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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
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Data from: Male phenotypes in a female framework: evidence for degeneration in sperm produced by male snails from asexual lineages
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Data from: Phenotypic diversity facilitates niche partitioning in a sky island assemblage of spiny lizards
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Data from: Gene editing to induce FOXP3 expression in human CD4+ T cells leads to a stable regulatory phenotype and function.
<p>Thymic regulatory T cells (tTreg) are potent inhibitors of autoreactive immune responses and loss of tTreg function results in fatal autoimmune disease. Defects in Treg number or function are also implicated in multiple autoimmune diseases, leading to growing interest in use of Treg as cell therapies to establish immune tolerance. Because tTreg are present at low numbers in circulating blood and may be challenging to purify and expand, and also inherently defective in some subjects, we designed an alternative strategy to creating autologous Treg-like cells from bulk CD4+ T cells. We utilized homology-directed-repair (HDR)-based gene-editing to enforce FOXP3 expression. Targeted insertion of a robust enhancer/promoter proximal to the first coding exon bypassed epigenetic silencing, permitting stable, high level endogenous FOXP3 expression. HDR-edited T cells, edTreg, manifested a transcriptional program leading to sustained expression of canonical markers and suppressive activity of tTreg. Both human and murine edTreg mediated immunosuppression in vivo in models of inflammatory disease. Further, this engineering strategy permitted generation of antigen-specific edTreg with robust in vitro and in vivo functional activity. Finally, edTreg could be enriched and expanded at scale using clinically-relevant methods. Together, these finding suggest edTreg production may permit broad future clinical application.</p>
Data from: Oxidative stress experienced during early development influences the offspring phenotype
<p>Oxidative stress (OS) experienced early in life can affect an individual's phenotype. However, its consequences for the next generation remain largely unexplored. We manipulated the OS level endured by zebra finches (<i>Taeniopygia guttata</i>) during their development by transitorily inhibiting the synthesis of the key antioxidant glutathione ('early-high-OS'). The offspring of these birds and control parents were cross-fostered at hatching to enlarge or reduce its brood size. Independently of parents' early-life OS levels, the chicks raised in enlarged broods showed lower erythrocyte glutathione levels, revealing glutathione sensitivity to environmental conditions. Control ("early-low-OS") biological mothers produced females, not males, that attained a higher body mass when raised in a benign environment (i.e. the reduced brood). In contrast, biological mothers exposed to early-life OS produced heavier males, not females, when allocated in reduced broods. Early-life OS also affected the parental rearing capacity because 12d-old nestlings raised by a foster pair with both early-high-OS members grew shorter legs (tarsus) than chicks from other groups. The results indicate that environmental conditions during development can affect early glutathione levels, which may, in turn, influence the next generation through both pre- and postnatal parental effects. The results also demonstrate that early-life OS can constrain the offspring phenotype.</p>
Data from: Ecology shapes epistasis in a genotype-phenotype-fitness map for stick insect colour
<p>Genetic interactions such as epistasis are widespread in nature and can shape evolutionary dynamics. Epistasis occurs due to non-linearity in biological systems, which can arise via cellular processes that convert genotype to phenotype and via selective processes that connect phenotype to fitness. Few studies in nature have connected genotype to phenotype to fitness for multiple potentially interacting genetic variants. Thus, the causes of epistasis in the wild remain poorly understood. Here, we show that epistasis for fitness is an emergent and predictable property of non-linear selective processes. We do so by measuring the genetic basis of cryptic colouration and survival in a field experiment with stick insects. We find that colouration exhibits a largely additive genetic basis, but with some effects of epistasis that enhance differentiation between colour morphs. In terms of fitness, different combinations of loci affecting colouration confer high survival in one host-plant treatment. Specifically, non-linear correlational selection for specific combinations of colour traits in this treatment drives the emergence of pairwise and higher-order epistasis for fitness at loci underlying colour. In turn, this results in a rugged fitness landscape for genotypes. In contrast, fitness epistasis was dampened in another treatment, where selection was weaker. Patterns of epistasis that are shaped by ecologically based selection could be common, and central to understanding fitness landscapes, the dynamics of evolution, and potentially other complex systems.</p>
Data from: High content imaging of unbiased chemical perturbations reveals that the phenotypic plasticity of the actin cytoskeleton is constrained
Although F-actin has a large number of binding partners and regulators, the number of phenotypic states available to the actin cytoskeleton is unknown. Here, we quantified 74 features defining F-actin and cellular morphology in >25 million cells after treatment with a library of 114,400 structurally diverse compounds. After reducing the dimensionality of these data, we found that only ~25 recurrent F-actin phenotypes emerged, each defined by distinct quantitative features that could be machine learned. We identified 2003 unknown compounds as inducers of actin-related phenotypes, including two that directly bind talin, a core regulator of integrin activity. Moreover, we observed that compounds with distinct molecular mechanisms could induce equivalent phenotypes and that initially divergent cellular responses could converge over time. These findings suggest a conceptual parallel between the actin cytoskeleton and gene regulatory networks; where the theoretical plasticity of interactions is nearly infinite, yet phenotypes observed in vivo are constrained into a limited subset of practicable configurations.
