Weak genetic signal for phenotypic integration implicates developmental processes as major regulators of trait covariation

Phenotypic integration is an important metric that describes the degree of covariation among traits in a population, and is hypothesized to arise due to selection for shared functional processes. Our ability to identify the genetic and/or developmental underpinnings of integration is marred by temporally overlapping cell-, tissue- and structure-level processes that serve to continually 'overwrite' the structure of covariation among traits through ontogeny. Here, we examine whether traits that are integrated at the phenotypic level also exhibit a shared genetic basis (e.g. pleiotropy). We micro-CT scanned two hard tissue traits, and two soft tissue traits (mandible, pectoral girdle, atrium and ventricle, respectively) from an F5 hybrid population of Lake Malawi cichlids, and used geometric morphometrics to extract 3D shape information from each trait. Given the large degree of asymmetric variation that may reflect developmental instability, we separated symmetric from asymmetric components of shape variation. We then performed quantitative trait loci (QTL) analysis to determine the degree of genetic overlap between shapes. While we found ubiquitous associations among traits at the phenotypic level, except for a handful of notable exceptions, our QTL analysis revealed few overlapping genetic regions. Taken together, this indicates developmental interactions can play a large role in determining the degree of phenotypic integration among traits, and likely obfuscate the genotype to phenotype map, limiting our ability to gain a comprehensive picture of the genetic contributors responsible for phenotypic divergence.

Stomatal and Leaf Morphology Response of European Beech (Fagus sylvatica L.) Provenances Transferred to Contrasting Climatic Conditions

Climate change-induced elevated temperatures and drought are considered to be serious threats to forest ecosystems worldwide, negatively affecting tree growth and viability. We studied nine European beech (Fagus sylvatica L.) provenances located in two provenance trial plots with contrasting climates in Central Europe. Stomata play a vital role in the water balance of plants by regulating gaseous exchanges between plants and the atmosphere. Therefore, to explain the possible adaptation and acclimation of provenances to climate conditions, stomatal (stomatal density, the length of guard cells, and the potential conductance index) and leaf morphological traits (leaf size, leaf dry weight and specific leaf area) were assessed. The phenotypic plasticity index was calculated from the variability of provenances’ stomatal and leaf traits between the provenance plots. We assessed the impact of various climatic characteristics and derived indices (e.g., ecodistance) on intraspecific differences in stomatal and leaf traits. Provenances transferred to drier and warmer conditions acclimated through a decrease in stomatal density, the length of guard cells, potential conductance index, leaf size and leaf dry weight. The reduction in stomatal density and the potential conductance index was proportional to the degree of aridity difference between the climate of origin and conditions of the new site. Moreover, we found that the climate heterogeneity and latitude of the original provenance sites influence the phenotypic plasticity of provenances. Provenances from lower latitudes and less heterogeneous climates showed higher values of phenotypic plasticity. Furthermore, we observed a positive correlation between phenotypic plasticity and mortality in the arid plot but not in the more humid plot. Based on these impacts of the climate on stomatal and leaf traits of transferred provenances, we can improve the predictions of provenance reactions for future scenarios of global climate change.

Size and shape regulation during larval growth in the lepidopteran Pieris brassicae

By adopting a longitudinal study design and through geometric morphometrics methods, we investigated size and shape regulation in the head capsule during the larval development of the cabbage butterfly Pieris brassicae under laboratory conditions. We found evidence of size regulation by compensatory growth, although not equally effective in all larval stages. Size compensation is not attained through the regulation of developmental timing, but rather through the modulation of per-time growth rate. As for the shape, neither the variance of the symmetric component of shape, nor the level of fluctuating asymmetry show any evidence of increase across stages, either at the population or individual level, which is interpreted as a mark of ontogenetic shape regulation. In addition, also the geometry of individual asymmetry is basically conserved across stages. While providing specific documentation on the ontogeny of size and shape variation in this insect, this study may contribute to a more general understanding of developmental regulation and its influence on phenotypic evolution.

