Source Of Variation For Traits Research Articles

Cis- and trans-regulatory contributions to a hierarchy of factors influencing gene expression variation

Gene expression variation results from numerous sources including genetic, environmental, life stage, and even the environment experienced by previous generations. While the importance of each has been demonstrated in diverse organisms, their relative contributions remain understudied because few investigations have simultaneously determined each within a single experiment. Here we quantified genome-wide gene expression traits in Drosophila, quantified the contribution of multiple different sources of trait variation and determined the molecular mechanisms underlying observed variation. Our results show that there is a clear hierarchy in our data with genome and developmental stage contributing on average considerably more than current and finally previous generation environmental effects. We also determined the role of cis and trans-regulatory changes across different sources of trait variation, highlighting their importance in adaptation and environmental responses and showing unexpectedly that transgenerational effects herein were predominantly associated with changes in trans-regulation.

Quantifying the capacity for contemporary trait changes to drive intermittent predator–prey cycles

AbstractA large and growing body of theory has demonstrated how the presence of trait variation in prey or predator populations may affect the amplitude and phase of predator–prey cycles. Less attention has been given to so‐called intermittent cycles, in which predator–prey oscillations recurrently disappear and re‐appear, despite such dynamics being observed in empirical systems and modeling studies. A comprehensive understanding of the conditions under which trait changes may drive intermittent predator–prey dynamics, as well as their potential ecological implications, is therefore missing. Here we provide a first systematic analysis of the eco‐evolutionary conditions that may give rise to intermittent predator–prey cycles, investigating 16 models that incorporate different types of trait variation within prey, predators, or both. Our results show that intermittent dynamics often arise through predator–prey coevolution, but only very rarely when only one trophic level can adapt. Additionally, the frequency of intermittent cycles depends on the source of trait variation (genetic variation or phenotypic plasticity) and the genetic architecture (Mendelian or quantitative traits), with intermittency occurring most commonly through Mendelian evolution, and very rarely through phenotypic plasticity. Further analysis identified three necessary conditions for when trait variation can drive intermittent cycles. First, the intrinsic stability of the predator–prey system must depend on the traits of prey, predators, or both. Second, there must be a mechanism causing the recurrent alternation between stable and unstable states, leading to a “trait” cycle superimposed on the population dynamics. Finally, these trait dynamics must be significantly slower than the predator–prey cycles. We show how these conditions explain all the abovementioned patterns. We further show an important unexpected consequence of these necessary conditions: they are most easily met when intraspecific trait variation is at high risk of being lost. As trait diversity is positively associated with ecosystem functioning, this can have potentially severe negative consequences. This novel result highlights the importance of identifying and understanding intermittent cycles in theoretical studies and natural systems. The new approach for detecting and quantifying intermittency we develop here will be instrumental in enabling future study.

Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traits.

DNA methylation is a chromatin modification that plays an essential role in regulating gene expression and genome stability and it is typically associated with gene silencing and heterochromatin. Owing to its heritability, alterations in the patterns of DNA methylation have the potential to provide for epigenetic inheritance of traits. Contemporary epigenomic technologies provide information beyond sequence variation and could supply alternative sources of trait variation for improvement in crops such as sorghum. Yet, compared with other species such as maize and rice, the sorghum DNA methylome is far less well understood. The distribution of CG, CHG, and CHH methylation in the genome is different compared with other species. CG and CHG methylation levels peak around centromeric segments in the sorghum genome and are far more depleted in the gene dense chromosome arms. The genes regulating DNA methylation in sorghum are also yet to be functionally characterised; better understanding of their identity and functional analysis of DNA methylation machinery mutants in diverse genotypes will be important to better characterise the sorghum methylome. Here, we catalogue homologous genes encoding methylation regulatory enzymes in sorghum based on genes in Arabidopsis, maize, and rice. Discovering variation in the methylome may uncover epialleles that provide extra information to explain trait variation and has the potential to be applied in epigenome-wide association studies or genomic prediction. DNA methylation can also improve genome annotations and discover regulatory elements underlying traits. Thus, improving our knowledge of the sorghum methylome can enhance our understanding of the molecular basis of traits and may be useful to improve sorghum performance.

Phylogenetic ANOVA: Group-clade aggregation, biological challenges, and a refined permutation procedure.