Data from: Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass
<p><span>Germplasm from perennial ryegrass (<i>Lolium perenne</i> L.) natural populations is useful for breeding because of its adaptation to a wide range of climates. Climate-adaptive genes can be detected from associations between genotype, phenotype and climate but an integrated framework for the analysis of these three sources of information is lacking.</span></p> <p><span>We used two approaches to identify adaptive loci in perennial ryegrass and their effect on phenotypic traits. First, we combined Genome-Environment Association (GEA) and GWAS analyses. Then, we implemented a new test based on a Canonical Correlation Analysis (CANCOR) to detect adaptive loci. Furthermore, we improved the previous perennial ryegrass gene set by <i>de novo</i> gene prediction and functional annotation of 39,967 genes.</span></p> <p><span>GEA-GWAS revealed eight outlier loci associated with both an environmental variable and a phenotypic trait. CANCOR retrieved 633 outlier loci associated with two climatic gradients, characterized by cold-dry vs mild-wet winter and long rainy season vs long summer, and pointed out traits putatively conferring adaptation at the extremes of these gradients. Our CANCOR test also revealed the presence of both polygenic and oligogenic climatic adaptations. Our gene annotation revealed that 374 of the CANCOR outlier loci were positioned within or close to a gene. Co-association networks of outlier loci revealed a potential utility of CANCOR for investigating the interaction of genes involved in polygenic adaptations.</span></p> <p><span>The CANCOR test provides an integrated framework to analyze adaptive genomic diversity and phenotypic responses to environmental selection pressures that could be used to facilitate the adaptation of plant species to climate change.</span></p>
Linkage maps and phenotypic data for Bainbridge et al. 2020
Limited genetic parallels underlie convergent evolution of quantitative pattern variation in mimetic butterflies <p>Mimetic systems allow us to address the question of whether the same genes control similar phenotypes in different species. Although widespread parallels have been found for major effect loci, much less is known about genes that control quantitative trait variation. In this study, we identify and compare the loci that control subtle changes in the size and shape of forewing pattern elements in two <i>Heliconius</i> butterfly co-mimics. We use quantitative trait locus (QTL) analysis with a multivariate phenotyping approach to map the variation in red pattern elements across the whole forewing surface of <i>Heliconius erato</i> and <i>Heliconius melpomene</i>. These results are compared to a QTL analysis of univariate trait changes, and show that our resolution for identifying small effect loci is somewhat improved with the multivariate approach, but also that different loci are detected with these different approaches. QTL likely corresponding to the known patterning gene <i>optix</i> were found in both species but otherwise, a remarkably low level of genetic parallelism was found. This lack of similarity indicates that the genetic basis of convergent traits may not be as predictable as assumed from studies that focus solely on Mendelian traits.</p>
Data from: Ecotypes or phenotypic plasticity - the aquatic and terrestrial forms of Helosciadium repens (Apiaceae)
<p> </p> <p>• Morphological and ecological differences of two forms of Helosciadium repens are known and described in the literature: aquatic and terrestrial. However, their taxonomic status is currently unknown. The question whether they are genotypically adapted to specific environmental conditions or are those differences a result of phenotypic plasticity is addressed in this study.<br> • SSR and ISSR data were used to uncover genotypic differences. Data from drought stress experiments (system water content and relative water content of leaves) were used to evaluate the response to water as an environmental factor. The stomatal index of both forms grown under different water treatments was analysed.<br> • The principal component analysis of the SSR and ISSR data revealed no clustering that would correspond with ecotypes. The diversity parameters of the SSR data showed no significant differences. Contrary to the expected pattern, the aquatic populations showed a tendency towards heterozygosity while the terrestrial ones showed a bias towards homozygosity. Both forms responded similarly to the changes in water availability, with newly produced leaves after drought stress that were better adapted to repeated drought stress. Stomatal indices were higher in plants from aquatic habitats, but these difference disappeared when the plants were grown in soil.<br> • The observed responses indicate that the differences between forms are due to phenotypic plasticity.</p> <p> </p>
Data from: Phenotypic plasticity in sexual communication signal of a noctuid moth
Variability within sex pheromone signalling systems is generally believed to be low because of strong stabilizing selection; yet the noctuid moth Heliothis subflexa (Hs) shows significant intraspecific variation. One possible explanation is that females may alter their sex pheromone blend depending on prevailing olfactory cues in the habitat, which we termed the "experience hypothesis". This could be adaptive if Hs females experiencing the pheromone of another species, Heliothis virescens (Hv), responded to reduce the frequency of heterospecific matings. We exposed Hs females to no pheromone, Hs pheromone, or Hv pheromone in the first 3 days of their adult lives. Hs females in the latter treatment produced signficantly more of the acetate Z11-16:OAc, which inhibits the attraction of Hv males. To our knowledge, this is the first study showing adaptive phenotypic plasticity in a moth sex pheromone, and suggests that behavioral differentiation may precede genetic divergence in the sexual signals of moths.
