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6,234 results for “phenotypes”
Data from: Experimental evolution with a multicellular host causes diversification within and between microbial parasite populations – differences in emerging phenotypes of two different parasite strains
Host-parasite coevolution is predicted to have complex evolutionary consequences, potentially leading to the emergence of genetic and phenotypic diversity for both antagonists. However, little is known about variation in phenotypic responses to coevolution between different parasite strains exposed to the same experimental conditions. We infected Caenorhabditis elegans with one of two strains of Bacillus thuringiensis and either allowed the host and the parasite to experimentally coevolve (coevolution treatment) or allowed only the parasite to adapt to the host (one-sided parasite adaptation). By isolating single parasite clones from evolved populations, we found phenotypic diversification of the ancestral strain into distinct clones, which varied in virulence towards ancestral hosts and competitive ability against other parasite genotypes. Parasite phenotypes differed remarkably not only between the two strains, but also between and within different replicate populations, indicating diversification of the clonal population caused by selection. This study highlights that the evolutionary selection pressure mediated by a multicellular host causes phenotypic diversification, but not necessarily with the same phenotypic outcome for different parasite strains.
Data from: Testing the phenotype-linked fertility hypothesis in the presence and absence of inbreeding
The phenotype-linked fertility hypothesis suggests that females can judge male fertility by inspecting male phenotypic traits. This is because male sexually selected traits might correlate with sperm quality if both are sensitive to factors that influence male condition. A recent meta-analysis found little support for this hypothesis, suggesting little or no shared condition dependence. However, we recently reported that in captive zebra finches (Taeniopygia guttata) inbreeding had detrimental effects both on phenotypic traits and on measures of sperm quality, implying that variation in inbreeding could induce positive covariance between indicator traits and sperm quality. Therefore, we here assess empirically the average strength of correlations between phenotypic traits (courtship rate, beak colour, tarsus length) and measures of sperm quality (proportion of functional sperm, sperm velocity, sperm length) in populations of only outbred individuals and in mixed populations consisting of inbreds (F = 0.25) and outbreds (F = 0). As expected, phenotype sperm-trait correlations were stronger when the population contained a mix of inbred and outbred individuals. We also found unexpected heterogeneity between our two study populations, with correlations being considerably stronger in a domesticated population than in a recently wild-derived population. Correlations ranged from essentially zero among outbred-only wild-derived birds (mean Fisher's Zr ± SE = 0.03 ± 0.10) to moderately strong among domesticated birds of mixed inbreeding status (Zr ± SE = 0.38 ± 0.08). Our results suggest that, under some conditions, the phenotype-linked fertility hypothesis might apply.
Data from: Evolution of phenotype-environment associations by genetic responses to selection and phenotypic plasticity in a temporally autocorrelated environment
Covariation between population-mean phenotypes and environmental variables, sometimes termed a 'phenotype-environment association' (PEA), can result from phenotypic plasticity, genetic responses to natural selection, or both. PEAs can potentially provide information on the evolutionary dynamics of a particular set of populations, but this requires a full theoretical characterization of PEAs and their evolution. Here, we derive formulas for the expected PEA in a temporally fluctuating environment for a quantitative trait with a linear reaction norm. We compare several biologically relevant scenarios, including constant versus evolving plasticity, and the situation where an environment affects both development and selection but at different time periods. We find that PEAs are determined not only by biological factors (e.g., magnitude of plasticity, genetic variation), but also environmental factors, such as the association between the environments of development and of selection, and in some cases the level of temporal autocorrelation. We also describe how a PEA can be used to estimate the relationship between an optimum phenotype and an environmental variable (i.e., the environmental sensitivity of selection), an important parameter for determining the extinction risk of populations experiencing environmental change. We illustrate this ability using published data on the predator-induced morphological responses of tadpoles to predation risk.
Data from: Does multiple paternity explain phenotypic variation among offspring in wild boar?
