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6,234 results for “phenotypes”
Data from: Comparative analyses of QTLs influencing obesity and metabolic phenotypes in pigs and humans
The pig is a well-known animal model used to investigate genetic and mechanistic aspects of human disease biology. They are particularly useful in the context of obesity and metabolic diseases because other widely used models (e.g. mice) do not completely recapitulate key pathophysiological features associated with these diseases in humans. Therefore, we established a F2 pig resource population (n = 564) designed to elucidate the genetics underlying obesity and metabolic phenotypes. Segregation of obesity traits was ensured by using breeds highly divergent with respect to obesity traits in the parental generation. Several obesity and metabolic phenotypes were recorded (n = 35) from birth to slaughter (242 ± 48 days), including body composition determined at about two months of age (63 ± 10 days) via dual-energy x-ray absorptiometry (DXA) scanning. All pigs were genotyped using Illumina Porcine 60k SNP Beadchip and a combined linkage disequilibrium-linkage analysis was used to identify genome-wide significant associations for collected phenotypes. We identified 229 QTLs which associated with adiposity- and metabolic phenotypes at genome-wide significant levels. Subsequently comparative analyses were performed to identify the extent of overlap between previously identified QTLs in both humans and pigs. The combined analysis of a large number of obesity phenotypes has provided insight in the genetic architecture of the molecular mechanisms underlying these traits indicating that QTLs underlying similar phenotypes are clustered in the genome. Our analyses have further confirmed that genetic heterogeneity is an inherent characteristic of obesity traits most likely caused by segregation or fixation of different variants of the individual components belonging to cellular pathways in different populations. Several important genes previously associated to obesity in human studies, along with novel genes were identified. Altogether, this study provides novel insight that may further the current understanding of the molecular mechanisms underlying human obesity.
Data from: Habitat- and season-specific temperatures affect phenotypic development of hatchling lizards
Embryonic environments influence phenotypic development, but relatively few experiments have explored the effects of natural environmental variation. We incubated eggs of the lizard Anolis sagrei under conditions that mimicked natural spatial and temporal thermal variation to determine their effects on offspring morphology and performance. Incubation temperatures mimicked two microhabitats (open, shade) at two different times of the incubation season (April, July). Egg survival, incubation duration and offspring size were influenced by interactions between habitat- and season-specific nest temperatures, and locomotor performance was influenced primarily by temporal factors. These findings highlight the importance of spatial and temporal environmental variation in generating variation in fitness-related phenotypes.
Data from: Selection on outlier loci and their association with adaptive phenotypes in Littorina saxatilis contact zones
A fundamental issue in speciation research is to evaluate phenotypic variation and the genomics driving the evolution of reproductive isolation between sister taxa. Above all, hybrid zones are excellent study systems for researchers to examine the association of genetic differentiation, phenotypic variation and the strength of selection. We investigated two contact zones in the marine gastropod Littorina saxatilis and utilized landmark-based geometric morphometric analysis together with amplified fragment length polymorphism (AFLP) markers to assess phenotypic and genomic divergence between ecotypes under divergent selection. From genetic markers, we calculated the cline width, linkage disequilibrium and the average effective selection on a locus. Additionally, we conducted an association analysis linking the outlier loci and phenotypic variation between ecotypes and show that a proportion of outlier loci are associated with key adaptive phenotypic traits.
Data from: Genetic basis of amphibian larval development along a latitudinal gradient: gene diversity, selection and links with phenotypic variation in transcription factor C/EBP-1
Ectotherm development rates often show adaptive divergence along climatic gradients, but the genetic basis for this variation is rarely studied. Here, we investigated the genetic basis for phenotypic variation in larval development in the moor frog Rana arvalis from five regions along a latitudinal gradient from Germany to northern Sweden. We focused on the C/EBP-1 gene, a transcription factor associated with larval development time. Allele frequencies at C/EBP-1 varied strongly among geographic regions. Overall, the distribution of alleles along the gradient was in concordance with the dual postglacial colonization routes into Scandinavia, with a large number of alleles exclusively present along the southern colonization route. Only three of 38 alleles were shared between the routes. Analysis of contemporary selection on C/EBP-1 showed divergent selection among the regions, likely reflecting adaptation to the local environmental conditions, although this was especially strong between southern and northern regions coinciding also with lineages from different colonization routes. Overall, the C/EBP-1 gene has historically been under purifying selection, however, two specific amino acid positions showed significant signals of positive selection. These positions showed divergence between southern and northern regions, and we suggest that they are functionally involved in the climatic adaptation of larval development. Using phenotypic data from a common garden experiment, we found evidence for specific C/EBP-1 alleles being correlated with larval development time, suggesting a functional role in adaptation of larval development to large-scale climatic variation.