Phylogenetic regression is frequently used in macroevolutionary studies, and its statistical properties have been thoroughly investigated. By contrast, phylogenetic ANOVA has received relatively less attention, and the conditions leading to incorrect statistical and biological inferences when comparing multivariate phenotypes among groups remain underexplored. Here, we propose a refined method of randomizing residuals in a permutation procedure (RRPP) for evaluating phenotypic differences among groups while conditioning the data on the phylogeny. We show that RRPP displays appropriate statistical properties for both phylogenetic ANOVA and regression models, and for univariate and multivariate datasets. For ANOVA, we find that RRPP exhibits higher statistical power than methods utilizing phylogenetic simulation. Additionally, we investigate how group dispersion across the phylogeny affects inferences, and reveal that highly aggregated groups generate strong and significant correlations with the phylogeny, which reduce statistical power and subsequently affect biological interpretations. We discuss the broader implications of this phylogenetic group aggregation, and its relation to challenges encountered with other comparative methods where one or a few transitions in discrete traits are observed on the phylogeny. Finally, we recommend that phylogenetic comparative studies of continuous trait data use RRPP for assessing the significance of indicator variables as sources of trait variation.

Decomposing functional trait associations in a Chinese subtropical forest.

Functional traits, properties of organisms correlated with ecological performance, play a central role in plant community assembly and functioning. To some extents, functional traits vary in concert, reflecting fundamental ecological strategies. While “trait syndromes” characteristic of e.g. fast-growing, early-successional vs. competitive, late-successional species are recognized in principle, less is known about the environmental and genetic factors at the source of trait variation and covariation within plant communities. We studied the three leaf traits leaf half-life (LHL), leaf mass per area (LMA) and nitrogen concentration in green leaves (Ngreen) and the wood trait wood density (WD) in 294 individuals belonging to 45 tree or shrub species in a Chinese subtropical forest from September 2006 to January 2009. Using multilevel ANOVA and decomposition of sums of products, we estimated the amount of trait variation and covariation among species (mainly genetic causes), i.e. plant functional type (deciduous vs. evergreen species), growth form (tree vs. shrub species), family/genus/species differences, and within species (mainly environmental causes), i.e. individual and season. For single traits, the variation between functional types and among species within functional types was large, but only LMA and Ngreen varied significantly among families and thus showed phylogenetic signal. Trait variation among individuals within species was small, but large temporal variation due to seasonal effects was found within individuals. We did not find any trait variation related to soil conditions underneath the measured individuals. For pairs of traits, variation between functional types and among species within functional types was large, reflecting a strong evolutionary coordination of the traits, with LMA, LHL and WD being positively correlated among each other and negatively with Ngreen. This integration of traits was consistent with a putative stem-leaf economics spectrum ranging from deciduous species with thin, high-nitrogen leaves and low-density wood to evergreen species with thick, low-nitrogen leaves and dense wood and was not influenced by phylogenetic history. Trait coordination within species was weak, allowing individual trees to deviate from the interspecific trait coordination and thus respond flexibly to environmental heterogeneity. Our findings suggest that within a single woody plant community variation and covariation in functional traits allows a large number of species to co-exist and cover a broad spectrum of multivariate niche space, which in turn may increase total resource extraction by the community and community functioning.

Eco-evolutionary dynamics: investigating multiple causal pathways linking changes in behavior, population density and natural selection

Correlations between population density, natural selection and phenotypic change are widespread and may comprise an eco-evolutionary feedback loop, yet we still know very little about the causes of connections between them. Isolating the mechanistic links in eco-evolutionary feedback loops, both in terms of identifying sources of variation in traits and in terms of determining how and why natural selection varies with population density, can provide key insight into avian population dynamics. Here, we summarize more than a decade of findings in western bluebirds (Sialia mexicana) to illustrate the multiple and potentially interacting mechanisms that can cause simultaneous changes in traits and population density. In previous work, we discovered correlated changes in aggression, population density and natural selection during the process of colonization. Here we provide evidence that density-dependent selection, maternal effects and demographic consequences of selection on aggression may all play a role in driving feedback between phenotypic change and population density. Thus, this system provides an example of the multiple mechanistic links that can produce such feedback loops and emphasizes the importance of investigating alternative hypotheses for correlated patterns of ecological and phenotypic change even when there is strong evidence that natural selection is acting on a trait. Ultimately, identifying these mechanisms is crucial, as eco-evolutionary feedback have the potential to explain avian population cycles, range dynamics, population persistence, and even patterns of species coexistence.