Data from: Phenotypic plasticity, but not adaptive tracking, underlies seasonal variation in post-cold hardening freeze tolerance of Drosophila melanogaster
<p> In temperate regions, an organism's ability to rapidly adapt to seasonally varying environments is essential for its survival. In response to seasonal changes in selection pressure caused by variation in temperature, humidity, and food availability, some organisms exhibit plastic changes in phenotype. In other cases, seasonal variation in selection pressure can rapidly increase the frequency of genotypes that offer survival or reproductive advantages under the current conditions. Little is known about the relative influences of plastic and genetic changes in short lived organisms experiencing seasonal environmental fluctuations. Cold hardening is a seasonally relevant plastic response in which exposure to cool, but nonlethal, temperatures significantly increases the organism's ability to later survive at freezing temperatures. In the present study, we demonstrate seasonal variation in cold hardening in <em>Drosophila melanogaster</em> and test the extent to which plasticity and adaptive tracking underlie that seasonal variation. We measured the post-cold hardening freeze tolerance of flies from outdoor mesocosms over the summer, fall, and winter. We bred outdoor mesocosm-caught flies for two generations in the lab and matched each outdoor cohort to an indoor control cohort of similar genetic background. We cold hardened all flies under controlled laboratory conditions and then measured their post-cold hardening freeze tolerance. Comparing indoor and field-caught flies and their laboratory-reared G1 and G2 progeny allowed us to determine the roles of seasonal environmental plasticity, parental effects, and genetic changes on cold hardening. We also tested the relationship between cold hardening and other factors, including age, developmental density, food substrate, presence of antimicrobials, and supplementation with live yeast. We found strong plastic responses to a variety of field- and lab-based environmental effects, but no evidence of seasonally varying parental or genetic effects on cold hardening. We therefore conclude that seasonal variation in post-cold hardening freeze tolerance results from environmental influences and not genetic changes. </p>
Data from: Plasticity matches phenotype to local conditions despite genetic homogeneity across 13 snake populations
<p><span>In a widespread species, a matching of phenotypic traits to local environmental optima is generally attributed to site-specific adaptation. However, the same matching can occur via adaptive plasticity, without requiring genetic differences among populations. Adult sea kraits (<i>Laticauda saintgironsi</i>) are highly philopatric to small islands, but the entire population within the Neo-Caledonian lagoon is genetically homogenous because females migrate to the mainland to lay their eggs at communal sites; recruits disperse before settling, mixing up alleles. Consequently, any adaptive matching between local environments (e.g., prey sizes) and snake phenotypes (e.g., body sizes and relative jaw sizes) must be achieved via phenotypic plasticity rather than spatial heterogeneity in gene frequencies. We sampled 13 snake colonies spread along a ~200km northwest-southeast gradient (N>4,500 individuals) to measure two morphological features that affect maximum ingestible prey size in gape-limited predators: body size and relative jaw size. As proxies of habitat quality, we used protection status, fishing pressure and lagoon characteristics (lagoon width and distance of islands to the barrier reef). In both sexes, spatial variation in body sizes and relative jaw sizes was linked to habitat quality; albeit in different ways, consistent with sex-based divergences in foraging ecology. Strong spatial divergence in morphology among snake colonies, despite genetic homogeneity, supports the idea that phenotypic plasticity can facilitate speciation by creating multiple phenotypically distinct sub-populations shaped by their environment.</span></p>
Data from: Telomere length reflects phenotypic quality and costs of reproduction in a long-lived seabird
Telomere length is associated with cellular senescence, lifestyle and ageing. Short telomeres indicate poor health in humans and reduced life expectancy in several bird species, but little is known about telomeres in relation to phenotypic quality in wild animals. We investigated telomere lengths in erythrocytes of known-age common terns (Sterna hirundo), a migratory seabird, in relation to arrival date and reproductive performance. Cross-sectional data revealed that, independent of age, individuals with short telomeres performed better: they arrived and reproduced earlier in the season and had more chicks in the nest. The latter effect was stronger the older the brood and stronger in males, which do most of the chick provisioning. Longitudinal data confirmed this pattern: compared with birds that lost their brood, birds that raised chicks beyond the 10th nestling day experienced higher telomere attrition from one year to the next. However, more detailed analysis revealed that the least and most successful individuals lost the fewest base pairs compared with birds with intermediate success. Our results suggest that reproductive success is achieved at the expense of telomeres, but that individual heterogeneity in susceptibility to such detrimental effects is important, as indicated by low telomere loss in the most successful birds.
