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1,363 results for “phenotypic data”
Data from: A camera trap based assessment of climate-driven phenotypic plasticity of seasonal moulting in an endangered carnivore
<p>For many species, the ability to rapidly adapt to changes in seasonality is essential for long-term survival. In the Arctic, seasonal moulting is a key life history event that provides year-round camouflage and thermal protection. However, increased seasonal variability can lead to phenological mismatch. In this study, we investigated whether winter-white (white morph) and winter-brown (blue morph) Arctic foxes (<em>Vulpes lagopus</em>) could adjust their winter-to-summer moult to match local environmental conditions. We used camera trap images spanning an eight-year period to quantify the timing and rate of fur change in a polymorphic subpopulation in south-central Norway. Seasonal snow cover duration and temperature governed the phenology of the spring moult. We observed a later onset and longer moulting duration with decreasing temperature and longer snow season. Additionally, white foxes moulted earlier than blue in years with shorter periods of snow cover and warmer temperatures. These results suggest that phenotypic plasticity allows Arctic foxes to modulate the timing and rate of their spring moult as snow conditions and temperatures fluctuate. With the Arctic warming at an unprecedented rate, understanding the capacity of polar species to physiologically adapt to a changing environment is urgently needed in order to develop adaptive conservation efforts. Moreover, we provide the first evidence for variations in the moulting phenology of blue and white Arctic foxes. Our study underlines the different intraspecific selective pressures that can exist in populations where several morphs co-occur, and illustrates the importance of integrating morph-based differences in future management strategies of such polymorphic species.</p>
Data from: Detecting macroevolutionary genotype-phenotype associations using error-corrected rates of protein convergence
<p><span>On macroevolutionary timescales, extensive mutations and phylogenetic uncertainty mask the signals of genotype-phenotype associations underlying convergent evolution. To overcome this problem, we extended the widely used framework of nonsynonymous-to-synonymous substitution rate ratios and developed the novel metric <em>ω<sub>C</sub></em>, which measures the error-corrected convergence rate of protein evolution. While </span><span><em>ω<sub>C</sub></em></span><span> distinguishes natural selection from genetic noise and phylogenetic errors in simulation and real examples, its accuracy allows an exploratory genome-wide search of adaptive molecular convergence without phenotypic hypothesis or candidate genes. Using gene expression data, we explored over 20 million branch combinations in vertebrate genes and identified the joint convergence of expression patterns and protein sequences with amino acid substitutions in functionally important sites, providing hypotheses on undiscovered phenotypes. We further extended our method with a heuristic algorithm to detect highly repetitive convergence among computationally nontrivial higher-order phylogenetic combinations. Our approach allows bidirectional searches for genotype-phenotype associations, even in lineages that diverged for hundreds of millions of years.</span></p>
FIGURE 31 in Anatolian endemic genus Bolua (Orthoptera: Tettigoniidae: Tettigoniinae): genetic and phenotypic data indicate inconsistent diversity and evolutionary patterns
FIGURE 31. The ML tree showing unique base changes per phylogroups of Bolua, obtained by maximum parsimony analysis (the base position indicates by the position number in the concatenated matrix)
FIGURES 28–30 in Anatolian endemic genus Bolua (Orthoptera: Tettigoniidae: Tettigoniinae): genetic and phenotypic data indicate inconsistent diversity and evolutionary patterns
FIGURES 28–30. Song in Bolua (28—B. balikesirensis from Balıkesir; 29—and 30—B. bursaensis from Bursa and Kütahya, respectively; A, B and C show song at three different time scale)
FIGURES 18–26. 18–20 in Anatolian endemic genus Bolua (Orthoptera: Tettigoniidae: Tettigoniinae): genetic and phenotypic data indicate inconsistent diversity and evolutionary patterns
FIGURES 18–26. 18–20. Female head+pronotum+tegmina in Bolua (18—B. turkiyae, 19—B. balıkesirensis, 20—B. bursaensis; D—dorsal view, L—lateral view). 21–23. Female subgenital plate in Bolua (21—B. turkiyae, 22—B. balıkesirensis, 23—B. bursaensis; V—ventral view, L-lateral view). 24–26. Ovipositor in Bolua (24—B. turkiyae, 25—B. balıkesirensis, 26— B. bursaensis)
FIGURE 2 in Anatolian endemic genus Bolua (Orthoptera: Tettigoniidae: Tettigoniinae): genetic and phenotypic data indicate inconsistent diversity and evolutionary patterns
FIGURE 2. Phylogenetic tree, chronogram and taxonomic pattern obtained from the matrix constituted by concatenation of COI+NAD2+VAL+ITS sequences. The bootstrap (ML)/ posterior probability (BI) supports to the node are given above the node and the time to the most recent common ancestor (TMRCA) and the 95% HPD as million years below the node. The results from the species delimitation test are indicated by a bar line.