Phenotypic plasticity influences the eco‐evolutionary dynamics of a predator–prey system

There is increasing evidence that rapid phenotypic evolution can strongly influence population dynamics, but how are such eco‐evolutionary dynamics influenced by the source of trait variation (i.e., genetic variation or phenotypic plasticity)? To investigate this, we used rotifer–algae microcosm experiments to test how the phenotypic and genetic composition of prey populations affect predator–prey population dynamics. We chose four genetically distinct strains of the green alga Chlamydomonas reinhardtii that varied in their growth rate, standing levels of defense, and inducible defense. To additionally test for strain specificity of plasticity responses, we quantified protein expression of each strain in the presence and absence of rotifer predators (Brachionus calyciflorus). We then tested how different strain combinations influenced the outcome of pairwise competition trials with and without rotifer predation. We tracked individual strain frequencies using quantitative polymerase chain reaction (qPCR), and compared the observed dynamics to a suite of eco‐evolutionary models of varying complexity. We found that variation in trade‐offs between growth and defense between algal strains strongly influenced the outcome of competition and the overall predator–prey dynamics. Our purely ecological model of the observed dynamics, which allowed for the presence of phenotypic plasticity but no trait variation between strains, never outperformed any of our eco‐evolutionary models in which strains could have different trait values. Our best fitting eco‐evolutionary model allowed strains to differ in an inducible defense trait. Overall, our results provide some of the first experimental evidence that variation in phenotypically plastic responses among prey genotypes can be an important component of eco‐evolutionary dynamics in a predator–prey system.

Evolutionary community ecology of plant‐associated arthropods in terrestrial ecosystems

AbstractIn the 21st century, researchers have attempted a synthesis between community ecology and evolutionary biology. This emerging research area, which aims to synthesize community ecology and evolutionary biology, is evolutionary community ecology. Evolutionary community ecology addresses how intraspecific trait variation in community members is essential for predicting community properties and, how community properties are a key component of the selective forces that determine genetic and phenotypic variation in a community member. In this paper, I review recent findings in evolutionary community ecology in plant‐associated arthropods in terrestrial ecosystems. I discuss roles of both genetic variation and phenotypic plasticity as a source of trait variation in plants in shaping plant‐associated arthropod communities. Also, I discuss effects of genetic variation in herbivores on plant‐associated arthropod communities. Furthermore, I highlight community context evolution in which multiple species interactions and community composition affect trait evolution of a community member. Finally, I argue that future studies should investigate a feedback loop between community and evolutionary dynamics beyond unidirectional studies on effects of evolution on a community or vice versa. This approach will provide major insights into mechanistic principles for making predictions of community ecology.

Maternal effects vary between source populations in the Atlantic tomcod Microgadus tomcod

Identifying the sources of variation in traits of larvae is one of the first steps in interpreting the role of phenotypic variation in recruitment. We examined the contributions of geographic source and parentage to phenotypic variation in offspring traits in a gadid, Microgadus tomcod, from 2 contrasting yet nearby locations. Adults were collected from the Hudson River (HR), a polluted riverine estuary with strong freshwater and tidal fluxes, and Shinnecock Bay (SB), a relatively clean barrier beach and lagoon system with minimal freshwater inflows. Eggs were stripped from fish in the laboratory and incubated in a common environment. Female and offspring traits varied substantially between populations. Females from SB had a higher ovary weight and gonado-somatic index (GSI) relative to body length, and produced larger eggs. Contrary to expectation, higher female condition did not result in larvae of better condition. SB offspring had smaller yolk reserves at hatch and were less resistant to starvation than offspring from HR, though size at hatching did not differ between the 2 populations. SB offspring took 25% longer to hatch, thereby increasing dependence on yolk reserves as embryos. This may represent a trade-off in time to hatching versus quality at hatching in tomcod from different environments. Geographic source accounted for more variance than maternal effects in time to hatch (90%) and yolk volume at hatch (42%). Maternal influence accounted for more variance in egg diameter (90%), length at hatch (33%) and starvation resistance (30%), though none of these measures was correlated to female size or age. These results emphasize differences in early life history traits across a small geographic scale and the extent to which offspring differences due to maternal effects depend on the local environment.

Non-genetic source of variation for traits measured in performance test of simmental bulls: (II) Body development traits

Data of 371 Simmental bulls tested at the A.I. Centre "Velika Plana" were analyzed in order to estimate year and month of birth, test-group, herd of origin and body weight effects on body measurements and body development indices. These two groups of traits were considering as body development traits. All observed traits were measured at the start as well as at the end of test. Birth year was significant source of variation for all body development traits, while significance of month of birth was expressed at different statistical levels. Herd of origin effect was gradually reduced over the test, while test-group effect was significance only for body measurements. For body development indices herd of origin have no effect, while test-group effect was significant at different statistical levels. Body weight was very significant source of variation for all body development traits. .