Data from: The architecture of an empirical genotype-phenotype map
Recent advances in high-throughput technologies are bringing the study of empirical genotype-phenotype (GP) maps to the fore. Here, we use data from protein binding microarrays to study an empirical GP map of transcription factor (TF) binding preferences. In this map, each genotype is a DNA sequence. The phenotype of this DNA sequence is its ability to bind one or more TFs. We study this GP map using genotype networks, in which nodes represent genotypes with the same phenotype, and edges connect nodes if their genotypes differ by a single small mutation. We describe the structure and arrangement of genotype networks within the space of all possible binding sites for 525 TFs from three eukaryotic species encompassing three kingdoms of life (animal, plant, and fungi). We thus provide a high-resolution depiction of the architecture of an empirical GP map. Among a number of findings, we show that these genotype networks are "small-world" and assortative, and that they ubiquitously overlap and interface with one another. We also use polymorphism data from Arabidopsis thaliana to show how genotype network structure influences the evolution of TF binding sites in vivo. We discuss our findings in the context of regulatory evolution.
Data from: What can aquatic gastropods tell us about phenotypic plasticity? A review and meta-analysis
There have been few attempts to synthesise the growing body of literature on phenotypic plasticity to reveal patterns and generalities about the extent and magnitude of plastic responses. Here, we conduct a review and meta-analysis of published literature on phenotypic plasticity in aquatic (marine and freshwater) gastropods, a common system for studying plasticity. We identified 96 studies, using pre-determined search terms, published between 1985 and November 2013. The literature was dominated by studies of predator-induced shell form, snail growth rates and life history parameters of a few model taxa, accounting for 67% of all studies reviewed. Meta-analyses indicated average plastic responses in shell thickness, shell shape, and growth and fecundity of freshwater species was at least three times larger than in marine species. Within marine gastropods, species with planktonic development had similar average plastic responses to species with benthic development. We discuss these findings in the context of the role of costs and limits of phenotypic plasticity and environmental heterogeneity as important constraints on the evolution of plasticity. We also consider potential publication biases and discuss areas for future research, indicating well-studied areas and important knowledge gaps.
Data from: Phenotype-dependent selection underlies patterns of sorting across habitats: the case of stream-fishes
Spatial and temporal heterogeneity within landscapes influences the distribution and phenotypic diversity of individuals both within and across populations. Phenotype-habitat correlations arise either through phenotypes within an environment altering through the process of natural selection or plasticity, or phenotypes remaining constant but individuals altering their distribution across environments. The mechanisms of non-random movement and phenotype-dependent habitat choice may account for associations within highly heterogeneous systems, such as streams, where local adaptation may be negated, plasticity too costly and movement is particularly important. Despite growing attention, however, few empirical tests have yet to be conducted. Here we provide a test of phenotype-dependent habitat choice and ask: 1) if individuals collected from a single habitat type continue to select original habitat; 2) if decisions are phenotype-dependent and functionally related to habitat requirements; and 3) if phenotypic-sorting continues despite increasing population density. To do so we both conducted experimental trials manipulating the density of four stream-fish species collected from either a single riffle or pool and developed a game-theoretical model exploring the influence of individuals' growth rate, sampling and competitive abilities as well as interference on distribution across two habitats as a function of density. Our experimental trials show individuals selecting original versus alternative habitats differed in their morphologies, that morphologies were functionally related to habitat-type swimming demands, and that phenotypic-sorting remained significant (although decreased) as density increased. According to our model this only occurs when phenotypes have contrasting habitat preferences and only one phenotype disperses (i.e. selects alternatives) in response to density pressures. This supports our explanation that empirical habitat selection was due to a combination of collecting a fraction of mobile individuals with different habitat preferences and the exclusion of individuals via scramble competition at increased densities. Phenotype-dependent habitat choice can thereby account for observed patterns of natural stream-fish distribution.