Data from: Changes in predator exposure, but not diet induce phenotypic plasticity in scorpion venom
Animals embedded between trophic levels must simultaneously balance pressures to deter predators and acquire resources. Venomous animals may use venom toxins to mediate both pressures, and thus changes in this balance may alter the composition of venoms. Basic theory suggests that greater exposure to a predator should induce a larger proportion of defensive venom components relative to offensive venom components, while increases in arms races with prey will elicit the reverse. Alternatively, reducing the need for venom expenditure for food acquisition, for example because of an increase in scavenging, may reduce the production of offensive venom components. Here, we investigated changes in scorpion venom composition using a mesocosm experiment where we manipulated scorpions' exposure to a surrogate vertebrate predator and live and dead prey. After six weeks, scorpions exposed to surrogate predators exhibited significantly different venom chemistry compared with naive scorpions. This change included a relative increase in some compounds toxic to vertebrate cells and a relative decrease in some compounds effective against their invertebrate prey. Our findings provide, to our knowledge, the first evidence for adaptive plasticity in venom composition. These changes in venom composition may increase the stability of food webs involving venomous animals.
Data from: The level of an intracellular antioxidant during development determines the adult phenotype in a bird species: a potential organizer role for glutathione
Life-history traits are often involved in trade-offs whose outcome would depend on the availability of resources but also on the state of specific molecular signals. Early conditions can influence trade-offs and program the phenotype throughout the lifetime, with oxidative stress likely involved in many taxa. Here we address the potential regulatory role of a single intracellular antioxidant in life-history trade-offs. Blood glutathione levels were reduced in a large sample of birds (zebra finch Taeniopygia guttata) during development using the synthesis inhibitor buthionine sulfoximine (BSO). Results revealed several modifications in the adult phenotype. BSO-treated nestlings showed lower glutathione and plasma antioxidant levels. In adulthood, BSO birds endured greater oxidative damage in erythrocytes but stronger expression of a sexual signal. Moreover, adult BSO females also showed weaker resistance to oxidative stress but were heavier and showed better body condition. Results suggest that low glutathione values during growth favor the investment in traits that should improve fitness returns, probably in the form of early reproduction. Higher oxidative stress in adulthood may be endured if this cost is paid later in life. Either the presence of specific signaling mechanisms or the indirect effect of increased oxidative stress can explain our findings.
Data from: How phenotypic convergence arises in experimental evolution
Evolutionary convergence is a core issue in the study of adaptive evolution, as well as a highly debated topic at present. Few studies have analyzed this issue using a "real-time" or evolutionary trajectory approach. Do populations that are initially differentiated converge to a similar adaptive state when experiencing a common novel environment? Drosophila subobscura populations founded from different locations and years showed initial differences and variation in evolutionary rates in several traits during short-term (~20 generations) laboratory adaptation. Here we extend that analysis to 40 more generations to analyze (1) how differences in evolutionary dynamics between populations change between shorter and longer time spans, and (2) whether evolutionary convergence occurs after sixty generations of evolution in a common environment. We found substantial variation in longer-term evolutionary trajectories and differences between short and longer-term evolutionary dynamics. Though we observed pervasive patterns of convergence towards the character values of long-established populations, populations still remain differentiated for several traits at the final generations analyzed. This pattern might involve transient divergence, as we report in some cases, indicating that more generations should lead to final convergence. These findings highlight the importance of longer-term studies for understanding convergent evolution.
Data from: The contribution of phenotypic plasticity to the evolution of insecticide tolerance in amphibian populations
Understanding population responses to rapid environmental changes caused by anthropogenic activities, such as pesticides, is a research frontier. Genetic assimilation (GA), a process initiated by phenotypic plasticity, is one mechanism potentially influencing evolutionary responses to novel environments. While theoretical and laboratory research suggests that GA has the potential to influence evolutionary trajectories, few studies have assessed its role in the evolution of wild populations experiencing novel environments. Using the insecticide, carbaryl, and 15 wood frog populations distributed across an agricultural gradient, we tested whether GA contributed to the evolution of pesticide tolerance. First, we investigated the evidence for evolved tolerance to carbaryl and discovered that population-level patterns of tolerance were consistent with evolutionary responses to pesticides; wood frog populations living closer to agriculture were more tolerant than populations living far from agriculture. Next, we tested the potential role of GA in the evolution of pesticide tolerance by assessing whether patterns of tolerance were consistent with theoretical predictions. We found that populations close to agriculture displayed constitutive tolerance to carbaryl whereas populations far from agriculture had low naïve tolerance but high magnitudes of induced tolerance. These results suggest GA could play a role in evolutionary responses to novel environments in nature.