Epistatic Pleiotropy and the Genetic Architecture of Covariation Within Early and Late-Developing Skull Trait Complexes in Mice

The role of epistasis as a source of trait variation is well established, but its role as a source of covariation among traits (i.e., as a source of "epistatic pleiotropy") is rarely considered. In this study we examine the relative importance of epistatic pleiotropy in producing covariation within early and late-developing skull trait complexes in a population of mice derived from an intercross of the Large and Small inbred strains. Significant epistasis was found for several pairwise combinations of the 21 quantitative trait loci (QTL) affecting early developing traits and among the 20 QTL affecting late-developing traits. The majority of the epistatic effects were restricted to single traits but epistatic pleiotropy still contributed significantly to covariances. Because of their proportionally larger effects on variances than on covariances, epistatic effects tended to reduce within-group correlations of traits and reduce their overall degree of integration. The expected contributions of single-locus and two-locus epistatic pleiotropic QTL effects to the genetic covariance between traits were analyzed using a two-locus population genetic model. The model demonstrates that, for single-locus or epistatic pleiotropy to contribute to trait covariances in the study population, both traits must show the same pattern of single-locus or epistatic effects. As a result, a large number of the cases where loci show pleiotropic effects do not contribute to the covariance between traits in this population because the loci show a different pattern of effect on the different traits. In general, covariance patterns produced by single-locus and epistatic pleiotropy predicted by the model agreed well with actual values calculated from the QTL analysis. Nearly all single-locus and epistatic pleiotropic effects contributed positive components to covariances between traits, suggesting that genetic integration in the skull is achieved by a complex combination of pleiotropic effects.

The implications and applications of resource capture concepts to crop improvement by plant breeding

Models relating crop production to resource capture and resource use efficiency (RESCAP) may be combined with the phenotype model applied in breeding that identifies sources of variation for traits. Estimating the parameters of the RESCAP models with low-cost non-destructive methods can improve the attribution of sources of variation in the phenotype model and, therefore, improve breeding efficiency. Since the resource captured is largely environmental(E), determining the contributions to yield from this source can leave a better estimate of the genetic(G) and G× E contributions to the phenotype. Some of the potential or existing applications include: (a) breeding for productivity through improved resource capture and/or use efficiency, and screening materials for difficult traits such as root traits in drought resistance/tolerance breeding programs; (b) evaluation of crop improvement strategies. Decisions about selection priorities and sequences depend on the relative extent of genetic and environmental contributions to variation. The RESCAP approach allows the relative components of the phenotype model to be estimated cheaply and aids in their interpretation; (c) improving statistical analysis of breeding trials by exploiting the non-destructive growth analysis of plot yields to isolate the genetic contributions to yield within trials with large error terms due to non-systematic environmental effects and (d) improved selection for yield in early generation segregating populations. RESCAP based on non-destructive single plant and small plot (row) growth analysis and the different contributions of RESCAP model parameters to the phenotype model terms effectively increase the heritability of yield with the attendant possible changes in plant breeding efficiency and practice.

Individual variation in male vocal traits and female mating preferences inBufo americanus

We investigated the amount of variation in mating behaviour between and within individual male and female American toads, because both sources of trait variation can influence the course of sexual selection. Males varied in all four call parameters investigated (dominant call frequency, pulse rate, call rate and call duration). Individual males lowered the dominant frequency of their call when they interacted vocally with nearby males. Dominant call frequency was more highly correlated with body size in vocally interacting males than in non-interacting males. Pulse rate of calls primarily varied with water temperature. Call rate and call duration showed the most variation of the four call properties, but this variation was unrelated to male morphology or social interactions. Females varied in three aspects of mating behaviour: two measures of pair formation and their preference for dominant frequency of male calls. The body size of paired males varied between females both in pairings initiated by either sex and in pairings initiated only by females. Males chosen by females were usually larger than average, although age and prior breeding experience of females did not affect mate choice. Playback experiments indicated that female preference for calls of low dominant frequency depended on the temporal patterning of alternative calls presented. Each of the four male vocal properties showed significant repeatability, but only one of the three aspects of female mating behaviour was repeatable. We discuss how different degrees of repeatability in sexual traits of males and females may influence the action and detection of sexual selection in this and other species.

The Maintenance of Phenotypic Plasticity as a Signal Detection Problem

The Maintenance of Phenotypic Plasticity as a Signal Detection Problem