Data from: Testing mechanisms of Bergmann's rule: phenotypic but no genetic change in body size in three passerine bird populations
Bergmann's rule predicts a decrease in body size with increasing temperature and has much empirical support. Surprisingly, we know very little about whether 'Bergmann size clines' are due to a genetic response or is a consequence of phenotypic plasticity. Here we use data on body size (mass and tarsus length) from three long-term (1979-2008) study populations of great tits (Parus major), in which there has been a temperature increase, to examine mechanisms behind Bergmann's rule. We show that adult body mass decreased over the study period in all populations and that tarsus length increased in one population. Both body mass and tarsus length were heritable and under weak positive directional selection, predicting an increase, rather than decrease, in body mass. There was no support for micro-evolutionary change and thus the observed declines in body mass were a result of phenotypic plasticity. Interestingly, this plasticity was not in direct response to temperature changes but seemed to be due to changes in prey dynamics. Our results caution against interpreting recent phenotypic body size declines as an adaptive evolutionary response to temperature changes and highlight the importance of considering alternative environmental factors when testing size clines.
Data from: Rapid local adaptation linked with phenotypic plasticity
<p>Models of 'plasticity-first' evolution are attractive because they explain the rapid evolution of new complex adaptations. Nevertheless, it is unclear whether plasticity can facilitate rapid microevolutionary change between diverging populations. Here we show how plasticity may have generated adaptive differences in fecundity between neighbouring wild populations of burying beetles <i>Nicrophorus vespilloides</i>. These populations occupy distinct Cambridgeshire woodlands that are just 2.5km apart and that probably originated from a common ancestral population c. 1000-4000 years ago. We find that populations are divergently adapted to breed on differently-sized carrion. Adaptive differences in clutch size and egg size are associated with divergence at loci connected with oogenesis. The populations differ specifically in the elevation of the reaction norm linking clutch size to carrion size (i.e. genetic accommodation), and in the likelihood that surplus offspring will be lost after hatching. We suggest that these two processes may have facilitated rapid local adaptation on a fine-grained spatial scale.</p>
Data from: Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies
The reality of larger and larger molecular databases and the need to integrate data scalably have presented a major challenge for the use of phenotypic data. Morphology is currently primarily described in discrete publications, entrenched in noncomputer readable text, and requires enormous investments of time and resources to integrate across large numbers of taxa and studies. Here we present a new methodology, using ontology-based reasoning systems working with the Phenoscape Knowledgebase (KB; kb.phenoscape.org), to automatically integrate large amounts of evolutionary character state descriptions into a synthetic character matrix of neomorphic (presence/absence) data. Using the KB, which includes more than 55 studies of sarcopterygian taxa, we generated a synthetic supermatrix of 639 variable characters scored for 1051 taxa, resulting in over 145,000 populated cells. Of these characters, over 76% were made variable through the addition of inferred presence/absence states derived by machine reasoning over the formal semantics of the source ontologies. Inferred data reduced the missing data in the variable character-subset from 98.5% to 78.2%. Machine reasoning also enables the isolation of conflicts in the data, that is, cells where both presence and absence are indicated; reports regarding conflicting data provenance can be generated automatically. Further, reasoning enables quantification and new visualizations of the data, here for example, allowing identification of character space that has been undersampled across the fin-to-limb transition. The approach and methods demonstrated here to compute synthetic presence/absence supermatrices are applicable to any taxonomic and phenotypic slice across the tree of life, providing the data are semantically annotated. Because such data can also be linked to model organism genetics through computational scoring of phenotypic similarity, they open a rich set of future research questions into phenotype-to-genome relationships.
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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.