona and Iris fulva, and to investigate, using a Bayesian Genomic Cline (BGC) framework, patterns of genomic introgression in a large and phenotypically diverse hybrid zone in southern Louisiana. Many loci of small effect-size were consistently found to be associated with phenotypic variation across all traits, and several individual loci were revealed to influence phenotypic variation across multiple traits. Patterns of genomic introgression were quite heterogeneous throughout the Louisiana Iris genome, with I. hexagona alleles tending to be favored over those of I. fulva. Loci that were found to have exceptional patterns of introgression were also found to be significantly associated with phenotypic variation in a small number of morphological traits. However, this was the exception rather than the rule, as most loci that were associated with morphological trait variation were not significantly associated with excess ancestry. These findings provide insights into the complexity of the genomic architecture of phenotypic differences and are a first step towards identifying loci that are associated with both trait variation and reproductive isolation in nature.
Associations between metabolic traits and growth rate in brown trout (Salmo trutta) depend on thermal regime
<p class="academicstyle"><span><span><span><span><span><span><span><span><span><span><span>Metabolism defines the energetic cost of life, yet we still know relatively little about why intraspecific variation in metabolic rate arises and persists. Spatiotemporal variation in selection potentially maintains differences, but relationships between metabolic traits (standard metabolic rate (SMR), maximum metabolic rate (MMR), and aerobic scope) and fitness across contexts are unresolved. We show that associations between SMR, MMR, and growth rate (a key fitness-related trait) vary depending on thermal regime (a potential selective agent) in offspring of wild-sampled brown trout from two populations reared for ~15 months in either a cool or warm (+ 1.8°C) regime.<i> </i>SMR was positively related to growth in the cool, but negatively related in the warm regime. The opposite patterns were found for MMR and growth associations (positive in warm, negative in cool regime). Mean SMR, but not MMR, was lower in warm regimes within both populations (i.e., basal metabolic costs were reduced at higher temperatures), consistent with an adaptive acclimation response that optimises growth. Metabolic phenotypes thus exhibited a thermally sensitive metabolic 'floor' and a less flexible metabolic 'ceiling'. Our findings suggest a role for growth-related fluctuating selection in shaping patterns of metabolic variation that is likely important in adapting to climate change.</span></span></span></span></span></span></span></span></span></span></span></p>
Trait-habitat associations explain novel bird assemblages mixing native and alien species across New-Zealand landscapes
<p><strong>Aim</strong>: Species introductions have reshaped island faunas for the last 200 years, often threatening native biodiversity. Approximately equal numbers of native and alien species currently co-occur in the New Zealand avifauna, but they show distinct habitat use. Antagonistic interactions, habitat affinities and legacies of introduction history may concur to explain their segregation along habitat gradients. To investigate these processes, we explored how habitat, ecological traits and introduction history relate with the current composition of bird assemblages.</p> <p><strong>Location</strong>: New Zealand</p> <p><strong>Taxon</strong>: Birds</p> <p><strong>Methods</strong>: We analysed 917 bird point counts spread along habitat and elevation gradients in the Canterbury region, South Island, and related 10 ecological traits to landscape composition using a three-table ordination method known as 'RLQ analysis', accounting for spatial autocorrelation and phylogeny. We tested whether alien species' positions in the RLQ were related to proxies of introduction history.</p> <p><strong>Results</strong>: Eighteen endemic, 11 native and 19 alien species were distributed along a gradient from forest to open-habitat assemblages, in relation to foraging mode, nesting site and body size. A second gradient segregated species between native and exotic forests according to territoriality, sedentarity and diet. Traits accounted for the separation of native and alien bird species in forests, but not in open habitats. Phylogenetic signals emerged from the separation of native and alien species by forest type, and spatial structures suggested a landscape-level, rather than regional or local determinism. These correlations were independent of introduction history, although open-habitat assemblages tended to host alien species introduced later in time. </p> <p><strong>Main conclusions: </strong>Habitat type and resource availability explain the spatial partitioning of New Zealand bird assemblages between native and alien species more consistently than competitive exclusion. We conclude that trait-mediated ecological differences among species have likely played a predominant role in species' segregation among landscapes, while maintaining endemic bird assemblages in native forests. </p>
