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186 results for “Quantitative genetics”
Data from: Quantitative genetic variance in experimental fly populations evolving with or without environmental heterogeneity
Heterogeneous environments are typically expected to maintain more genetic variation in fitness within populations than homogeneous environments. However, the accuracy of this claim depends on the form of heterogeneity as well as the genetic basis of fitness traits and how similar the assay environment is to the environment of past selection. Here we measure quantitative genetic variance for three traits important for fitness using replicated experimental populations of Drosophila melanogaster evolving under four selective regimes: constant salt-enriched medium (Salt), constant cadmium-enriched medium (Cad), and two heterogeneous regimes that vary either temporally (Temp) or spatially (Spatial). As theory predicts, we found that Spatial populations tend to harbor more genetic variation than Temp populations or those maintained in a constant environment that is the same as the assay environment. Contrary to expectation, Salt populations tend to have more genetic variation than Cad populations in both assay environments. We discuss the patterns for quantitative genetic (QG) variances across regimes in relation to previously reported data on genome-wide sequence diversity. For some traits, the QG patterns are similar to the diversity patterns of ecological selected SNPs whereas the QG patterns for some other traits resembled that of neutral SNPs.
Data from: Quantitative genetic analysis of subspecific differences in body shape in the snail-feeding carabid beetle Damaster blaptoides
A dimorphic pattern of macrocephalic (wide, short) and stenocephalic (narrow, long) body shapes is observed in snail-feeding carabid beetles globally. The former exhibits high performance in crushing snail shells with powerful jaws, whereas the latter specializes in eating snails' soft body directly by inserting the head into the shell. In the snail-feeding species Damaster blaptoides, the subspecies D. b. capito has a wide short forebody, and D. b. fortunei has a narrow, long forebody. They exhibit distinct morphologies despite their geographic and phylogenetic proximity. To examine the genetic basis of the morphological differences between these two subspecies, we conducted quantitative genetic analyses by crossing these subspecies and producing F_1 and backcross hybrids. The hybrids had body shapes intermediate between the parental subspecies. The variation between wide, short and narrow, long forebodies was based on negative geneti c correlations between width and length of the head and thorax. Between one and eight genetic factors were involved in the morphological differences between subspecies. We suggest that the morphological integration of forebody parts in a small number of loci has facilitated the marked morphological diversification between subspecies of D. blaptoides.
Data from: Quantitative genetic insights into the coevolutionary dynamics of male and female genitalia
The spectacular variability that typically characterizes male genital traits has largely been attributed to the role of sexual selection. Among the evolutionary mechanisms proposed to account for this diversity, two processes in particular have generated considerable interest. On the one hand, females may exploit postcopulatory mechanisms of selection to favour males with preferred genital traits (cryptic female choice; CFC), while on the other hand females may evolve structures or behaviours that mitigate the direct costs imposed by male genitalia (sexual conflict; SC). A critical but rarely explored assumption underlying both processes is that male and female reproductive traits coevolve, either via the classic Fisherian model of preference-trait coevolution (CFC) or through sexually antagonistic selection (SC). Here, we provide evidence for this prediction in the guppy (Poecilia reticulata), a polyandrous livebearing fish in which males transfer sperm internally to females via consensual and forced matings. Our results from a paternal half-sibling breeding design reveal substantial levels of additive genetic variation underlying male genital size and morphology—two traits known to predict mating success during non-consensual matings. Our subsequent finding that physically interacting female genital traits exhibit corresponding levels of genetic (co)variation reveals the potential intersexual coevolutionary dynamics of male and female genitalia, thereby fulfilling a fundamental assumption underlying CFC and SC theory.
