PHENOTYPIC PLASTICITY AND EPIGENETIC MARKING: AN ASSESSMENT OF EVIDENCE FOR GENETIC ACCOMMODATION

The relationship between genotype (which is inherited) and phenotype (the target of selection) is mediated by environmental inputs on gene expression, trait development, and phenotypic integration. Phenotypic plasticity or epigenetic modification might influence evolution in two general ways: (1) by stimulating evolutionary responses to environmental change via population persistence or by revealing cryptic genetic variation to selection, and (2) through the process of genetic accommodation, whereby natural selection acts to improve the form, regulation, and phenotypic integration of novel phenotypic variants. We provide an overview of models and mechanisms for how such evolutionary influences may be manifested both for plasticity and epigenetic marking. We point to promising avenues of research, identifying systems that can best be used to address the role of plasticity in evolution, as well as the need to apply our expanding knowledge of genetic and epigenetic mechanisms to our understanding of how genetic accommodation occurs in nature. Our review of a wide variety of studies finds widespread evidence for evolution by genetic accommodation.     

不同能量供需下雌性棕色田鼠胃运动的变化

用PowerLab/8sp生理信号采集分析系统记录哺乳雌鼠、禁食1d和3d雌鼠及正常对照雌鼠胃内压、胃收缩幅值及收缩频率,以研究在不同能量需求与供应状态下,棕色田鼠(Lasiopodomys mandarinus)胃运动的适应性变化。结果显示,禁食组和哺乳期雌鼠的胃内压及胃收缩幅值均显著高于正常对照雌鼠组(P0.05),禁食组胃内压、胃收缩幅值较哺乳组有所下降,且禁食3d组胃内压明显下降(P0.05)。说明在不同生理状态下,能量需求与供应不同,消化道活动发生适应性变化,且消化道生理功能变化与能量胁迫程度相关。     

Risk‐Group‐Specific Dose Finding Based on an Average Toxicity Score

Summary We propose a Bayesian dose‐finding design that accounts for two important factors, the severity of toxicity and heterogeneity in patients' susceptibility to toxicity. We consider toxicity outcomes with various levels of severity and define appropriate scores for these severity levels. We then use a multinomial‐likelihood function and a Dirichlet prior to model the probabilities of these toxicity scores at each dose, and characterize the overall toxicity using an average toxicity score (ATS) parameter. To address the issue of heterogeneity in patients' susceptibility to toxicity, we categorize patients into different risk groups based on their susceptibility. A Bayesian isotonic transformation is applied to induce an order‐restricted posterior inference on the ATS. We demonstrate the performance of the proposed dose‐finding design using simulations based on a clinical trial in multiple myeloma.     

Internal pilots for observational studies

Study planning often involves selecting an appropriate sample size. Power calculations require specifying an effect size and estimating “nuisance” parameters, e.g. the overall incidence of the outcome. For observational studies, an additional source of randomness must be estimated: the rate of the exposure. A poor estimate of any of these parameters will produce an erroneous sample size. Internal pilot (IP) designs reduce the risk of this error ‐ leading to better resource utilization ‐ by using revised estimates of the nuisance parameters at an interim stage to adjust the final sample size. In the clinical trials setting, where allocation to treatment groups is pre‐determined, IP designs have been shown to achieve the targeted power without introducing substantial inflation of the type I error rate. It has not been demonstrated whether the same general conclusions hold in observational studies, where exposure‐group membership cannot be controlled by the investigator. We extend the IP to observational settings. We demonstrate through simulations that implementing an IP, in which prevalence of the exposure can be re‐estimated at an interim stage, helps ensure optimal power for observational research with little inflation of the type I error associated with the final data analysis.     

The adaptive dynamics of the evolution of host resistance to indirectly transmitted microparasites

We use adaptive dynamics and pairwise invadability plots to examine the evolutionary dynamics of host resistance to microparasitic infection transmitted indirectly via free stages. We investigate trade-offs between pathogen transmission rate and intrinsic growth rate. Adaptive dynamics distinguishes various evolutionary outcomes associated with repellors, attractors or branching points. We find criteria corresponding to these and demonstrate that a major factor deciding the evolutionary outcome is whether trade-offs are acceleratingly or deceleratingly costly. We compare and contrast two models and show how the differences between them lead to different evolutionary outcomes.     