Data set for: Genetic dissection of marker trait associations for grain micro-nutrients and thousand grain weight under heat and moisture deficit stress conditions in wheat
<p>The study material in the GWAS panel with 193 bread wheat genotypes from Indian and exotic collections was selected to map the genomic regions responsible for grain iron and Zinc content under drought and heat stress treatments.</p> <p>Phenotypic data:</p> <p>The GWAS panel was evaluated at IARI, New Delhi - DL (28.6550° N, 77.1888° E, MSL 228.61 m) under Irrigated (IR), Restricted Irrigated (RI) and Late sown (LS) treatment conditions over 2 years i.e. 2020 and 2021 with augmented RCBD design. Data was collected on Grain Iron and Grain zinc content along with thousand-grain weight. Around 20 g of grain sample from each of 282 genotypes from the GWAS panel under all three conditions were used for phenotyping GFeC and GZnC through high-throughput Energy Dispersive X-ray Fluorescence (ED-XRF) machine (model X-Supreme 8000; Oxford Instruments plc, Abingdon, United Kingdom) calibrated with glass beads-based values. To record TGW, manual counting of grains was followed and the weight of the grains was recorded in grams with an electronic balance.</p> <p>Genotypic data:</p> <p>Genomic DNA of the GWAS panel was extracted from the leaves of seedlings by Cetyl Trimethyl Ammonium Bromide (CTAB) method. The panel was genotyped using Axiom Wheat Breeder's Genotyping Array (Affymetrix, Santa Clara, CA, United States) having 35,143 genome-wide SNPs. The monomorphic, markers with minor allele frequency (MAF) of <5%, missing data of >10%, and heterozygote frequency >50% were removed from the analysis. The remaining set of 13,947 high-quality SNPs was used in GWAS analysis.</p>
Data and code for: Functional traits mediate individualistic species-environment distributions at broad spatial scales while fine-scale species' associations remain unpredictable
<p>Ecological communities are structured by a diverse set of processes acting at different spatial scales. In plant communities, assembly processes like ecological sorting, limiting similarity, and stochastic events are all expected to influence plant distributions and co-occurrence patterns. We assembled a data set describing the distribution of 139 herbaceous plant species within and among 257 forest stands in Wisconsin (USA) to elucidate the spatial scales at which these assembly processes operate. Analyses of these data in conjunction with detailed information about environmental conditions, plant functional traits, and phylogenetic relationships provided new insights into the scale-dependent drivers of plant community assembly in temperate forest understories. Traits like leaf height, specific leaf area, and seed mass all influenced individualistic plant distributions along landscape-scale gradients in soil texture, soil fertility, light availability, and climate while phylogenetic relationships did not predict species-environment relationships. These findings point to the importance of trait-mediated ecological sorting in shaping individualistic plant distributions at broad spatial scales. Contrary to our expectations about the importance of limiting similarity at local scales, neither functionally similar nor phylogenetically related herbs segregated among microsites within forest stands. We hypothesize strong ecological sorting among forest stands coupled with stochastic fine-scale interactions among species appear deterministic, niche-based assembly processes at local scales.</p>
Data from: Dual function and associated costs of a highly exaggerated trait in a cichlid fish
<p><span><span><span><span><span><span><span><span><span><span><span>Exaggerated secondary sexual characteristics are apparently costly and seem to defy natural selection. This conundrum prompted Charles Darwin to propose the theory of sexual selection. Accordingly, exaggerated secondary sexual characteristics might be ornaments on which female choice is based and/or armaments used during male-male competition. Males of many cichlid fish species, including the adaptive radiation of Nicaraguan Midas cichlids, develop a highly exaggerated nuchal hump, which is thought to be a sexually selected trait. To test this hypothesis, we conducted a series of behavioral assays in F2 hybrids obtained from crossing a species with a relatively small hump and one with an exaggerated hump. Mate-choice experiments showed a clear female preference for males with large humps. In an open-choice experiment with limited territories, couples including large humped males were more successful in acquiring these territories. Therefore, nuchal humps appear to serve dual functions as an ornament for attracting mates and as an armament for direct contest with rivals. Although being beneficial in terms of sexual selection, this trait also imposes fitness costs on males possessing disproportionally large nuchal humps since they exhibit decreased endurance and increased energetic costs when swimming. We conclude that these costs illustrate trade-offs associated with large hump size between sexual and natural selection, which causes the latter to limit further exaggeration of this spectacular male trait.</span></span></span></span></span></span></span></span></span></span></span></p>