During pregnancy, littermates compete to extract maternal resources from the placenta. Unequal extraction of resources leads to developmental differences among offspring and thus within-litter variation in offspring mass. Because competition among littermates can be stronger among half-sibs, multiple paternity may represent an adaptive strategy allowing females to increase within-litter phenotypic variation among offspring when facing variable environments. Wild boar (Sus scrofa) females produce large litters with diversified offspring in terms of body mass. Additionally, multiple paternity within a litter has been observed in this promiscuous species. One can hypothesize that multiple paternity represents the mechanism by which females increase within-litter phenotypic variation. Combining long-term monitoring data with paternity analyses in a wild boar population, we tested whether the increase in the number of fathers within a litter explained the increase in within-litter variation in offspring mass observed in large litters. We showed that heavy females mated earlier during the rut, produced larger litters with a higher number of fathers and more variable fetus mass than lighter females. Within-litter variation of offspring mass increased with gestation stage and litter size, suggesting differential allocation of maternal resource among offspring in utero. However, we found only a weak paternal effect on offspring mass and no direct effect of the number of fathers on the within-litter variation in offspring mass. These results indicate that differential maternal allocation to offspring during pregnancy is unlikely related to paternal identity in this species.
Data from: Reverting ontogeny: rapid phenotypic plasticity of color vision in cichlid fish
Phenotypic plasticity, particularly during development, allows organisms to rapidly adjust to different environmental conditions. Yet, it is often unclear whether the extent and direction of plastic changes are restricted by an individual's ontogeny. Many species of cichlid fishes go through ontogenetic changes in visual sensitivity, from short to long wavelengths, by switching expression of cone opsin genes crucial for color vision. During this progression, individuals often exhibit phenotypic plasticity to the ambient light conditions. However, it is commonly assumed that once an adult visual phenotype is reached, reverting to an earlier ontogenetic state with higher sensitivity at shorter wavelengths is not common. In this study, we experimentally demonstrate that four-month-old Midas cichlid fish (Amphilophus astorquii) show plasticity in single cone opsin expression after experiencing drastic changes in light conditions. Resulting shifts of visual sensitivity occurred presumably in an adaptive direction - towards shorter or longer wavelengths when exposed to short or long wavelength light, respectively. Single cone opsin expression changed within only a few days and went through a transitional phase of co-expression. When the environment was experimentally enriched in long wavelength light, the corresponding change occurred gradually along a dorsoventral gradient within the retina. This plasticity allowed individuals to revert earlier ontogenetic changes and return to a more juvenile visual phenotype demonstrating previously unrecognized insights into temporal and spatial dynamics of phenotypic plasticity of the visual system in response to ambient light.
Data from: Inferring bounded evolution in phenotypic characters from phylogenetic comparative data
Our understanding of phenotypic evolution over macroevolutionary timescales largely relies on the use of stochastic models for the evolution of continuous traits over phylogenies. The two most widely used models, Brownian motion and the Ornstein–Uhlenbeck (OU) process, differ in that the latter includes constraints on the variance that a trait can attain in a clade. The OU model explicitly models adaptive evolution toward a trait optimum and has thus been widely used to demonstrate the existence of stabilizing selection on a trait. Here we introduce a new model for the evolution of continuous characters on phylogenies: Brownian motion between two reflective bounds, or Bounded Brownian Motion (BBM). This process also models evolutionary constraints, but of a very different kind. We provide analytical expressions for the likelihood of BBM and present a method to calculate the likelihood numerically, as well as the associated R code. Numerical simulations show that BBM achieves good performance: parameter estimation is generally accurate but more importantly BBM can be very easily discriminated from both BM and OU. We then analyze climatic niche evolution in diprotodonts and find that BBM best fits this empirical data set, suggesting that the climatic niches of diprotodonts are bounded by the climate available in Australia and the neighboring islands but probably evolved with little additional constraints. We conclude that BBM is a valuable addition to the macroevolutionary toolbox, which should enable researchers to elucidate whether the phenotypic traits they study are evolving under hard constraints between bounds.