Data from: Parental care and sibling competition independently increase phenotypic variation among burying beetle siblings
Several recent hypotheses suggest that parental care can influence the extent of phenotypic variation within populations; however, there have been few tests of these ideas. We exploited the facultative nature of post-hatching parental care in the burying beetle, Nicrophorus vespilloides, to test whether parental care influences the expression of phenotypic variation in an important fitness trait (body size). We found that parental care and brood size (which influences sibling competition) had positive and independent effects on variation in body size. First, the mean coefficient of variation (CV) of body size was significantly greater in broods that received care than in those that did not. Second, CV body size increased with brood size in both parental care treatments. These results are not consistent with predictions from recent hypotheses that predict parental care will reduce phenotypic variation among siblings. The positive effects of parental care and brood size on phenotypic variation that we observed are likely due to sibling competition for access to provisioning parents and competition for limiting resources contained in the breeding carcass. Our results suggest that future theory linking parental care to the generation and maintenance of phenotypic variation must integrate the nature of interactions among family members.
Data from: Nonrandom dispersal drives phenotypic divergence within a bird population
Gene flow through dispersal has traditionally been thought to function as a force opposing evolutionary differentiation. However, directional gene flow may actually reinforce divergence of populations in close proximity. This study documents the phenotypic differentiation over more than two decades in body size (tarsus length) at a very short spatial scale (1.1 km) within a population of pied flycatchers Ficedula hypoleuca inhabiting deciduous and coniferous habitats. Unlike females, males breeding in the deciduous forest were consistently larger than those from the managed coniferous forest. This assortment by size is likely explained by preset habitat preferences leading to dominance of the largest males and exclusion of the smallest ones toward the nonpreferred coniferous forest coupled with directional dispersal. Movements of males between forests were nonrandom with respect to body size and flow rate, which might function to maintain the phenotypic variation in this heritable trait at such a small spatial scale. However, a deeply rooted preference for the deciduous habitat might not be in line with its quality due to the increased levels of breeding density of hole-nesting competitors therein. These results illustrate how eco-evolutionary scenarios can develop under directional gene flow over surprisingly small spatial scales. Our findings come on top of recent studies concerning new ways in which dispersal and gene flow can influence microevolution.
Data from: Evidence of weaker phenotypic plasticity by prey to novel cues from non-native predators
A central question in evolutionary biology is how coevolutionary history between predator and prey influences their interactions. Contemporary global change and range expansion of exotic organisms impose a great challenge for prey species, which are increasingly exposed to invading non-native predators, with which they share no evolutionary history. Here, we complete a comprehensive survey of empirical studies of coevolved and naive predator−prey interactions to assess whether a shared evolutionary history with predators influences the magnitude of predator-induced defenses mounted by prey. Using marine bivalves and gastropods as model prey, we found that coevolved prey and predator-naive prey showed large discrepancies in magnitude of predator-induced phenotypic plasticity. Although naive prey, predominantly among bivalve species, did exhibit some level of plasticity – prey exposed to native predators showed significantly larger amounts of phenotypic plasticity. We discuss these results and the implications they may have for native communities and ecosystems.
Data from: Evidence for adaptive phenotypic differentiation in Baltic Sea sticklebacks
The evidence for adaptive phenotypic differentiation in mobile marine species remains scarce, partly due to the difficulty of obtaining quantitative genetic data to demonstrate the genetic basis of the observed phenotypic differentiation. Using a combination of phenotypic and molecular genetic approaches, we elucidated the relative roles of natural selection and genetic drift in explaining lateral plate number differentiation in threespine sticklebacks (Gasterosteus aculeatus) across the entire Baltic Sea basin (ca. 392 000 km2). We found that phenotypic differentiation (PST = 0.213) in plate number exceeded that in neutral markers (FST = 0.008), suggesting an adaptive basis for the observed differentiation. Since a close correspondence was found between plate phenotype and genotype at a QTL (STN381) tightly linked to the gene (Ectodysplasin) underlying plate variation, the evidence for adaptive differentiation was confirmed by comparison of FST at the QTL (FSTQ = 0.089) with FST at neutral marker loci. Hence, the results provide a comprehensive demonstration of adaptive phenotypic differentiation in a high gene flow marine environment with direct, rather than inferred, verification for the genetic basis of this differentiation. In general, the results illustrate the utility of PST – FST – FSTQ comparisons in uncovering footprints of natural selection and evolution, and add to the growing evidence for adaptive genetic differentiation in high-gene flow marine environments, including that of the relatively young Baltic Sea.