A heuristic model of the effects of phenotypic robustness in adaptive evolution

A recent theoretical, deterministic model of the effects of phenotypic robustness on adaptive evolutionary dynamics showed that a certain level of phenotypic robustness (critical robustness) is a required condition for adaptation to occur and to be maintained during evolution in most real organismal systems. We built an individual-based heuristic model to verify the soundness of these theoretical results through computer simulation, testing expectations under a range of scenarios for the relevant parameters of the evolutionary dynamics. These include the mutation probability, the presence of stochastic effects, the introduction of environmental influences and the possibility for some features of the population (like selection coefficients and phenotypic robustness) to change themselves during adaptation. Overall, we found a good match between observed and expected results, even for evolutionary parameter values that violate some of the assumptions of the deterministic model, and that robustness can itself evolve. However, from more than one simulation it appears that very high robustness values, higher than the critical value, can limit or slow-down adaptation. This possible trade-off was not predicted by the deterministic model.

When European meets African honeybees (Apis mellifera L.) in the tropics: Morphological changes related to genetics in Mauritius Island (South-West Indian Ocean)

The previous genetic characterization of the honeybee population of Mauritius Island (Indian Ocean) revealed an ongoing process of hybridization between the first established African subspecies Apis mellifera unicolor and recently imported European subspecies (A. m. ligustica, A. m. carnica and A. m. mellifera). This context offers the rare opportunity to explore the influence of hybridization between African and European honeybees on phenotypic traits out of the case largely studied of the Africanized honeybee (hybrid between A. m. scutellata from South Africa and European subspecies). We thus conducted geometric morphometric analyses on forewings of 283 workers genetically characterized at 14 microsatellite loci to evaluate (1) if the morphological variability coincides well with the neutral genetic variability, (2) if hybrids exhibited rather parental, intermediate or transgressive traits, and (3) to test if fluctuating asymmetry (FA) of size and shape, as a measure of developmental stability, was elevated in hybrids (due to genetic stress) and/or European bees (due to unsuitable environment) compared to African bees. A strong concordance was found between morphological variability and neutral genetic variability, especially for wing shape, based on partial least-square analyses (PLS). However, on average, the morphology of hybrids was more similar to the African bees, potentially reflecting the dynamics and direction of introgression. Significant FA for wing size as well as wing shape was detected, suggesting the overall presence of stress during the development of the studied individuals. In contrast, the asymmetry levels do not differ according to the ancestry (African, European or hybrid) of the individuals. Therefore, if ongoing hybridization contributed to increasing the genetic and phenotypic diversity of the populations and influences its adaptive potential, developmental stressors could not be identified and their evolutionary consequences remain uncertain.

Extreme developmental instability associated with wing plasticity in pea aphids

A key focus of evolutionary developmental biology is on how phenotypic diversity is generated. In particular, both plasticity and developmental instability contribute to phenotypic variation among genetically identical individuals, but the interactions between the two phenomena and their general fitness impacts are unclear. We discovered a striking example of asymmetry in pea aphids: the presence of wings on one side and the complete or partial absence of wings on the opposite side. We used this asymmetric phenotype to study the connection between plasticity, developmental instability and fitness. We found that this asymmetric wing development (i) occurred equally on both sides and thus is a developmental instability; (ii) is present in some genetically unique lines but not others, and thus has a genetic basis; and (iii) has intermediate levels of fecundity, and thus does not necessarily have negative fitness consequences. We conclude that this dramatic asymmetry may arise from incomplete switching between developmental targets, linking plasticity and developmental instability. We suspect that what we have observed may be a more widespread phenomenon, occurring across species that routinely produce distinct, alternative phenotypes.