FIGURE 27 in Anatolian endemic genus Bolua (Orthoptera: Tettigoniidae: Tettigoniinae): genetic and phenotypic data indicate inconsistent diversity and evolutionary patterns
FIGURE 27. The PCA plots and trait contribution prepared from the metric data sets of male and female individuals belonging to Bolua
FIGURE 1 in Anatolian endemic genus Bolua (Orthoptera: Tettigoniidae: Tettigoniinae): genetic and phenotypic data indicate inconsistent diversity and evolutionary patterns
FIGURE 1. Distribution of Bolua [for detail of the localities see material examined per species; Bolu(1), Kastamonu (2,3,4, 6), Karabük (5), Çankırı (7), Balıkesir (8), Bursa (9, 10), Kütahya (11) and Kocaeli (12, 13)]
FIGURES 3–17. 3–5 in Anatolian endemic genus Bolua (Orthoptera: Tettigoniidae: Tettigoniinae): genetic and phenotypic data indicate inconsistent diversity and evolutionary patterns
FIGURES 3–17. 3–5. Male head+pronotum+tegmina in Bolua (3—B. turkiyae, 4—B. balıkesirensis, 5—B. bursaensis; D— dorsal view, L—lateral view). 6–8. Male anal tergite in Bolua (6—B. turkiyae, 7—B. balıkesirensis, 8—B. bursaensis). 9–11. Male cercus in Bolua (9—B. turkiyae, 10—B. balıkesirensis, 11—B. bursaensis). 12–14. Male subgenital plate in Bolua (12—B. turkiyae, 13—B. balıkesirensis, 14—B. bursaensis). 15–17. Titillators in Bolua (15—B. turkiyae, 16—B. balıkesirensis, 17—B. bursaensis)
Data for the Arcadia Phenotype-o-mat pub
<p>This is the data used in the Arcadia phenotype-o-mat pub which is available <a href="https://doi.org/10.57844/arcadia-112f-5023">here</a>.</p> <p>The repository containing the analysis code for these data is available <a href="https://github.com/Arcadia-Science/2024-phenotypeomat">here</a>.</p> <p>This data repository contains two data sets from two species, <em>Chlamydomonas reinhardtii </em>and <em>Chlamydomonas smithii.</em></p> <p>The data sets are chlorophyll fluorescence from colonies streaked on petri dishes (chlorophyll_fluorescence_data.tar.gz) and multi-wavelength reflectance data from colonies in 96 well format (reflectance_data.tar.gz).</p>
Data for: Phenotypic variation of hydraulic traits for woody species
<p>Hydraulic traits are major determinants of plant fitness, thus exerting control over vegetation structure, function and distribution. Yet it remains unclear whether and how hydraulic traits respond to environmental stimuli (i.e., phenotypic variation of hydraulic traits; PVHT), and if the coordination between different hydraulic traits and the trait-climate relationship are affected by PVHT.</p> <p>Here, we synthesized data of PVHT (maximum hydraulic conductivity and water potential inducing 50% loss of hydraulic conductivity) as well as potentially related morphological and anatomical traits (e.g. sapwood density, branch Huber value, mean and hydraulic weighted conduit diameter). We analyzed the magnitude, direction and source of variation of the plastic response, as well as the influence of environmental factors on trait coordination. Additionally, we compared the intra- and inter- specific variation between key hydraulic traits and climate metrics (mean annual precipitation and mean annual temperature) at the site of growth, as well as across the population range.</p> <p>PVHT was highly variable in both magnitude and direction, which was contingent on the environmental factor. The variation in PVHT mainly occurred at high taxonomic levels (i.e., family and genus), whereas phenology explained little variation for PVHT. Despite the high variability, trait correlation remained robust in the presence of environmental stimuli. Moreover, trait-climate relationships differed at inter-specific and intra-specific levels. The intra-specific variation of hydraulic traits in most species showed no correlation with climate metrics compared with the high correlation of hydraulic traits with climate metrics across species.</p> <p>Our findings suggest that the high variability of PVHT does not affect the trait correlation which may be valuable in predicting vegetation dynamics under varying environments. The distinct trait-climate relationships highlight the need to unravel the driving force of PVHT, as well as the adaptive strategy across populations.</p>
Data from: Pilot study demonstrating potential association between breast cancer image-based risk phenotypes and genomic biomarkers.
