Phenotypic noise and the cost of complexity

Experimental studies demonstrate the existence of phenotypic diversity despite constant genotype and environment. Theoretical models based on a single phenotypic character predict that during an adaptation event, phenotypic noise should be positively selected far from the fitness optimum because it increases the fitness of the genotype, and then be selected against when the population reaches the optimum. It is suggested that because of this fitness gain, phenotypic noise should promote adaptive evolution. However, it is unclear how the selective advantage of phenotypic noise is linked to the rate of evolution, and whether any advantage would hold for more realistic, multidimensional phenotypes. Indeed, complex organisms suffer a cost of complexity, where beneficial mutations become rarer as the number of phenotypic characters increases. Using a quantitative genetics approach, we first show that for a one-dimensional phenotype, phenotypic noise promotes adaptive evolution on plateaus of positive fitness, independently from the direct selective advantage on fitness. Second, we show that for multidimensional phenotypes, phenotypic noise evolves to a low-dimensional configuration, with elevated noise in the direction of the fitness optimum. Such a dimensionality reduction of the phenotypic noise promotes adaptive evolution and numerical simulations show that it reduces the cost of complexity.     

Joint Variable Selection for Fixed and Random Effects in Linear Mixed‐Effects Models

Summary It is of great practical interest to simultaneously identify the important predictors that correspond to both the fixed and random effects components in a linear mixed‐effects (LME) model. Typical approaches perform selection separately on each of the fixed and random effect components. However, changing the structure of one set of effects can lead to different choices of variables for the other set of effects. We propose simultaneous selection of the fixed and random factors in an LME model using a modified Cholesky decomposition. Our method is based on a penalized joint log likelihood with an adaptive penalty for the selection and estimation of both the fixed and random effects. It performs model selection by allowing fixed effects or standard deviations of random effects to be exactly zero. A constrained expectation–maximization algorithm is then used to obtain the final estimates. It is further shown that the proposed penalized estimator enjoys the Oracle property, in that, asymptotically it performs as well as if the true model was known beforehand. We demonstrate the performance of our method based on a simulation study and a real data example.     

SPATIOTEMPORAL VARIATION IN LINEAR NATURAL SELECTION ON BODY COLOR IN WILD GUPPIES (POECILIA RETICULATA)

We conducted 10 mark–recapture experiments in natural populations of Trinidadian guppies to test hypotheses concerning the role of viability selection in geographic patterns of male color variation. Previous work has reported that male guppies are more colorful in low‐predation sites than in high‐predation sites. This pattern of phenotypic variation has been theorized to reflect differences in the balance between natural (viability) selection that disfavors bright male color (owing to predation) and sexual selection that favors bright color (owing to female choice). Our results support the prediction that male color is disfavored by viability selection in both predation regimes. However, it does not support the prediction that viability selection against male color is weaker in low‐predation experiments. Instead, some of the most intense bouts of selection against color occurred in low‐predation experiments. Our results illustrate considerable spatiotemporal variation in selection among experiments, but such variation was not generally correlated with local patterns of color diversity. More complex selective interactions, possibly including the indirect effects of predators on variation in mating behavior, as well as other environmental factors, might be required to more fully explain patterns of secondary sexual trait variation in this system.     

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.     

Adaptive response and split-dose effect of radiation on the survival of mice

Although the importance of radiation-induced adaptive response has been recognized in human health, risk assessment and clinical application, the phenomenon has not been understood well in terms of survival of animals. To examine this aspect Swiss albino mice were irradiated with different doses (2–10 Gy) at 0015 Gy/s dose rate and observed on a regular basis for 30 days. Since almost 50% lethality was seen with 8 Gy, it was selected as the challenging dose for further studies. Irradiation of mice with conditioning doses (0.25 or 0.5 Gy) and subsequent exposure to 8 Gy caused significant increase in the survival of mice compared to irradiated control. The splitting of challenging dose did not influence the efficiency of conditioning doses (0.25 Gy and 0.5 Gy) to induce an adaptive response. However conditioning doses given in fractions (0.25 Gy + 0.25 Gy) or (0.5 Gy + 0.5 Gy) were able to modulate the response of challenging dose of 8 Gy. These results clearly showed the occurrence of adaptive response in terms of survival of animals. The conditioning dose given in small fractions seemed to be more effective. The findings have been discussed from a mechanistic point of view. The possible biological implications, potential medical benefits, uncertainties and controversies related to adaptive response have also been addressed     