Variation in Leaf Size and Fluctuating Asymmetry of Mountain Birch (Betula pubescens var. pumila) in Space and Time: Implications for Global Change Research

Experimental, latitudinal, and historical approaches have been used to explore and/or predict the effects of global change on biota, and each approach has its own advantages and disadvantages. The weaknesses of these individual approaches can, potentially, be avoided by applying them simultaneously, but this is rarely done in global change research. Here, we explored the temporal and spatial variations in the leaf size and fluctuating asymmetry (FA) of mountain birch (Betula pubescens var. pumila) in the Murmansk region of Russia, with the aim of verifying the predictions derived from the responses of these traits to experimental manipulations of abiotic drivers of global change. The examination of herbarium specimens revealed that leaf length increased during the 20th century, whereas the FA in the number of leaf teeth decreased, presumably reflecting an increase in the carbon and nitrogen availability to plants in that century. Along a northward latitudinal gradient, leaf length decreased whereas FA increased, presumably due to the poleward decreases in air temperature. The study site, collection year, and latitude explained a larger part of the leaf length variation in mountain birch relative to the variation in FA. Leaf length is likely a better indicator than FA in studies addressing global environmental change impacts on plant performance.

Symmetric and Asymmetric Components of Shape Variation in the Diatom Genus Frustulia (Bacillariophyta)

Irregularities in cell division can produce asymmetry in symmetric structures, such as outlines of diatom cells, which can reflect genetic, environmental, or random variability in developmental processes. This study examined 12 phylogenetic lineages of the diatom genus Frustulia using landmark-based geometric morphometrics to assess the variation between cell segments separated by apical and transapical axes. Although asymmetric variation within cells differed in some lineages, these irregularities most likely did not reflect the evolutionary history of the lineages. The intraclonal phenotypic plasticity of diatom frustules was induced rather by nongenetic factors, i.e., inherited valve abnormalities, constraints of siliceous cell walls, and random developmental instability during morphogenesis. The positive correlations between the symmetric and asymmetric components of shape variation indicated that the morphogenesis of diatom cell walls affected irregularities within cells and variability among the symmetrized cells to a similar extent.

Schizophrenia: Developmental Variability Interacts with Risk Factors to Cause the Disorder: Nonspecific Variability-Enhancing Factors Combine with Specific Risk Factors to Cause Schizophrenia

A new etiological model is proposed for schizophrenia that combines variability-enhancing nonspecific factors acting during development with more specific risk factors. This model is better suited than the current etiological models of schizophrenia, based on the risk factors paradigm, for predicting and/or explaining several important findings about schizophrenia: high co-morbidity rates, low specificity of many risk factors, and persistence in the population of the associated genetic polymorphisms. Compared with similar models, e.g., de-canalization, common psychopathology factor, sexual-selection, or differential sensitivity to the environment, this proposal is more general and integrative. Recently developed research methods have proven the existence of genetic and environmental factors that enhance developmental variability. Applying such methods to newly collected or already available data can allow for testing the hypotheses upon which this model is built. If validated, this model may change the understanding of the etiology of schizophrenia, the research models, and preventionbrk paradigms.

Fluctuating Asymmetry, Developmental Noise and Developmental Stability: Future Prospects for the Population Developmental Biology Approach

Developmental noise—which level may vary within a certain backlash allowed by natural selection—is a reflection of the state of a developing system or developmental stability. Phenotypic variations inside the genetically determined norm observed in case of fluctuating asymmetry provide a unique opportunity for evaluating this form of ontogenetic variability. Low levels of developmental noise for the biologic system under study is observed under certain conditions, while its increase acts as a measure of stress. The concordance of changes in developmental stability with changes in other parameters of developmental homeostasis indicates the significance of fluctuating asymmetry estimates. All this determines the future prospects of the study of fluctuating asymmetry not only for developmental biology, but also for population biology. The study of developmental stability may act as the basis of an approach of population developmental biology to assess the nature of the phenotypic diversity and the state of natural populations under various impacts and during evolutionary transformations.