<p>Genotype data from</p> <p>Li H, Giger ML, Sun C, Ponsukcharoen U, Huo D, Lan L, Olopade OI, Jamieson AR, Brown JB, Di Rienzo A. (2014) Pilot study demonstrating potential association between breast cancer image-based risk phenotypes and genomic biomarkers. Med Phys. 41(3)</p>
Data from: Phenotypic correlates between clock genes and phenology among populations of Diederik cuckoo, Chrysococcyx caprius
<p>Dataset of Clock genes for Diederik Cuckoos collected as part of a migration genetics study.</p>
Phenotypic landscape of schizophrenia-associated genes defines candidates and their shared functions - behavior data
<p>Processed behavior data for all zebrafish behavior runs included in manuscript. This includes data such as bouts / minute. The raw data used to generate this processed output is available upon request (too large for any public repository). These files can be used to generate all statistics and graphs using the script statsandgraphs.py (https://github.com/sthyme/ZFSchizophrenia/tree/master/BehaviorAnalysis). Each directory also contains scripts used, genotyping information, and output files for the statistical analyses presented in the manuscript.</p>
Supporting data and code for: Dissecting the transcriptomic basis of phenotypic evolution in the aquatic keystone grazer Daphnia: Part I
<p>Main codes for Dissecting the transcriptomic basis of phenotypic evolution in the aquatic keystone grazer Daphnia.</p>
Simulation and empirical data for "Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations"
<p>Simulation data and empirical data used to generate figures from "Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations". Can be used with code provided on the associated github to regenerate the figures. </p>
BRESOV WP5 Common Bean, phenotypic data
<p>Partners P6-FiBL, P11-VRDS, P16-SERIDA, P18-ITAKA, P21-SECL conducted 2 years of trials except P11-VRDS who conducted 3 years, the first two of them in two locations each. The file BRESOV_BEAN_DATA_descriptors.xlsx contains the list of all the cultivars/lines tested per partner and year, as well as all the descriptors used in the data files. For each trait the average value of the repetitions is reported.</p> <p>P6-FiBL: <br>Trials were conducted in spring/summer 2020 and 2021 at an organic farming cooperative in Dietikon, Switzerland. Plots are randomly distributed per block. Blocks are four seed beds.<br>In 2020, the trial was sown on the 3rd of July (direct sowing), almost 2 months later than normal in this location due to the late availability of seeds from the seed multiplication. The 8 varieties were cultivated in 4 plots per variety for an outcome of approx. 25 Plants/m2 outcome, 9.375m2 per plot, half of each plot was harvested green (the data in this dataset) and the rest was left to be harvested as dry beans (dry beans data not included). <br>In 2021, seed were sown on 10.05.2021 in rows spaced 0.5m, at a density of 25-35 plant/m2, in 17.6m2 per variety plot and 4 repetitions per variety. No fertilizer was applied. The harvest of green beans was carried 3 times a week from 07 July to 09 August 2021. </p> <p>P11-VRDS<br>VRDS conducted trials in two location in 2020 and 2021, and for an additional year in one location in 2022. The two locations are a Romanian organic Farm (RO FARM) and P11-VRDS experimental farm on-station. Four plots (7.5 m2 and 80 plants/plot) per variety, were randomized on a field of 300m2, at each of the 2 locations and for each of the three trials years. every year of trial.</p> <p>P16-SERIDA<br>The trials of snap bean cultivars were carried out on the field of an organic farmer in Asturias, Spain under the supervision of SERIDA staff during the years 2020 and 2021. The field trial included 12 cultivars (in 2020) and three replicates per cultivar with 20-25 plants distributed in plots of 4.5 m2.<br>P18-ITAKA<br>ITAKA conducted 3 bean trials, two under greenhouse in 2020 and 2021 (September to December) and a third trial in open field in 2021. The trials were conducted with 4 replicates per variety on an area of 245 m2 (18m x 13,5m greenhouse) in the greenhouse trials and open field trial. Variety plots were randomly distributed within blocks. Each block consisted of one repetition of all varieties in the trial.</p> <p>P21-SECL<br>SECL conducted their bean variety trial on their organic experimental farm in open field from July to September 2020 and June to September 2021. A complete random block design with varieties and four replicates per variety were used. In 2020, each experimental unit consisted of 88 plants sown into two plots of 1.5m wide and 4m length (12m², 7.4 plants/m²). In 2021, each experimental plot was 5m in length and 1.5m in width and beans were sown at 13 plants/m².</p>
Data from: Endocrine phenotype, reproductive success and survival in the great tit, Parus major
A central goal in evolutionary ecology is to characterize and identify selection patterns on the optimal phenotype in different environments. Physiological traits, such as hormonal responses, provide important mechanisms by which individuals can adapt to fluctuating environmental conditions. It is therefore expected that selection shapes hormonal traits, but the strength and the direction of selection on plastic hormonal signals are still under investigation. Here, we determined whether, and in which way, selection is acting on the hormones corticosterone and prolactin by characterizing endocrine phenotypes and their relationship with fitness in free-living great tits, Parus major. We quantified variation in circulating concentrations of baseline and stress-induced corticosterone and in prolactin during the prebreeding (March) and the breeding season (May) for two consecutive years, and correlated these with reproductive success (yearly fledgling number) and overwinter survival in female and male individuals. In both years, individuals with high baseline corticosterone concentrations in March had the highest yearly fledgling numbers; while in May, individuals with low baseline corticosterone had the highest yearly reproductive success. Likewise, individuals that displayed strong seasonal plasticity in baseline corticosterone concentrations (high in March and low in May) had the highest reproductive success in each year. Prolactin concentrations were not related to reproductive success, but were positively correlated to the proximity to lay. Between-year plasticity in stress-induced corticosterone concentrations of males was related to yearly variation in food abundance, but not to overall reproductive success. These findings suggest that seasonally alternating directional selection is operating on baseline corticosterone concentrations in both sexes. The observed between-year consistency in selection patterns indicates that a one-time hormone sample in a given season can allow the prediction of individual fitness.