Studies on reproductive strategies of Vitex negundo L. var. heterophylla (Franch.) Rehder (Lamiaceae) based on morphological characteristics and SSR markers

Vitex negundo L. var. heterophylla (Franch.) Rehder (Lamiaceae) is an important tree species for soil and water conservation, yet the reproductive ecology of this species remains to be elucidated. To investigate the reproductive traits of V. negundo var. heterophylla, the phenology, morphological characteristics (a suite of characters was assessed: floral morphology, nectar production, pollen viability, and stigma receptivity) and mating system of this species were systematically revealed for the first time in this study. Phenological observations, morphological measurements, and nectar production analysis were conducted during anthesis. Pollen viability and stigma receptivity at different flowering stages were measured by biochemical methods. Finally, genetic analysis based on SSR markers was used to reveal the mating system; outcrossing index and pollen‐ovule ratio were also calculated to help analysis. V. negundo var. heterophylla showed several obvious characteristics of outcrossing, such as abundant and attractive flowers, secreting nectar, and emitting scent. In addition, mechanisms such as homogamy and a short anther‐stigma distance that can promote self‐fertilization were also identified in this species. The coexistence of selfing and outcrossing characteristics demonstrates a predominantly outcrossed mixed mating system (outcrossing rate, t = 95%). The scientific information provided by this study may contribute to conservation of V. negundo var. heterophylla from a reproductive perspective.     

Adaptive laboratory evolution and reverse engineering enhances autotrophic growth in Pichia pastoris

Synthetic biology offers several routes for CO₂ conversion into biomass or bio-chemicals, helping to avoid unsustainable use of organic feedstocks, which negatively contribute to climate change. The use of well-known industrial organisms, such as the methylotrophic yeast Pichia pastoris (Komagataella phaffii), for the establishment of novel C1-based bioproduction platforms could wean biotechnology from feedstocks with alternative use in food production. Recently, the central carbon metabolism of P. pastoris was re-wired following a rational engineering approach, allowing the resulting strains to grow autotrophically with a μ_max of 0.008 h⁻¹, which was further improved to 0.018 h⁻¹ by adaptive laboratory evolution. Using reverse genetic engineering of single-nucleotide (SNPs) polymorphisms occurring in the genes encoding for phosphoribulokinase and nicotinic acid mononucleotide adenylyltransferase after evolution, we verified their influence on the improved autotrophic phenotypes. The reverse engineered SNPs lead to lower enzyme activities in putative branching point reactions and in reactions involved in energy balancing. Beyond this, we show how further evolution facilitates peroxisomal import and increases growth under autotrophic conditions. The engineered P. pastoris strains are a basis for the development of a platform technology, which uses CO₂ for production of value-added products, such as cellular biomass, technical enzymes and chemicals and which further avoids consumption of organic feedstocks with alternative use in food production. Further, the identification and verification of three pivotal steps may facilitate the integration of heterologous CBB cycles or similar pathways into heterotrophic organisms.     

Darwin's ‘mystery of mysteries’: the role of sexual selection in plant speciation

Sexual selection is considered one of the key processes that contribute to the emergence of new species. While the connection between sexual selection and speciation has been supported by comparative studies, the mechanisms that mediate this connection remain unresolved, especially in plants. Similarly, it is not clear how speciation processes within plant populations translate into large-scale speciation dynamics. Here, we review the mechanisms through which sexual selection, pollination, and mate choice unfold and interact, and how they may ultimately produce reproductive isolation in plants. We also overview reproductive strategies that might influence sexual selection in plants and illustrate how functional traits might connect speciation at the population level (population differentiation, evolution of reproductive barriers; i.e. microevolution) with evolution above the species level (macroevolution). We also identify outstanding questions in the field, and suitable data and tools for their resolution. Altogether, this effort motivates further research focused on plants, which might potentially broaden our general understanding of speciation by sexual selection, a major concept in evolutionary biology.     