Data from: Local adaptation, phenotypic differentiation and hybrid fitness in diverged natural populations of Arabidopsis lyrata
Selection for local adaptation results in genetic differentiation in ecologically important traits. In a perennial, outcrossing model plant Arabidopsis lyrata, several differentiated phenotypic traits contribute to local adaptation, as demonstrated by fitness advantage of the local population at each site in reciprocal transplant experiments. Here we compared fitness components, hierarchical total fitness and differentiation in putatively ecologically important traits of plants from two diverged parental populations from different continents in the native climate conditions of the populations in Norway and in North Carolina (NC), USA. Survival and number of fruits per inflorescence indicated local advantage at both sites and aster life-history models provided additional evidence for local adaptation also at the level of hierarchical total fitness. Populations were also differentiated in flowering start date and floral display. We also included reciprocal experimental F1 and F2 hybrids to examine the genetic basis of adaptation. Surprisingly, the F2 hybrids showed heterosis at the study site in Norway, likely because of a combination of beneficial dominance effects from different traits. At the NC site, hybrid fitness was mostly intermediate relative to the parental populations. Local cytoplasmic origin was associated with higher fitness, indicating that cytoplasmic genomes also may contribute to the evolution of local adaptation.
Data from: The genetic inheritance of the blue-eyed white phenotype in alpacas (Vicugna pacos)
White spotting patterns in mammals can be caused by mutations in the gene KIT, whose protein is necessary for the normal migration and survival of melanocytes from the neural crest. The alpaca (Vicugna pacos) blue-eyed white phenotype (BEW) is characterized by two blue eyes and a solid white coat over the whole body. Breeders hypothesize that the BEW phenotype in alpacas is caused by the combination of the gene causing grey fleece and a white-spotting gene. We performed an association study using KIT flanking and intragenic markers with 40 unrelated alpacas, of which 17 were BEW. Two microsatellite alleles at KIT-related markers were significantly associated (P < 0.0001) with the BEW phenotype (bew1 and bew2). In a larger cohort of 171 related individuals we identify an abundance of an allele (bew1) in grey animals and the occurrence of bew2 homozygotes that are solid white with pigmented eyes. Association tests accounting for population structure and familial relatedness are consistent with a proposed model where these alleles are in linkage disequilibrium with a mutation or mutations that contribute to the BEW phenotype and to individual differences in fleece color.
Data from: Automated deep-phenotyping of the vertebrate brain
Here we describe an automated platform suitable for large-scale deep-phenotyping of zebrafish mutant lines, which uses optical projection tomography to rapidly image brain-specific gene expression patterns in 3D at cellular resolution. Registration algorithms and correlation analysis are then used to compare 3D expression patterns, to automatically detect all statistically significant alterations in mutants, and to map them onto a brain atlas. Automated deep-phenotyping of a mutation in the master transcriptional regulator fezf2 not only detects all known phenotypes but also uncovers important novel neural deficits that were overlooked in previous studies. In the telencephalon, we show for the first time that fezf2 mutant zebrafish have significant patterning deficits, particularly in glutamatergic populations. Our findings reveal unexpected parallels between fezf2 function in zebrafish and mice, where mutations cause deficits in glutamatergic neurons of the telencephalon-derived neocortex.
Data from: Experimental confirmation that body size determines mate preference via phenotype matching in a stickleback species pair
Mate choice by phenotype matching, whereby individuals prefer a mate whose phenotype is similar to their own, should facilitate speciation with gene flow. This is because the genes that control mate signal (the phenotype being matched) also determine the preferred mate signal ('mate preference'). Speciation is made even easier if phenotype matching is based on a trait under divergent natural selection. In this case, assortative mating should readily evolve as a by-product of divergent selection on the trait. Previous observational studies of assortative mating between sympatric, hybridizing threespine stickleback species (Gasterosteus aculeatus complex) suggested that phenotype matching might occur by body size, a trait under divergent natural selection. To test this we used experimental manipulation of body size to rule out the effects of confounding variables. We found that size-manipulated benthic and limnetic stickleback females prefer mates whose body size more closely matches their own. It is thus likely that assortative mating by phenotype matching has facilitated the origin and persistence of benthic and limnetic threespine sticklebacks in the face of gene flow.