Genetic and environmental canalization are not associated among altitudinally varying populations of Drosophila melanogaster

Organisms are exposed to environmental and mutational effects influencing both mean and variance of phenotypes. Potentially deleterious effects arising from this variation can be reduced by the evolution of buffering (canalizing) mechanisms, ultimately reducing phenotypic variability. There has been interest regarding the conditions enabling the evolution of canalization. Under some models, the circumstances under which genetic canalization evolves are limited despite apparent empirical evidence for it. It has been argued that genetic canalization evolves as a correlated response to environmental canalization (congruence model). Yet, empirical evidence has not consistently supported predictions of a correlation between genetic and environmental canalization. In a recent study, a population of Drosophila adapted to high altitude showed evidence of genetic decanalization relative to those from low altitudes. Using strains derived from these populations, we tested if they varied for multiple aspects of environmental canalization We observed the expected differences in wing size, shape, cell (trichome) density and mutational defects between high- and low-altitude populations. However, we observed little evidence for a relationship between measures of environmental canalization with population or with defect frequency. Our results do not support the predicted association between genetic and environmental canalization.

Network-regulated organ allometry: The developmental regulation of morphological scaling

Morphological scaling relationships, or allometries, describe how traits grow coordinately and covary among individuals in a population. The developmental regulation of scaling is essential to generate correctly proportioned adults across a range of body sizes, while the mis-regulation of scaling may result in congenital birth defects. Research over several decades has identified the developmental mechanisms that regulate the size of individual traits. Nevertheless, we still have poor understanding of how these mechanisms work together to generate correlated size variation among traits in response to environmental and genetic variation. Conceptually, morphological scaling can be generated by size-regulatory factors that act directly on multiple growing traits (trait-autonomous scaling), or indirectly via hormones produced by central endocrine organs (systemically regulated scaling), and there are a number of well-established examples of such mechanisms. There is much less evidence, however, that genetic and environmental variation actually acts on these mechanisms to generate morphological scaling in natural populations. More recent studies indicate that growing organs can themselves regulate the growth of other organs in the body. This suggests that covariation in trait size can be generated by network-regulated scaling mechanisms that respond to changes in the growth of individual traits. Testing this hypothesis, and one of the main challenges of understanding morphological scaling, requires connecting mechanisms elucidated in the laboratory with patterns of scaling observed in the natural world. This article is categorized under: Establishment of Spatial and Temporal Patterns > Regulation of Size, Proportion, and Timing Comparative Development and Evolution > Organ System Comparisons Between Species.

Sources of epigenetic variation and their applications in natural populations

Epigenetic processes manage gene expression and products in a real‐time manner, allowing a single genome to display different phenotypes. In this paper, we discussed the relevance of assessing the different sources of epigenetic variation in natural populations. For a given genotype, the epigenetic variation could be environmentally induced or occur randomly. Strategies developed by organisms to face environmental fluctuations such as phenotypic plasticity and diversified bet‐hedging rely, respectively, on these different sources. Random variation can also represent a proxy of developmental stability and can be used to assess how organisms deal with stressful environmental conditions. We then proposed the microbiome as an extension of the epigenotype of the host to assess the factors determining the establishment of the community of microorganisms. Finally, we discussed these perspectives in the applied context of conservation.

The weakest link: Haploid honey bees are more susceptible to neonicotinoid insecticides

Neonicotinoid insecticides are currently of major concern for the health of wild and managed insects that provide key ecosystem services like pollination. Even though sublethal effects of neonicotinoids are well known, there is surprisingly little information on how they possibly impact developmental stability, and to what extent genetics are involved. This holds especially true for haploid individuals because they are hemizygous at detoxification loci and may be more susceptible. Here we take advantage of haplodiploidy in Western honey bees, Apis mellifera, to show for the first time that neonicotinoids affect developmental stability in diploid females (workers), and that haploid males (drones) are even more susceptible. Phenotypic fore wing venation abnormalities and fluctuating wing asymmetry, as measures of developmental instability, were significantly increased under field-realistic neonicotinoid-exposure of colonies. The higher susceptibility of haploid drones suggests that heterozygosity can play a key role in the ability to buffer the sublethal effects of neonicotinoids. Aiming to improve conservation efforts, our findings highlight the urgent need to better understand the role that genetics plays at enabling non-target organisms to cope with insecticide exposure.