Divergent compensatory growth responses within species: linked to contrasting migrations in salmon?

Animals often exhibit accelerated or “compensatory” growth (CG) after periods of environmentally induced growth depression, raising important questions about how they cope with environmental variability. We tested an underexplored hypothesis regarding the evolutionary consequences of CG; namely, that natural populations differ in CG responses. Common-garden experiments were used to compare subadult growth following food restriction between groups (control, treatment) of two Atlantic salmon (Salmo salar) populations and their first-generation (F₁) hybrids. The populations are found at similar latitudes but characterized by differences in migration distance. We predicted that long-distance migrants would better maintain growth trajectories following food restriction than short-distance migrants because they: (1) require larger body sizes to offset energetic costs of migration and (2) face greater time constraints for growth as they must leave non-breeding areas earlier to return to breeding areas. Long-distance migrants grew faster, achieved quicker CG (relative to controls), and their overall body morphology was more streamlined (a trait known to improve swimming efficiency) than slower growing short-distance migrants. F₁ hybrids were generally intermediate in “normal” growth, CG, and body morphology. We concluded that CG responses may differ considerably among populations and that the conditions generating them are likely interconnected with selection on a suite of other traits.     

Effects of diet quality on phenotypic flexibility of organ size and digestive function in Mongolian gerbils (Meriones unguiculatus)

In the context of evolution and ecology, there is a trade-off between the benefits of processing food through a digestive system with specific phenotypic attributes and the cost of maintaining and carrying the digestive system. In this study, we tested the hypothesis that digestive modulations at several levels can match each other to meet the energy and nutrient demands of Mongolian gerbils, a small granivorous rodent species, by acclimating them to a high-quality diet diluted with alfalfa powder. Mongolian gerbils on the diluted diet maintained metabolizable energy intake by an integrated processing response (IPR), which included increases in dry matter intake, gut capacity and rate of digesta passage after 2-weeks of acclimation. Down-regulation of hydrolytic enzyme activity in the intestinal brush-border membrane supported the adaptive modulation hypothesis. The absence of up-modulation of summed enzyme hydrolytic capacity on the diluted diet indicated that greater mass of small intestine on a high-fibre diet is not a direct indicator of digestive or absorptive capacity. Changes in mass of vital organs and carcass suggested that the amount of energy allocated to various organs and hence physiological functions was regulated in response to diet shift.     

Ecological character displacement caused by reproductive interference

We carried out a theoretical investigation of whether ecological character displacement can be caused by reproductive interference. Our model assumes that a quantitative character is associated with both resource use and species recognition, and that heterospecific mating incurs costs. The model shows that ecological character displacement can occur as a consequence of evolution of premating isolation; this conclusion is based on the premise that resource competition is less intense between species than within species and that the ecological character also contributes to premating isolation. When resource competition between species is intense, extinction of either species may occur by competitive exclusion before ecological character divergence. Some observational studies have shown that character displacement in body size is associated with not only resources use but also species recognition. We propose that body size displacement can occur as a consequence of evolution of premating isolation. Our results suggest that ecological character displacement results from reproductive character displacement.     

Relation between complexity and stability in food webs with adaptive behavior

We investigate the influence of functional responses (Lotka-Volterra or Holling type), initial topological web structure (randomly connected or niche model), adaptive behavior (adaptive foraging and predator avoidance) and the type of constraints on the adaptive behavior (linear or nonlinear) on the stability and structure of food webs. Two kinds of stability are considered: one is the network robustness (i.e., the proportion of species surviving after population dynamics) and the other is the species deletion stability. When evaluating the network structure, we consider link density as well as the trophic level structure. We show that the types of functional responses and initial web structure do not have a large effect on the stability of food webs, but foraging behavior has a large stabilizing effect. It leads to a positive complexity-stability relationship whenever higher "complexity" implies more potential prey per species. The other type of adaptive behavior, predator avoidance behavior, makes food webs only slightly more stable. The observed link density after population dynamics depends strongly on the presence or absence of adaptive foraging, and on the type of constraints used. We also show that the trophic level structure is preserved under population dynamics with adaptive foraging.