Data from: Quantitative genetic variance and multivariate clines in the Ivyleaf morning glory, Ipomoea hederacea
Clinal variation is commonly interpreted as evidence of adaptive differentiation, although clines can also be produced by stochastic forces. Understanding whether clines are adaptive therefore requires comparing clinal variation to background patterns of genetic differentiation at presumably neutral markers. Although this approach has frequently been applied to single traits at a time, we have comparatively fewer examples of how multiple correlated traits vary clinally. Here, we characterize multivariate clines in the Ivyleaf morning glory, examining how suites of traits vary with latitude, with the goal of testing for divergence in trait means that would indicate past evolutionary responses. We couple this with analysis of genetic variance in clinally varying traits in 20 populations to test whether past evolutionary responses have depleted genetic variance, or whether genetic variance declines approaching the range margin. We find evidence of clinal differentiation in five quantitative traits, with little evidence of isolation by distance at neutral loci that would suggest non-adaptive or stochastic mechanisms. Within and across populations, the traits that contribute most to population differentiation and clinal trends in the multivariate phenotype are genetically variable as well, suggesting that a lack of genetic variance will not cause absolute evolutionary constraints. Our data are broadly consistent theoretical predictions of polygenic clines in response to shallow environmental gradients. Ecologically, our results are consistent with past findings of natural selection on flowering phenology, presumably due to season-length variation across the range.
Pedigree-free quantitative genetic approach provides evidence for heritability of movement tactics in wild roe deer
<p>Assessing the evolutionary potential of animal populations in the wild is crucial to understanding how they may respond to selection mediated by rapid environmental change (e.g. habitat loss and fragmentation). A growing number of studies have investigated the adaptive role of behaviour, but assessments of its genetic basis in a natural setting remain scarce. We combined intensive biologging technology with genome-wide data and a pedigree-free quantitative genetic approach to quantify repeatability, heritability and evolvability for a suite of behaviours related to the risk avoidance-resource acquisition trade-off in a wild roe deer (Capreolus capreolus) population inhabiting a heterogeneous, human-dominated landscape. These traits, linked to the stress response, movement and space-use behaviour, were all moderately to highly repeatable. Furthermore, the repeatable among-individual component of variation in these traits was partly due to additive genetic variance, with heritability estimates ranging from 0.19±0.07 to 0.71±0.11 and evolvability ranging from 1.1 to 4.3%. Changes in the trait mean can therefore occur under hypothetical directional selection over just a few generations. To the best of our knowledge, this is the first empirical demonstration of additive genetic variation in space-use behaviour in a free-ranging population based on genomic relatedness data. We conclude that wild animal populations may have the potential to adjust their spatial behaviour to human-driven environmental modifications through micro-evolutionary change.</p>
Data from: Age and sex affect quantitative genetic parameters for dominance rank and aggression in free-living greylag geese
Knowledge of the genetic and environmental influences on a character is pivotal for understanding evolutionary changes in quantitative traits in natural populations. Dominance and aggression are ubiquitous traits that are selectively advantageous in many animal societies and have the potential to impact the evolutionary trajectory of animal populations. Here we provide age- and sex-specific estimates of additive genetic and environmental components of variance for dominance rank and aggression rate in a free-living, human-habituated bird population subject to natural selection. We use a long-term data set on individually marked greylag geese (Anser anser) and show that phenotypic variation in dominance-related behaviours contains significant additive genetic variance, parental effects and permanent environment effects. The relative importance of these variance components varied between age and sex classes, whereby the most pronounced differences concerned non-genetic components. In particular, parental effects were larger in juveniles of both sexes than in adults. In paired adults, the partner's identity had a larger influence on male dominance rank and aggression rate than in females. In sex- and age-specific estimates, heritabilities did not differ significantly between age and sex classes. Adult dominance rank was only weakly genetically correlated between the sexes, leading to considerably higher heritabilities in sex-specific estimates than across sexes. We discuss these patterns in relation to selection acting on dominance rank and aggression in different life history stages and sexes and suggest that different adaptive optima could be a mechanism for maintaining genetic variation in dominance-related traits in free-living animal populations.