Phenotypic traits evolution and morphological traits associated with echolocation calls in cryptic horseshoe bats (Rhinolophidae)
<p><span>Bats provide an excellent case study for studying evolution due to their remarkable flight and echolocation capabilities. In this study, we sought to understand the phenotypic evolution of key traits in Rhinolophidae (horseshoe bats) using phylogenetic comparative methods. We aim to test the phylogenetic signals of traits and evaluated the best-fit evolutionary models given the data for each trait considering different traits may evolve under different models (i.e., Brownian Motion (BM), Ornstein-Uhlenbeck (OU) and Early Burst (EB)) and reconstruct ancestral character states. We examined how phenotypic characters are associated with echolocation calls and minimum detectable prey size. We measured 34 traits of 10 Asian rhinolophids species (187 individuals). We found that the majority of traits showed a high phylogenetic signal based on Blomberg's K and Pagel's λ, but each trait may evolve under different evolutionary models. Sella traits were shown to evolve under stabilizing selection based on OU models, indicating sella traits have the tendency to move forward along the branches toward some medial value in equilibrium. Our findings highlight the importance of sella characters in association with echolocation call emissions in Rhinolophidae, as calls are important for spatial cognition and also influence dietary preferences. Minimum detectable prey size in Rhinolophidae was associated with call frequency, bandwidth, call duration, wingspan and wing surface area. Ultimately, understanding trait evolution requires sensitivity due to the differential selective pressures which may apply to different characteristics.</span></p>
Data for: Dissecting the genetic architecture of leaf morphology traits in mungbean (Vigna radiata (L.) Wizcek) using genome‐wide association study
<p><span>Mungbean (<em>Vigna radiata</em> (L) Wizcek) is an important pulse crop, increasingly used as a source of protein, fiber, low fat, carbohydrates, minerals, and bioactive compounds in human diets. Mungbean is a dicot plant with trifoliate leaves. Leaves are central to various plant processes like photosynthesis, light interception, and overall canopy structure. The objectives were to study leaf morphological traits, use image analysis to extract leaf traits from images from the Iowa Mungbean Diversity (IMD) panel, develop a regression model for the prediction of leaflet area, and conduct association mapping for leaf morphological traits. We collected more than 5000 leaf images of the IMD panel consisting of 484 accessions over two years (2020 and 2021) with two replications per experiment. Leaf traits were extracted using image analysis, analyzed, and used for association mapping. Morphological diversity included leaflet type (oval or lobed), leaflet size (small, medium, large), lobed angle (shallow, deep), and vein coloration (green, purple). A regression model was developed to predict each ovate leaflet's area (adjusted R<sup>2</sup> = 0.97; residual standard errors of <= 1.10). The candidate genes <em>Vradi01g07560</em>, <em>Vradi05g01240</em>, <em>Vradi02g05730</em>, and <em>Vradi03g00440</em>, are associated with multiple traits (length, width, perimeter, and area) across the leaflets (left, terminal, and right). These are suitable candidate genes for further investigation in their role in leaf development, growth, and function. Future studies will be needed to correlate the observed traits discussed here with yield or important agronomic traits for use as phenotypic or genotypic markers in marker-aided selection methods for mungbean crop improvement.</span></p>
Variation and association of leaf traits for desert plants in the arid area, northwest China
<p><span>Characterizing variation and association of plant traits is critical for understanding plant adaptation strategies and community assembly mechanisms. However, little is known about the leaf trait variations of desert plants and their association with different life forms. We used principal component analysis, Pearson's correlation, phylogenetic independent contrasts, linear mixed model, and variance decomposition to explore the variation and association of 10 leaf traits in 22 desert plants in the arid area of northwest China. We found that: (1) the contribution of interspecific variation to the overall variation was greater than the intraspecific variation of all the studied leaf traits; (2) intraspecific and interspecific variation in leaf traits differed among life forms. Some leaf traits, such as tissue density of shrubs and specific leaf area of herbs, exhibited greater intraspecific than interspecific variation, while other traits exhibited the inverse; (3) desert shrubs corroborate the leaf economic spectrum hypothesis and had a fast acquisitive resource strategy, but herbs may not conform to this hypothesis; (4) there were trade‐offs between leaf traits, which were mediated by phylogeny. Overall, our results suggest that interspecific variation of leaf traits significantly contributes to the total leaf traits variation in desert plants. However, intraspecific variation should not be overlooked. There are contrasts in the resource acquisition strategies between plants life forms. Our results support understanding of the mechanisms underlying community assembly in arid regions and suggest that future works may focus on the variation and association of plant traits at both intra‐ and interspecific scales.</span></p>