Can indicator species predict restoration outcomes early in the monitoring process? a case study with peatlands

Success in ecological restoration is rarely assessed rigorously due to insufficient planning for post-restoration monitoring programs, limited funding and, especially, lack of scientifically validated evaluation criteria and protocols. In this article, we propose the use of the Indicator Value Index technique (IndVal), which statistically determines the association of species to one or several particular site types, to obtain indicators of success at the early stages of the recovery process in restoration projects. Peat bogs extracted by the vacuum method, subsequently restored by a moss-transfer technique and regularly monitored for ~10 years were used as a model system to test this approach. We first identified 34 restored sectors of ~10 ha from 4 to 11 years old in twelve eastern-Canadian bogs. These sectors were then classified according to their degree of success in recovering a typical sphagnum moss carpet (restoration goal). Then, we retrospectively reviewed vegetation communities recorded at the third year after restoration to identify indicator species of different categories of restoration success, using the IndVal methodology. By identifying early indicator species, our method provides a tool that guides intervention soon after restoration if a site is not on a desired successional trajectory. Typical bog species, namely the bryophytes S. rubellum and Mylia anomala and the tree Picea mariana, were indicative of successful restoration; while bare peat, lichens and one species of ericaceous shrubs (Empetrum nigrum), which cope better under drier conditions, indicated sites where restoration failed. A surprising finding was that the moss Polytrichum strictum, which is known to facilitate the colonization of sphagnum in disturbed peatlands, is an early indicator of unsuccessful restoration. This finding made us question the nursing role of P. strictum at a cover threshold above ca. 30%, when P. strictum could be outcompeting sphagnum and become dominant. We conclude that the IndVal method is an effective tool to identify early indicators of restoration success when combined with a thoughtful examination of species frequency and cover within each site type.     

A structured decision making analysis to increase a Red-cockaded Woodpecker population and balance stakeholder objectives for a National Forest

Longleaf pine (Pinus palustris) savanna is a biodiverse ecosystem native to the southeastern United States. Due to fire suppression and timber harvest, longleaf pine has declined to 3% of its original range. The extant forest provides habitat for many threatened and endangered species, including the endangered Red-cockaded Woodpecker (Picoides borealis; RCW), a cavity-nesting bird that co-evolved with fire-maintained forest, resulting in savanna-like old-growth forest as the bird’s preferred habitat. Our study site, the Oakmulgee Ranger District of the Talladega National Forest, harbors the largest RCW population in Alabama and is managed with an emphasis on RCW conservation. The United States Forest Service (USFS) also manages the Oakmulgee for uses such as wildlife conservation, recreation, and timber harvest. Despite efforts to restore RCW habitat and install artificial cavities in the Oakmulgee, the number of RCW groups has not exceeded 123, although the Recovery Plan objective is 394 groups. Our project was motivated by the USFS expressing interest in determining why the RCW population has not exceeded 123 groups. We proposed using structured decision making (SDM) with the USFS and other stakeholders to address this problem. Our goals were to explicitly define management objectives, build a Bayesian belief network with a model of how decision alternatives are believed to affect management objectives, and use a sensitivity analysis to determine the part of the model to which RCW population growth was most sensitive. Therefore, results from the analysis were expected to give insights into 1) ecological factors limiting RCW population growth, 2) how management can overcome these limits, plus 3) the relative expected ability of different decision alternatives to satisfy multiple objectives in addition to increasing RCW group number. We held four SDM workshops with representatives from the USFS, the Animal and Plant Health Inspection Service, the Longleaf Alliance, the Birmingham Audubon Society, and local residents. Stakeholder objectives consisted of maximizing the following: RCW group number, forest health, recreational enjoyment, community economic health, and aesthetics. Cavity insert installation had the greatest probability of increasing the number of RCW groups. The number of RCW groups was most affected by cavity availability, adult survival, reproductive output, food availability, and herbaceous understory. Prescribed burning was most likely to meet the combination of stakeholder objectives, followed by midstory removal. Our findings suggest that cavity installation efforts may need to be increased in the Oakmulgee to increase RCW group number. Also it could be beneficial to investigate how RCWs select cavity tree locations with the goal of increasing the chance that RCWs use artificial cavities to form new groups. The Bayesian belief network provided insights into factors limiting RCW population growth and how management can overcome these limits. The Bayesian belief network also can be used to prioritize management methods in the Oakmulgee given stakeholder objectives and time constraints.