Data from: Uncovering the genetic signature of quantitative trait evolution with replicated time series data
The genetic architecture of adaptation in natural populations has not yet been resolved: it is not clear to what extent the spread of beneficial mutations (selective sweeps) or the response of many quantitative trait loci drive adaptation to environmental changes. Although much attention has been given to the genomic footprint of selective sweeps, the importance of selection on quantitative traits is still not well studied, as the associated genomic signature is extremely difficult to detect. We propose 'Evolve and Resequence' as a promising tool, to study polygenic adaptation of quantitative traits in evolving populations. Simulating replicated time series data we show that adaptation to a new intermediate trait optimum has three characteristic phases that are reflected on the genomic level: (1) directional frequency changes towards the new trait optimum, (2) plateauing of allele frequencies when the new trait optimum has been reached and (3) subsequent divergence between replicated trajectories ultimately leading to the loss or fixation of alleles while the trait value does not change. We explore these 3 phase characteristics for relevant population genetic parameters to provide expectations for various experimental evolution designs. Remarkably, over a broad range of parameters the trajectories of selected alleles display a pattern across replicates, which differs both from neutrality and directional selection. We conclude that replicated time series data from experimental evolution studies provide a promising framework to study polygenic adaptation from whole-genome population genetics data.
Data from: Population size is weakly related to quantitative genetic variation and trait differentiation in a stream fish
How population size influences quantitative genetic variation and differentiation among natural, fragmented populations remains unresolved. Small, isolated populations might occupy poor quality habitats and lose genetic variation more rapidly due to genetic drift than large populations. Genetic drift might furthermore overcome selection as population size decreases. Collectively, this might result in directional changes in additive genetic variation (VA) and trait differentiation (QST) from small to large population size. Alternatively, small populations might exhibit larger variation in VA and QST if habitat fragmentation increases variability in habitat types. We explored these alternatives by investigating VA and QST using nine fragmented populations of brook trout varying 50-fold in census size N (179-8416) and 10-fold in effective number of breeders, Nb (18-135). Across 15 traits, no evidence was found for consistent differences in VA and QST with population size and almost no evidence for increased variability of VA or QST estimates at small population size. This suggests that (i) small populations of some species may retain adaptive potential according to commonly adopted quantitative genetic measures and (ii) populations of varying sizes experience a variety of environmental conditions in nature, however extremely large studies are likely required before any firm conclusions can be made.
Data from: Multiple mating but not recombination causes quantitative increase in offspring genetic diversity for varying genetic architectures
Explaining the evolution of sex and recombination is particularly intriguing for some species of eusocial insects because they display exceptionally high mating frequencies and genomic recombination rates. Explanations for both phenomena are based on the notion that both increase colony genetic diversity, with demonstrated benefits for colony disease resistance and division of labor. However, the relative contributions of mating number and recombination rate to colony genetic diversity have never been simultaneously assessed. Our study simulates colonies, assuming different mating numbers, recombination rates, and genetic architectures, to assess their worker genotypic diversity. The number of loci has a strong negative effect on genotypic diversity when the allelic effects are inversely scaled to locus number. In contrast, dominance, epistasis, lethal effects, or limiting the allelic diversity at each locus does not significantly affect the model outcomes. Mating number increases colony genotypic variance and lowers variation among colonies with quickly diminishing returns. Genomic recombination rate does not affect intra- and inter-colonial genotypic variance, regardless of mating frequency and genetic architecture. Recombination slightly increases the genotypic range of colonies and more strongly the number of workers with unique allele combinations across all loci. Overall, our study contradicts the argument that the exceptionally high recombination rates cause a quantitative increase in offspring genotypic diversity across one generation. Alternative explanations for the evolution of high recombination rates in social insects are therefore needed. Short-term benefits are central to most explanations of the evolution of multiple mating and high recombination rates in social insects but our results also apply to other species.