Data from: Prednisolone induces osteoporosis-like phenotypes via focal adhesion signaling pathway in zebrafish larvae
Patients taking glucocorticoid or glucocorticoid-like drugs for an extended period of time may develop osteoporosis, termed glucocorticoid-induced osteoporosis (GIOP). GIOP is the most common form of secondary osteoporosis, but the mechanism underlying its development is unclear. In the present study, we used prednisolone to treat zebrafish larvae to investigate GIOP. Our RNA deep-sequencing (RNA-seq) results show that prednisolone affects genes known to act in the extracellular region. Therefore the extracellular region, extracellular matrix, and collagen trimer might be involved in glucocorticoid-induced osteoporosis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the focal adhesion signaling pathway is the most enriched signaling pathway in terms of differentially expressed genes (DEGs). In this pathway, integrin subunit alpha 10 (itga10) and integrin subunit beta like 1 (itgbl1), genes encoding two adapter proteins, were down-regulated in the prednisolone-treated larvae. Further experiments showed that prednisolone contributes to GIOP by down-regulating itga10 and itgbl1.
Data from: Selection in a fluctuating environment leads to decreased genetic variation and facilitates the evolution of phenotypic plasticity
Changes in the environment are expected to induce changes in the quantitative genetic variation, which influences the ability of a population to adapt to environmental change. Furthermore, environmental changes are not constant in time, but fluctuate. Here we investigate the effect of rapid, continuous and/or fluctuating temperature changes in the seed beetle Callosobruchus maculatus, using an evolution experiment followed by a split brood experiment. In line with expectations, individuals responded in a plastic way and had an overall higher potential to respond to selection after a rapid change in the environment. After selection in an environment with increasing temperature, plasticity remained unchanged (or decreased) and environmental variation decreased, especially when fluctuations were added; these results were unexpected. As expected, the genetic variation decreased after fluctuating selection. Our results suggest that fluctuations in the environment have major impact on the response of a population to environmental change; in a highly variable environment with low predictability a plastic response might not be beneficial and the response is genetically and environmentally canalized resulting in a low potential to respond to selection and low environmental sensitivity. Interestingly, we found greater variation for phenotypic plasticity after selection, suggesting that the potential for plasticity to evolve is facilitated after exposure to environmental fluctuations. Our study highlights that environmental fluctuations should be considered when investigating the response of a population to environmental change.
Data from: Heritable variation in an extended phenotype: the case of a parasitoid manipulated by a virus
In host-symbiont interactions, the genes of both host and symbiont can influence phenotypic traits. In the context of a conflict of interest, fitness-related traits are subjected to opposing selective pressures in the genomes of the partners. In the Drosophila parasitoid Leptopilina boulardi, females usually avoid laying eggs into already parasitized larvae. However, when infected by the virus LbFV, they readily lay additional eggs into parasitized larvae. Inducing superparasitism allows the virus to colonize uninfected parasitoid lineages, but is usually mal-adaptive for the parasitoid. We tested for the presence of resistance genes to this behavioural manipulation in the parasitoid genotype by sampling 30 lines from 5 populations with contrasting viral prevalence, after infecting them with a reference viral isolate. No geographical differentiation was observed although some genotypes underwent less manipulation than others and these differences were heritable across generations. The viral titre was not correlated to these differences, although fecundity differed between extreme lines.
Data from: Phenotypic shift in Wolbachia virulence towards its native host across serial horizontal passages
Vertical transmission mode is predicted to decrease the virulence of symbionts. However, Wolbachia, a widespread vertically transmitted endosymbiont, exhibits both negative and beneficial effects on arthropod fitness. This 'Jekyll and Hyde' behaviour, as well as its ability to live transiently outside host cells and to establish new infections via horizontal transmission, may reflect the capacity of Wolbachia to exhibit various phenotypes depending on the prevailing environmental constraints. To study the ability of Wolbachia to readily cope with new constraints, we forced this endosymbiont to spread only via horizontal transmission. To achieve this, we performed serial horizontal transfers of haemolymph from Wolbachia-infected to naive individuals of the isopod Armadillidium vulgare. Across passages, we observed phenotypic changes in the symbiotic relationship: (i) The Wolbachia titre increased in both haemolymph and nerve cord but remained stable in ovaries; (ii) Wolbachia infection was benign at the beginning of the experiment, but highly virulent, killing most hosts after only a few passages. Such a phenotypic shift after recurrent horizontal passages demonstrates that Wolbachia can rapidly change its virulence when facing new environmental constraints. We thoroughly discuss the potential mechanism(s) underlying this phenotypic change, which are likely to be crucial for the ongoing radiation of Wolbachia in arthropods.