Effects of long-term mowing on leaf- and root-associated bacterial community structures are linked to functional traits in 11 plant species from a temperate steppe
<ol> <li><span>Long-term mowing can cause morphological stuntedness of plants, thus reducing grassland productivity and exacerbating grassland degradation. Although plant microbiomes can enhance plant resistance against disturbance, considerable uncertainty exists regarding how mowing and mowing-induced plant trait plasticity affect plant microbiomes in natural grasslands. </span></li> <li><span>Here we examined the responses of leaf-/root-associated bacterial (LAB/RAB) communities of 11 dominant herbaceous perennials (6 replicates per species) to a 17-year mowing treatment in a temperate grassland. We also measured leaf/root physiological and morphological traits and analyzed the relationships among mowing practice, bacterial community structures, and leaf/root trait parameters. </span></li> <li><span>We found that both leaf and root functional traits showed interspecific variations (variations across different plant species), while only the leaf traits exhibited intraspecific variation (treatment-induced variations within plant species) between the treatments. Similarly, the LAB community structure was more sensitive to mowing but less influenced by host species identity, compared to the RAB community. The RAB community structure was primarily shaped by host species identity, while mowing was a secondary influencing factor. </span></li> <li> <span>The different patterns of LAB and RAB communities in response to mowing could be specifically explained by the inter-/intraspecific variations of the related leaf and root traits. The LAB community was strongly correlated with the leaf traits which exhibited mowing-induced plasticity (intraspecific variation), with the correlations with nitrogen resorption efficiency and aboveground dry weight being the greatest. The root traits were important indicators of bacterial community structure in the root compartment across the hosts, rather than between the treatments. Root tissue density</span> <span>showed the strongest interspecific variation, and was identified as an overwhelming driver of the RAB community. The shifts in LAB/RAB communities under mowing were largely attributed to the increased proportions of Actinobacteria. The high mowing sensitivity of the LAB community was associated with the enrichment of soil-derived Actinobacteria in leaves under mowing. Actinobacteria were also the main keystone taxa in the bacterial community networks under mowing.</span> </li> <li><span>Our results demonstrate that the magnitude of plant-associated microbial community response to long-term mowing is plant compartment- and trait-variation-dependent, and advance our understanding of the leaf/root microbiome-trait relationships in complex plant communities.</span></li> </ol>
Winter range shifts and their associations with species traits are heterogeneous in eastern North American birds
<p>Many species' distributions are shifting in response to climate change. Many distributional shifts are predictably poleward or higher in elevation, but heterogeneity in the rate and direction of shifts both within and between species appears to be common. We found high heterogeneity in the trajectory of winter range shifts for 65 species of birds across eastern North America and in the different traits and trait interactions associated with these shifts across the spatial scales we examined. We used data from the Christmas Bird Count to quantify the trajectory of winter latitudinal center of abundance range shifts over four decades (1980–2019) for 65 species of songbirds and woodpeckers in North America, both across eastern North America (ENA) as a whole and for the Atlantic (ATL) and Mississippi (MISS) flyways separately. We then used linear models and AICc model selection to test whether species traits could explain variation in range shifts or flyway discrepancies. Across ENA, most species showed northward latitudinal range shifts, but some showed no latitudinal shift while others shifted southwards. Amongst ATL and MISS, we documented both within- and between-species differences in the rate and direction of latitudinal shifts, complicating the results from across ENA. No single trait emerged as a dominant driver of range shift differences at the ENA and flyway scales. Migration strategy interacted with insectivory to explain variation at the largest spatial scale (ENA), whereas frugivory and mean winter latitude explained much of the variation in ATL and MISS, respectively. Exploring heterogeneity in range shifts within and between species, and in the associations between range shifts and life history traits, will help us better understand the mechanisms that mediate differing responses to environmental change and predict which species will be better able to adapt to those changes. </p>