Data from: The genetic basis of discrete and quantitative colour variation in the polymorphic lizard, Ctenophorus decresii
Background: Colour polymorphic species provide invaluable insight into processes that generate and maintain intra-specific variation. Despite an increasing understanding of the genetic basis of discrete morphs, sources of colour variation within morphs remain poorly understood. Here we use the polymorphic tawny dragon lizard Ctenophorus decresii to test simple Mendelian models for the inheritance of discrete morphs, and to investigate the genetic basis of continuous variation among individuals across morphs. Males of this species express either orange, yellow, orange surrounded by yellow, or grey throats. Although four discrete morphs are recognised, the extent of orange and yellow varies greatly. We artificially elevated testosterone in F0 females and F1 juveniles to induce them to express the male throat colour polymorphism, and quantified colour variation across the pedigree. Results: Inheritance of discrete morphs in C. decresii best fit a model whereby two autosomal loci with complete dominance respectively determine the presence of orange and yellow. However, a single locus model with three co-dominant alleles for orange, yellow and grey could not be definitively rejected. Additionally, quantitative expression of the proportion of orange and yellow on the throat was strongly heritable (orange: h2 = 0.84 ± 0.14; yellow: h2 = 0.67 ± 0.19), with some evidence for covariance between the two. Conclusions: Our study supports the theoretical prediction that polymorphism should be governed by few genes of major effect, but implies broader genetic influence on variation in constituent morph traits.
Data from: Identification of quantitative genetic components of fitness variation in farmed, hybrid and native salmon in the wild
Feral animals represent an important problem in many ecosystems due to interbreeding with wild conspecifics. Hybrid offspring from wild and domestic parents are often less adapted to local environment and ultimately, can reduce the fitness of the native population. This problem is an important concern in Norway, where each year, hundreds of thousands of farm Atlantic salmon escape from fish farms. Feral fish outnumber wild populations, leading to a possible loss of local adaptive genetic variation and erosion of genetic structure in wild populations. Studying the genetic factors underlying relative performance between wild and domesticated conspecific can help to better understand how domestication modifies the genetic background of populations, and how it may alter their ability to adapt to the natural environment. Here, based upon a large-scale release of wild, farm and wild x farm salmon crosses into a natural river system, a genome-wide quantitative trait locus (QTL) scan was performed on the offspring of 50 full-sib families, for traits related to fitness (length, weight, condition factor and survival). Six QTLs were detected as significant contributors to the phenotypic variation of the first three traits, explaining collectively between 9.8 and 14.8% of the phenotypic variation. The seventh QTL had a significant contribution to the variation in survival, and is regarded as a key factor to understand the fitness variability observed among salmon in the river. Interestingly, strong allelic correlation within one of the QTL regions in farmed salmon might reflect a recent selective sweep due to artificial selection.
Data from: Social cues affect quantitative genetic variation and covariation in animal personality traits
The social environment is expected to have substantial effects on behavior, and as a consequence its heritability and evolvability. We investigated these effects by exposing Australian field crickets (Teleogryllus oceanicus) to either silence or recordings of male acoustic sexual signals. We used a combined pedigree and full-sib/half-sib breeding design to estimate the repeatability, heritability, and evolvability of behaviors related to boldness, exploration, and activity. All behaviors measured were significantly repeatable in both social environments. Additionally, most behaviors showed significant heritabilities in the two environments. We found no difference in repeatabilities between the silent and the acoustic environment but did find significant differences in the heritabilities and evolvabilities between these environments. There was a high degree of similarity between the phenotypic covariance matrices across the two environments, while the genotypic covariance matrices were highly dissimilar. Reflecting this, we found significant genotype-by-environment interactions for most of the behaviors. Lastly, we found that the repeatable aspect of behavior ('personality') was significantly heritable for most behaviors, but that these heritabilities were higher in the acoustic than in the silent environment. We conclude that the social environment can have a significant impact on the heritability and evolvability of behavior, and argue that evolutionary inferences from phenotypic studies should be made with caution.