Data from: Phenotypic plasticity of mate recognition systems prevents sexual interference between two sympatric leaf beetle species
Maladaptive sexual interactions among heterospecific individuals (sexual interference) can prevent the coexistence of animal species. Thus, the avoidance of sexual interference by divergence of mate recognition systems is crucial for a stable coexistence in sympatry. Mate recognition systems are thought to be under tight genetic control. However, we demonstrate that mate recognition systems of two closely related sympatric leaf beetle species show a high level of host-induced phenotypic plasticity. Mate choice in the mustard leaf beetles, Phaedon cochleariae and P. armoraciae, is mediated by cuticular hydrocarbons (CHCs). Divergent host plant use causes a divergence of CHC phenotypes, whereas similar host use leads to their convergence. Consequently, both species exhibit significant behavioral isolation when they feed on alternative host species, but mate randomly when using a common host. Thus, sexual interference between these syntopic leaf beetles is prevented by host-induced phenotypic plasticity rather than by genotypic divergence of mate recognition systems.
Data from: Independence among physiological traits suggests flexibility in the face of ecological demands on phenotypes
Phenotypic flexibility allows animals to adjust their physiology to diverse environmental conditions encountered over the year. Examining how these varying traits covary gives insights into potential constraints or freedoms that may shape evolutionary trajectories. In this study we examined relationships among hematocrit, baseline corticosterone concentration, constitutive immune function and basal metabolic rate in red knot Calidris canutus islandica individuals subjected to experimentally manipulated temperature treatments over an entire annual cycle. If covariation among traits is constrained, we predict consistent covariation within and among individuals. We further predict consistent correlations between physiological and metabolic traits if constraints underlie species level patterns found along the slow-fast pace-of-life continuum. We found no consistent correlations among hematocrit, baseline corticosterone concentration, immune function and basal metabolic rate either within or among individuals. This provides no evidence for constraints limiting relationships among these measures of the cardiovascular, endocrine, immune and metabolic systems in individual red knots. Rather, our data suggest that knots are free to adjust individual parts of their physiology independently. This makes good sense if one places the animal within its ecological context where different aspects of the environment might put different pressures on different aspects of physiology.
Data from: Does phenotypic plasticity for adult size versus food level in Drosophila melanogaster evolve in response to adaptation to different rearing densities?
Recent studies using inbred lines of Drosophila have suggested that there is extensive genetic variability for phenotypic plasticity of body size versus food level. If true, we expect that the outcome of evolution at very different food levels should yield genotypes whose adult sizes show different patterns of phenotypic plasticity. We have tested this prediction with six independent populations of Drosophila melanogaster kept at extreme (low vs. high) densities for 125 generations. We found that the phenotypic plasticity of body size versus food level is not affected by selection or the presence of competitors of a different genotype. However, we document increasing among population variation in phenotypic plasticity due to random genetic drift. Several reasons are explored to explain these results including the possibility that the use of highly inbred lines to make inferences about the evolution of genetically variable populations may be misleading.
Data from: Experimental evolution reveals differences between phenotypic and evolutionary responses to population density
Group living can select for increased immunity, given the heightened risk of parasite transmission. Yet, it also may select for increased male reproductive investment, given the elevated risk of female multiple mating. Trade-offs between immunity and reproduction are well documented. Phenotypically, population density mediates both reproductive investment and immune function in the Indian meal moth, Plodia interpunctella. However, the evolutionary response of populations to these traits is unknown. We created two replicated populations of P. interpunctella, reared and mated for 14 generations under high or low population densities. These population densities cause plastic responses in immunity and reproduction: at higher numbers, both sexes invest more in one index of immunity (phenoloxidase (PO) activity) and males invest more in sperm. Interestingly, our data revealed divergence in PO and reproduction in a different direction to previously reported phenotypic responses. Males evolving at low population densities transferred more sperm and both males and females displayed higher PO than individuals at high population densities. These positively correlated responses to selection suggest no apparent evolutionary trade-off between immunity and reproduction. We speculate that the reduced PO activity and sperm investment when evolving under high population density may be due to the reduced population fitness predicted under increased sexual conflict and/or to trade-offs between pre- and post-copulatory traits.
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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)
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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.