Data from: Phenotypic plasticity through transcriptional regulation of the evolutionary hotspot gene tan in Drosophila melanogaster
Phenotypic plasticity is the ability of a given genotype to produce different phenotypes in response to distinct environmental conditions. Phenotypic plasticity can be adaptive. Furthermore, it is thought to facilitate evolution. Although phenotypic plasticity is a widespread phenomenon, its molecular mechanisms are only beginning to be unravelled. Environmental conditions can affect gene expression through modification of chromatin structure, mainly via histone modifications, nucleosome remodelling or DNA methylation, suggesting that phenotypic plasticity might partly be due to chromatin plasticity. As a model of phenotypic plasticity, we study abdominal pigmentation of Drosophila melanogaster females, which is temperature sensitive. Abdominal pigmentation is indeed darker in females grown at 18°C than at 29°C. This phenomenon is thought to be adaptive as the dark pigmentation produced at lower temperature increases body temperature. We show here that temperature modulates the expression of tan (t), a pigmentation gene involved in melanin production. t is expressed 7 times more at 18°C than at 29°C in female abdominal epidermis. Genetic experiments show that modulation of t expression by temperature is essential for female abdominal pigmentation plasticity. Temperature modulates the activity of an enhancer of t without modifying compaction of its chromatin or level of the active histone mark H3K27ac. By contrast, the active mark H3K4me3 on the t promoter is strongly modulated by temperature. The H3K4 methyl-transferase involved in this process is likely Trithorax, as we show that it regulates t expression and the H3K4me3 level on the t promoter and also participates in female pigmentation and its plasticity. Interestingly, t was previously shown to be involved in inter-individual variation of female abdominal pigmentation in Drosophila melanogaster, and in abdominal pigmentation divergence between Drosophila species. Sensitivity of t expression to environmental conditions might therefore give more substrate for selection, explaining why this gene has frequently been involved in evolution of pigmentation.
Data from: Integrating molecular, phenotypic and environmental data to elucidate patterns of crocodile hybridization in Belize
The genus Crocodylus comprises 12 currently recognized species, many of which can be difficult to differentiate phenotypically. Interspecific hybridization among crocodiles is known to occur in captivity and has been documented between some species in the wild. The identification of hybrid individuals is of importance for management and monitoring of crocodilians, many of which are Convention on International Trade in Endangered Species (CITES) listed. In this study, both mitochondrial and nuclear DNA markers were evaluated for their use in confirming a suspected hybrid zone between American crocodile (Crocodylus acutus) and Morelet's crocodile (Crocodylus moreletii) populations in southern Belize where individuals and nests exhibiting atypical phenotypic features had previously been observed. Patterns observed in both phenotypic and molecular data indicate possible behavioural and ecological characteristics associated with hybridization events. The results of the combined analyses found that the majority of suspected hybrid samples represent crosses between female C. acutus and male C. moreletii. Phenotypic data could statistically identify hybrids, although morphological overlap between hybrids and C. moreletii reduced reliability of identification based solely on field characters. Ecologically, C. acutus was exclusively found in saline waters, whereas hybrids and C. moreletii were largely absent in these conditions. A hypothesized correlation between unidirectional hybridization and destruction of C. acutus breeding habitats warrants additional research.
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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.