Data from: QTL and quantitative genetic analysis of beak morphology reveals patterns of standing genetic variation in an Estrildid finch
The intra- and interspecific diversity of avian beak morphologies is one of the most compelling examples for the power of natural selection acting on a morphological trait. The development and diversification of the beak has also become a textbook example for evolutionary developmental biology, and variation in expression levels of several genes is known to causally affect beak shape. However, until now no genomic polymorphisms have been identified that are related to beak morphology in birds. QTL mapping does reveal the location of causal polymorphisms, albeit with poor spatial resolution. Here we estimate heritability and genetic correlations for beak length, depth and width and perform a QTL linkage analysis for these traits based on 1,404 informative single nucleotide polymorphisms genotyped in a four generation pedigree of 992 captive zebra finches (Taeniopygia guttata). Beak size, relative to body size, was sexually dimorphic (larger in males). Heritability estimates ranged from 0.47 for beak length to 0.74 for beak width. QTL mapping revealed four to five regions of significant or suggestive genome-wide linkage for each of the three beak dimensions (nine different regions in total). Eight out of eleven genes known to influence beak morphology are located in these nine peak regions. Five QTL do not cover known candidates demonstrating that yet unknown genes or regulatory elements may influence beak morphology in the zebra finch.
Data from: Drosophila wing modularity revisited through a quantitative genetic approach
To predict the response of complex morphological structures to selection it is necessary to know how the covariation among its different parts is organized. Two key features of covariation are modularity and integration. The Drosophila wing is currently considered a fully integrated structure. Here, we study the patterns of integration of the Drosophila wing and test the hypothesis of the wing being divided into two modules along the proximo-distal axis, as suggested by developmental, biomechanical, and evolutionary evidence. To achieve these goals we perform a multilevel analysis of covariation combining the techniques of geometric morphometrics and quantitative genetics. Our results indicate that the Drosophila wing is indeed organized into two main modules, the wing base and the wing blade. The patterns of integration and modularity were highly concordant at the phenotypic, genetic, environmental, and developmental levels. Besides, we found that modularity at the developmental level was considerably higher than modularity at other levels, suggesting that in the Drosophila wing direct developmental interactions are major contributors to total phenotypic shape variation. We propose that the precise time at which covariance-generating developmental processes occur and/or the magnitude of variation that they produce favor proximo-distal, rather than anterior-posterior, modularity in the Drosophila wing.
Data from: Quantitative genetics of female mate preferences in an ancestral and a novel environment
A female's mate preference is a potentially complex function relating variation in multiple male phenotypes with her probability of accepting individual males as a mate. Estimating the quantitative genetic basis of preference functions within a population is empirically challenging yet key to understanding preference evolution. We employed a recently described approach that uses random-coefficient mixed models in the analysis of function-valued traits. Using a half-sibling breeding design in a laboratory-adapted Drosophila serrata population, we estimated the genetic (co)variance function of female preference for male sexual displays composed of nine contact pheromones. The breeding design was performed across two environments: the food to which the population was well adapted and a novel food that reduced average female productivity by 35%. Significant genetic variance in female preference was detected and the majority (64.2%) was attributable to a single genetic dimension (eigenfunction), suggesting that preferences for different pheromones are not genetically independent. The second eigenfunction, accounting for 24% of the total genetic variance, approached significance in a conservative test, suggesting the existence of a second, independent genetic dimension. There was no evidence that the genetic basis of female preference differed between the two environments, suggesting the absence of genotype-by-environment interactions and hence a lack of condition-dependent preference expression.
Data from: The evolution of genetic architectures underlying quantitative traits
In the classic view introduced by R. A. Fisher, a quantitative trait is encoded by many loci with small, additive effects. Recent advances in quantitative trait loci mapping have begun to elucidate the genetic architectures underlying vast numbers of phenotypes across diverse taxa, producing observations that sometimes contrast with Fisher's blueprint. Despite these considerable empirical efforts to map the genetic determinants of traits, it remains poorly understood how the genetic architecture of a trait should evolve, or how it depends on the selection pressures on the trait. Here, we develop a simple, population-genetic model for the evolution of genetic architectures. Our model predicts that traits under moderate selection should be encoded by many loci with highly variable effects, whereas traits under either weak or strong selection should be encoded by relatively few loci. We compare these theoretical predictions with qualitative trends in the genetics of human traits, and with systematic data on the genetics of gene expression levels in yeast. Our analysis provides an evolutionary explanation for broad empirical patterns in the genetic basis for traits, and it introduces a single framework that unifies the diversity of observed genetic architectures, ranging from Mendelian to Fisherian.