Data from: Crowdsourced geometric morphometrics enable rapid large-scale collection and analysis of phenotypic data
1. Advances in genomics and informatics have enabled the production of large phylogenetic trees. However, the ability to collect large phenotypic datasets has not kept pace. 2. Here, we present a method to quickly and accurately gather morphometric data using crowdsourced image-based landmarking. 3. We find that crowdsourced workers perform similarly to experienced morphologists on the same digitization tasks. We also demonstrate the speed and accuracy of our method on seven families of ray-finned fishes (Actinopterygii). 4. Crowdsourcing will enable the collection of morphological data across vast radiations of organisms, and can facilitate richer inference on the macroevolutionary processes that shape phenotypic diversity across the tree of life.
Data from: Inferring the potentially complex genetic architectures of adaptation, sexual dimorphism, and genotype by environment interactions by partitioning of mean phenotypes.
Genetic architecture fundamentally affects the way that traits evolve. However, the mapping of genotype to phenotype includes complex interactions with the environment or even the sex of an organism that can modulate the expressed phenotype. Line cross analysis is a powerful quantitative genetics method to infer genetic architecture by analyzing the mean phenotype value of two diverged strains and a series of subsequent crosses and backcrosses. However, it has been difficult to account for complex interactions with the environment or sex within this framework. We have developed extensions to line cross analysis that allow for gene by environment and gene by sex interactions. Using extensive simulations studies and reanalysis of empirical data, we show that our approach can account for both unintended environmental variation when crosses cannot be reared in a common garden and can be used to test for the presence of gene by environment or gene by sex interactions. In analyses that fail to account for environmental variation between crosses we find that line cross analysis has low power and high false positive rates. However, we illustrate that accounting for environmental variation allows for the inference of adaptive divergence, and that accounting for sex differences in phenotypes allows practitioners to infer the genetic architecture of sexual dimorphism.
Data from: Phenotypic integration of the cervical vertebrae in the Hominoidea (Primates)
Phenotypic integration and modularity represent important factors influencing evolutionary change. The mammalian cervical vertebral column is particularly interesting in regards to integration and modularity because it is highly constrained to seven elements, despite widely variable morphology. Previous research has found a common pattern of integration among quadrupedal mammals, but integration patterns also evolve in response to locomotor selective pressures like those associated with hominin bipedalism. Here, I test patterns of covariation in the cervical vertebrae of three hominoid primates (Hylobates, Pan, Homo) who engage in upright postures and locomotion. Patterns of integration in the hominoid cervical vertebrae correspond generally to those previously found in other mammals, suggesting that integration in this region is highly conserved, even among taxa that engage in novel positional behaviors. These integration patterns reflect underlying developmental as well as functional modules. The strong integration between vertebrae suggests that the functional morphology of the cervical vertebral column should be considered as a whole, rather than in individual vertebrae. Taxa that display highly derived morphologies in the cervical vertebrae are likely exploiting these integration patterns, rather than reorganizing them. Future work on vertebrates without cervical vertebral number constraints will further clarify the evolution of integration in this region.