Developmental bias in the fossil record

The role of developmental bias and plasticity in evolution is a central research interest in evolutionary biology. Studies of these concepts and related processes are usually conducted on extant systems and have seen limited investigation in the fossil record. Here, I identify plasticity-led evolution (PLE) as a form of developmental bias accessible through scrutiny of paleontological material. I summarize the process of PLE and describe it in terms of the environmentally mediated accumulation and release of cryptic genetic variation. Given this structure, I then predict its manifestation in the fossil record, discuss its similarity to quantum evolution and punctuated equilibrium, and argue that these describe macroevolutionary patterns concordant with PLE. Finally, I suggest methods and directions towards providing evidence of PLE in the fossil record and conclude that such endeavors are likely to be highly rewarding.

An amino-terminal threonine/serine motif is necessary for activity of the Crp/Fnr homolog, MrpC and for Myxococcus xanthus developmental robustness

The Crp/Fnr family of transcriptional regulators play central roles in transcriptional control of diverse physiological responses, and are activated by a surprising diversity of mechanisms. MrpC is a Crp/Fnr homolog that controls the Myxococcus xanthus developmental program. A long-standing model proposed that MrpC activity is controlled by the Pkn8/Pkn14 serine/threonine kinase cascade, which phosphorylates MrpC on threonine residue(s) located in its extreme amino-terminus. In this study, we demonstrate that a stretch of consecutive threonine and serine residues, T₂₁ T₂₂ S₂₃ S_24, is necessary for MrpC activity by promoting efficient DNA binding. Mass spectrometry analysis indicated the TTSS motif is not directly phosphorylated by Pkn14 in vitro but is necessary for efficient Pkn14-dependent phosphorylation on several residues in the remainder of the protein. In an important correction to a long-standing model, we show Pkn8 and Pkn14 kinase activities do not play obvious roles in controlling MrpC activity in wild-type M. xanthus under laboratory conditions. Instead, we propose Pkn14 modulates MrpC DNA binding in response to unknown environmental conditions. Interestingly, substitutions in the TTSS motif caused developmental defects that varied between biological replicates, revealing that MrpC plays a role in promoting a robust developmental phenotype.

Genomics of Developmental Plasticity in Animals

Developmental plasticity refers to the property by which the same genotype produces distinct phenotypes depending on the environmental conditions under which development takes place. By allowing organisms to produce phenotypes adjusted to the conditions that adults will experience, developmental plasticity can provide the means to cope with environmental heterogeneity. Developmental plasticity can be adaptive and its evolution can be shaped by natural selection. It has also been suggested that developmental plasticity can facilitate adaptation and promote diversification. Here, we summarize current knowledge on the evolution of plasticity and on the impact of plasticity on adaptive evolution, and we identify recent advances and important open questions about the genomics of developmental plasticity in animals. We give special attention to studies using transcriptomics to identify genes whose expression changes across developmental environments and studies using genetic mapping to identify loci that contribute to variation in plasticity and can fuel its evolution.

Testing the evolutionary constraints of metamorphosis: The ontogeny of head shape in Triturus newts

In vertebrates with complex, biphasic, life cycles, larvae have a distinct morphology and ecological preferences compared to metamorphosed juveniles and adults. In amphibians, abrupt and rapid metamorphic changes transform aquatic larvae to terrestrial juveniles. The main aim of this study is to test whether, relative to larval stages, metamorphosis (1) resets the pattern of variation between ontogenetic stages and species, (2) constrains intraspecific morphological variability, and (3) similar to the "hour-glass" model reduces morphological disparity. We explore postembryonic ontogenetic trajectories of head shape (from hatching to completed metamorphosis) of two well-defined, morphologically distinct Triturus newts species and their F1 hybrids. Variation in head shape is quantified and compared on two levels: dynamic (across ontogenetic stages) and static (at a particular stage). Our results show that the ontogenetic trajectories diverge early during development and continue to diverge throughout larval stages and metamorphosis. The high within-group variance and the largest disparity level (between-group variance) characterize the metamorphosed stage. Hence, our results indicate that metamorphosis does not canalize head shape variation generated during larval development and that metamorphosed phenotype is not more constrained relative to larval ones. Therefore, metamorphosis cannot be regarded as a developmental constraint, at least not for salamander head shape.