Data from: Quantitative trait loci from the host genetic background modulate the durability of a resistance gene: a rational basis for sustainable resistance breeding in plants
The combination of major resistance genes with quantitative resistance factors is hypothesized as a promising breeding strategy to preserve the durability of resistant cultivar, as recently observed in different pathosystems. Using the pepper (Capsicum annuum)/Potato virus Y (PVY, genus Potyvirus) pathosystem, we aimed at identifying plant genetic factors directly affecting the frequency of virus adaptation to the major resistance gene pvr23 and at comparing them with genetic factors affecting quantitative resistance. The resistance breakdown frequency was a highly heritable trait (h²=0.87). Four loci including additive quantitative trait loci (QTLs) and epistatic interactions explained together 70% of the variance of pvr23 breakdown frequency. Three of the four QTLs controlling pvr23 breakdown frequency were also involved in quantitative resistance, strongly suggesting that QTLs controlling quantitative resistance have a pleiotropic effect on the durability of the major resistance gene. With the first mapping of QTLs directly affecting resistance durability, this study provides a rationale for sustainable resistance breeding. Surprisingly, a genetic trade-off was observed between the durability of PVY resistance controlled by pvr23 and the spectrum of the resistance against different potyviruses. This trade-off seemed to have been resolved by the combination of minor-effect durability QTLs under long term farmer selection.
Fig. 1 in Quantitative genetics of gastrointestinal strongyle burden and associated body condition in feral horses
Fig. 1. Map of Sable Island, Nova Scotia, Canada, showing its position relative to the Canadian mainland and the predominant land cover types.
Data from: Quantitative genetics of immunity and life history under different photoperiods
Insects with complex life-cycles should optimize age and size at maturity during larval development. When inhabiting seasonal environments, organisms have limited reproductive periods and face fundamental decisions: individuals that reach maturity late in season have to either reproduce at a small size or increase their growth rates. Increasing growth rates is costly in insects due to higher juvenile mortality, decreased adult survival, or increased susceptibility to parasitism by bacteria and viruses via compromised immune function. Environmental changes such as seasonality can also alter the quantitative genetic architecture. Here we explore the quantitative genetics of life history and immunity traits under two experimentally induced seasonal environments in the cricket Gryllus bimaculatus. Seasonality affected the life history but not the immune phenotypes. Individuals under decreasing day length developed slower and grew to a bigger size. We found ample additive genetic variance and heritability for components of immunity (haemocyte densities, proPhenoloxidase activity, resistance against Serratia marcescens), and for the life history traits, age and size at maturity. Despite genetic covariance among traits, the structure of G was inconsistent with genetically based trade-off between life history and immune traits (e.g., a strong positive genetic correlation between growth rate and haemocyte density was estimated). However, conditional evolvabilities support the idea that genetic covariance structure limits the capacity of individual traits to evolve independently. We found no evidence for GxE interactions arising from the experimentally induced seasonality.
Data from: Comparison of non-Gaussian quantitative genetic models for migration and stabilizing selection
The balance between stabilizing selection and migration of maladapted individuals has formerly been modeled using a variety of quantitative genetic models of increasing complexity, including models based on a constant expressed genetic variance and models based on normality. The infinitesimal model can accommodate non-normality and a non-constant genetic variance as a result of linkage disequilibrium. It can be seen as a parsimonious one-parameter model which approximates the underlying genetic details well when a large number of loci are involved. Here, the performance of this model is compared to several more realistic explicit multilocus models, with either two, several or a large number of alleles per locus with unequal effect sizes. Predictions for the deviation of the population mean from the optimum are highly similar across the different models, so that the non-Gaussian infinitesimal model forms a good approximation. It does however generally estimate a higher genetic variance than the multilocus models, with the difference decreasing with an increasing number of loci. The difference between multilocus models depends more strongly on the effective number of loci, accounting for relative contributions of loci to the variance, than on the number of alleles per locus.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.