Populations of a widespread invader and co-occurring native species vary in phenotypic plasticity
<p class="MsoListBulletCxSpFirst"><span>Phenotypic plasticity can promote plant invasions and enhance impacts on native species but little is known about variation in plasticity among invader populations compared to native species. Variation in plasticity among invader populations could inform more precise predictions of invader spread and impacts across heterogeneous resource environments.</span></p> <p class="MsoListBulletCxSpMiddle"><span> We used a common garden experiment with sun and shade treatments to test for variation in plasticity among 12 populations of an invasive grass, and to determine if the invader exhibited greater plasticity than six native species that co-occur in the Southeast US.</span></p> <p class="MsoListBulletCxSpMiddle"><span>Principal component analysis revealed that invader populations from different native ranges consistently varied from each other and native species in traits linked to more favorable phenotypes under resource limitation. Overall, the invader exhibited greater plasticity than native species, as demonstrated by higher plasticity index values for traits such as plant height, leaf mass ratio, and root shoot ratio.</span></p> <p class="MsoListBulletCxSpLast"><span>Variation in phenotypic plasticity among invader<i> </i>populations suggests the potential for evolution of plasticity, and greater plasticity of invader populations than native species may underlie invader dominance. Differences in plasticity among populations appears to play an important role in predictions of the spread and potentially the impacts of invasive species.</span></p>
Data from: Heritability, evolvability, phenotypic plasticity and temporal variation in sperm-competition success of Drosophila melanogaster
Sperm-competition success (SCS) is seen as centrally important for evolutionary change: superior fathers sire superior sons and thereby inherit the traits that make them superior. Additional hypotheses, that phenotypic plasticity in SCS and sperm ageing explain variation in paternity, are less considered. Even though various alleles have individually been shown to be correlated with variation in SCS, few studies have addressed the heritability, or evolvability, of overall SCS. Those studies that have, found low or no heritability and have not examined evolvability. They have further not excluded phenotypic plasticity, and temporal effects on SCS, despite their known dramatic effects on sperm function. In Drosophila melanogaster, we found that both standard components of sperm competition, sperm defence and sperm offence, showed non-significant or insignificant heritability across several offspring cohorts. Instead, our analysis revealed, for the first time, the existence of phenotypic plasticity in SCS across an extreme environment (5% CO2), and an influence of sperm ageing. Evolvability of SCS was substantial for sperm defence but virtually absent for sperm offence. Our results suggest that the paradigm of explaining evolution by sperm competition is more complex and will benefit from further experimental work on the heritability or evolvability of SCS, measuring phenotypic plasticity, and separating the effects of sperm competition and sperm ageing.
Data from: Environmental heterogeneity does not affect levels of phenotypic plasticity in natural populations of three Drosophila species
Adaptation of natural populations to variable environmental conditions may occur by changes in trait means and/or in the levels of plasticity. Theory predicts that environmental heterogeneity favors plasticity of adaptive traits. Here we investigated the performance in several traits of three sympatric Drosophila species freshly collected in two environments that differ in the heterogeneity of environmental conditions. Differences in trait means within species were found in several traits, indicating that populations differed in their evolutionary response to the environmental conditions of their origin. Different species showed distinct adaptation with a very different role of plasticity across species for coping with environmental changes. However, geographically distinct populations of the same species generally displayed the same levels of plasticity as induced by fluctuating thermal regimes. This indicates a weak and trait-specific effect of environmental heterogeneity on plasticity. Furthermore, similar levels of plasticity were found in a laboratory-adapted population of Drosophila melanogaster with a common geographic origin but adapted to the laboratory conditions for more than 100 generations. Thus, this study does not confirm theoretical predictions on the degree of adaptive plasticity among populations in relation to environmental heterogeneity but shows a very distinct role of species-specific plasticity.
Data from: Predation risk determines pigmentation phenotype in nuthatches by melanin-related gene expression effects
Pigments determine the appearance of organisms. However, pigment production can be associated to physiological constraints as in the case of pheomelanin, the sulphurated form of melanin whose synthesis in melanocytes consumes cysteine and consequently reduces the availability of glutathione (GSH) to exert antioxidant protection. Pheomelanogenesis may thus increase the susceptibility to suffer chronic oxidative stress. I investigated the possibility that environmental lability in the expression of genes regulating pheomelanogenesis protects from oxidative stress, a situation in which GSH is most required. By broadcasting adult alarm calls, I manipulated the perception of predation risk, a natural source of oxidative stress, in free-living Eurasian nuthatch Sitta europaea nestlings developing pheomelanin-pigmented flank feathers. The manipulation affected the consumption of GSH that resulted from the expression of two genes (Slc7a11 and Slc45a2) influencing cysteine/GSH availability in cells, as these genes were downregulated in the feather melanocytes of the nestlings with lowest intracellular antioxidant capacity (i.e., lowest GSH levels). Systemic oxidative damage increased with Slc7a11 expression in feather melanocytes, suggesting that the observed downregulation was physiologically advantageous. The nestlings exposed to an increased perception of predation risk developed flank feathers of reduced color intensity. These results indicate that perceived predation risk can determine the pigmentation phenotype by (probably epigenetic) effects on gene expression that protect from physiological constraints imposed by pheomelanin production.