Data from: Trait-dependent associations between early- and late-life reproduction in a wild mammal
<p>Early- versus late-life trade-offs are a central prediction of life-history theory that are expected to shape the evolution of ageing. While ageing is widely observed in wild vertebrates, evidence that early–late trade-offs influence ageing rates remains limited. Vertebrate reproduction is a complex, multi-stage process, yet few studies have examined how different aspects of early-life reproductive allocation shape late-life performance and ageing. Here, we use longitudinal data from a 36-year study of wild Soay sheep to show that early-life reproduction predicts late-life reproductive performance in a trait-dependent manner. Females that started breeding earlier showed more rapid declines in annual fecundity with age, consistent with a trade-off. However, age-related declines in offspring first-year survival and birth weight were not associated with early-life reproduction. Selective disappearance was evident in all three late-life reproductive measures, with longer-lived females having higher average performance. Our results provide mixed support for early–late reproductive trade-offs and show that the way early-life reproduction shapes late-life performance and ageing can differ among reproductive traits.</p>
PLINK association test statistics of UK Biobank blood traits
<p>PLINK association test statistics of UK Biobank blood traits generated for mvSuSiE fine-mapping analyses; see https://www.biorxiv.org/content/10.1101/2023.04.14.536893.</p>
Identification of quantitative trait loci and associated candidate genes for pregnancy success in Angus – Brahman crossbred heifers
<p>Development of genomic tools to identify females with high genetic merit for reproductive function could increase the profitability and sustainability of beef production. Here, genome-wide association studies (GWAS) were performed on pregnancy outcome traits from a population of Angus – Brahman crossbred heifers. Furthermore, a validation GWAS was performed using data from another location. Heifers were genotyped with the Bovine GGP F250 array that contains ~250,000 SNPs. In the discovery population, heifers were bred in winter breeding seasons involving a single round of timed artificial insemination (AI) followed by natural mating for three months. Three phenotypes were analyzed: pregnancy outcome to first-service AI (PAI; n = 1481), pregnancy status at the end of the breeding season (PEBS; n = 1725), and pregnancy score (Pregscore where 1 = pregnant to first-service AI, 2 = pregnant to bull, 3 = not pregnant; n =1481). The heritability for PAI was estimated as 0.149. One large quantitative trait locus (QTL) that explained ~3% of the genetic variation for PAI was found on BTA7, in a region containing a cluster of γ-protocadherin genes and SLC25A2. Other QTLs explaining between 0.5-1% of the genetic variation were found on BTA12 and 25. The heritability of PEBS was estimated at 0.122. A large QTL on BTA7 was synonymous with the QTL for PAI, with minor QTL located on BTA5, 9, 10, 11, 19, and 20. Estimated heritability for Pregscore was 0.189. There was a large QTL on BTA7 synonymous with the other two traits as well as smaller QTLs on BTA1, 10, 15, 18, 19, and 20. The validation population for pregnancy status at the end of the breeding season were Angus-Brahman crossbred heifers bred by natural mating. In concordance with the discovery population, the large QTL on BTA7 and QTL on BTA10, 12 and 18 were identified. In summary, QTL and candidate SNPs associated with pregnancy outcomes in beef heifers were identified, including a large QTL associated with a group of protocadherin genes. Confirmation of these associations with larger populations could lead to the development of genomic estimates of reproductive function in beef cattle.</p>
Data from: Loss of pigments in females is associated with sexual dichromatism in an ornamental trait
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Data set for: Genetic dissection of marker trait associations for grain micro-nutrients and thousand grain weight under heat and moisture deficit stress conditions in wheat
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Data from: Vertical niche usage and trait associations in Gabonese amphibians
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Data from: Genomic variation across two barn swallow hybrid zones reveals traits associated with divergence in sympatry and allopatry
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Data from: The effect of root-associated microbes on plant growth and chemical defence traits across two contrasted elevations,
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Static allometries of caste-associated traits vary with genotype but not environment in the clonal raider ant
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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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