Data from: Insect mating signal and mate preference phenotypes covary among host plant genotypes
Sexual selection acting on small initial differences in mating signals and mate preferences can enhance signal-preference co-divergence and reproductive isolation during speciation. However, the origin of initial differences in sexual traits remains unclear. We asked whether biotic environments, a source of variation in sexual traits, may provide a general solution to this problem. Specifically, we asked whether genetic variation in biotic environments provided by host plants can result in signal-preference phenotypic covariance in a host-specific, plant-feeding insect. We used a member of the Enchenopa binotata species complex of treehoppers (Hemiptera: Membracidae) to assess patterns of variation in male mating signals and female mate preferences induced by genetic variation in host plants. We employed a novel implementation of a quantitative genetics method, rearing field-collected treehoppers on a sample of naturally-occurring replicated host plant clone lines. We found remarkably high signal-preference covariance among host plant genotypes. Thus, genetic variation in biotic environments influences the sexual phenotypes of organisms living on those environment in a way that promotes assortative mating among environments. This consequence arises from conditions likely to be common in nature (phenotypic plasticity and variation in biotic environments). It therefore offers a general answer to how divergent sexual selection may begin.
Data from: microCT-based phenomics in the zebrafish skeleton reveals virtues of deep phenotyping in a distributed organ system
Phenomics, which ideally involves in-depth phenotyping at the whole-organism scale, may enhance our functional understanding of genetic variation. Here, we demonstrate methods to profile hundreds of phenotypic measures comprised of morphological and densitometric traits at a large number of sites within the axial skeleton of adult zebrafish. We show the potential for vertebral patterns to confer heightened sensitivity, with similar specificity, in discriminating mutant populations compared to analyzing individual vertebrae in isolation. We identify phenotypes associated with human brittle bone disease and thyroid stimulating hormone receptor hyperactivity. Finally, we develop allometric models and show their potential to aid in the discrimination of mutant phenotypes masked by alterations in growth. Our studies demonstrate virtues of deep phenotyping in a spatially distributed organ system. Analyzing phenotypic patterns may increase productivity in genetic screens, and facilitate the study of genetic variants associated with smaller effect sizes, such as those that underlie complex diseases.
Data from: Male phenotypic diversity experienced during ontogeny mediates female mate choice in guppies
Early social experience can be important in shaping female mate choice. Previous work has shown that females adjust their decisions based on the distribution of male sexual trait values encountered during development. However, other phenotypic features could be important in the formation of mate preferences if, for example, they provide additional information about the males available. Here, we examined how the level of overall phenotypic variance (independent of trait values) experienced during ontogeny, mediated female choice in guppies, Poecilia reticulata. Developing females were reared with males either all different in colouration or all similar in colouration or with adult females representing high variance, low variance and no experience of male variance respectively. We found that females were more sexually responsive when reared with females only than in either of the male treatments. When reared with males, responsiveness was greater in the low-variance compared to the high variance treatment. Moreover, females had stronger sexual preferences following rearing in the high variance compared to the low variance condition. In turn, males switched mating tactics, increasing the rate of coerced copulation attempts when facing choosier females, possibly to balance the loss in mating opportunities. Taken together, these results demonstrate the adaptive plasticity of female mating decisions and the dynamic selection pressures they might impose on the evolution of male sexual traits, potentially contributing to the maintenance of the extreme polymorphism found in male colour patterns.
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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.