Divergent selection and the evolution of signal traits and mating preferences

Mating preferences are common in natural populations, and their divergence among populations is considered an important source of reproductive isolation during speciation. Although mechanisms for the divergence of mating preferences have received substantial theoretical treatment, complementary experimental tests are lacking. We conducted a laboratory evolution experiment, using the fruit fly Drosophila serrata, to explore the role of divergent selection between environments in the evolution of female mating preferences. Replicate populations of D. serrata were derived from a common ancestor and propagated in one of three resource environments: two novel environments and the ancestral laboratory environment. Adaptation to both novel environments involved changes in cuticular hydrocarbons, traits that predict mating success in these populations. Furthermore, female mating preferences for these cuticular hydrocarbons also diverged among populations. A component of this divergence occurred among treatment environments, accounting for at least 17.4% of the among-population divergence in linear mating preferences and 17.2% of the among-population divergence in nonlinear mating preferences. The divergence of mating preferences in correlation with environment is consistent with the classic by-product model of speciation in which premating isolation evolves as a side effect of divergent selection adapting populations to their different environments.     

Stable carbon isotopes of lipid biomarkers: analysis of metabolites and metabolic fates of environmental microorganisms

Lipid biomarkers are specific compounds that are characteristic of certain groups or species of microorganisms. The use of natural or labeled carbon isotopes of lipid biomarkers has enabled a better understanding of carbon flow pathways at the molecular level. Recent advances include, but are not limited to, the elucidation of mechanisms of anaerobic methane oxidation mediated by syntrophic sulfate-reducing bacteria and Archaea, linking microbial populations with specific microbial processes or bacterial transport mechanisms in natural or contaminated environments, and elucidation of the biosynthetic pathways of cellular material.     

The dynamics of diversification in evolving Pseudomonas populations

Determining the mechanisms that promote the evolution of diversity is a central problem in evolutionary biology. Previous studies have demonstrated that diversification occurs in complex environments and that genotypes specialized on alternative resources can be maintained over short time scales. Here, we describe a selection experiment that has tracked the dynamics of adaptive diversification within selection lines of the asexual bacteria Pseudomonas fluorescens over about 900 generations. We cultured experimental populations from the same two isogenic ancestral strains in simple, single-substrate environments or in complex, four-substrate environments. Following selection we assayed the growth of genotypes from each population on each substrate individually. We estimated mutational heritability, Vm/VE, as 1 x 10(-3) per generation in simple environments and 3 x 10(-3) per generation in complex environments. These values are roughly consistent with estimates reported in other systems. Populations selected in complex environments evolved into genetically diverse communities. Genotypes exhibited greater metabolic differentiation from other genotypes in their own population than to genotypes evolving in other populations, presumably as a result of resource competition. In populations selected in simple environments, little genetic diversity evolved, and genotypes shared very similar phenotypes. Our findings suggest that ecological opportunity provided by environmental complexity plays a major role in the evolution and maintenance of diversity.     

The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps

The accumulation of adaptive mutations is essential for survival in novel environments. However, in clonal populations with a high mutational supply, the power of natural selection is expected to be limited. This is due to clonal interference - the competition of clones carrying different beneficial mutations - which leads to the loss of many small effect mutations and fixation of large effect ones. If interference is abundant, then mechanisms for horizontal transfer of genes, which allow the immediate combination of beneficial alleles in a single background, are expected to evolve. However, the relevance of interference in natural complex environments, such as the gut, is poorly known. To address this issue, we have developed an experimental system which allows to uncover the nature of the adaptive process as Escherichia coli adapts to the mouse gut. This system shows the invasion of beneficial mutations in the bacterial populations and demonstrates the pervasiveness of clonal interference. The observed dynamics of change in frequency of beneficial mutations are consistent with soft sweeps, where different adaptive mutations with similar phenotypes, arise repeatedly on different haplotypes without reaching fixation. Despite the complexity of this ecosystem, the genetic basis of the adaptive mutations revealed a striking parallelism in independently evolving populations. This was mainly characterized by the insertion of transposable elements in both coding and regulatory regions of a few genes. Interestingly, in most populations we observed a complete phenotypic sweep without loss of genetic variation. The intense clonal interference during adaptation to the gut environment, here demonstrated, may be important for our understanding of the levels of strain diversity of E. coli inhabiting the human gut microbiota and of its recombination rate.     

Natural selection and genital variation: a role for the environment,parasites and sperm ageing?

Male genitalia are more variable between species (and populations) than other organs, and are more morphologically complex in polygamous compared to monogamous species. Therefore, sexual selection has been put forward as the major explanation of genital variation and complexity, in particular cryptic female choice for male copulatory courtship. As cryptic female choice is based on differences between males it is somewhat paradoxical that there is such low within-species variation in male genitalia that they are a prime morphological identification character for animal species. Processes other than sexual selection may also lead to genitalia variation but they have recently become neglected. Here I focus on pleiotropy and natural selection and provide examples how they link genitalia morphology with genital environments. Pleiotropy appears to be important because most studies that specifically tested for pleiotropic effects on genital morphology found them. Natural selection likely favours certain genital morphology over others in various environments, as well as by reducing re-infection with sexually transmitted diseases or reducing the likelihood of fertilisation with aged sperm. Both pleiotropy and natural selection differ locally and between species so may contribute to local variation in genitalia and sometimes variation between monogamous and polygamous species. Furthermore, the multitude of genital environments will lead to a multitude of genital functions via natural selection and pleiotropy, and may also contribute to explaining the complexity of genitalia.     

Salinity Adaptation and the Contribution of Parental Environmental Effects in Medicago truncatula

High soil salinity negatively influences plant growth and yield. Some taxa have evolved mechanisms for avoiding or tolerating elevated soil salinity, which can be modulated by the environment experienced by parents or offspring. We tested the contribution of the parental and offspring environments on salinity adaptation and their potential underlying mechanisms. In a two-generation greenhouse experiment, we factorially manipulated salinity concentrations for genotypes of Medicago truncatula that were originally collected from natural populations that differed in soil salinity. To compare population level adaptation to soil salinity and to test the potential mechanisms involved we measured two aspects of plant performance, reproduction and vegetative biomass, and phenological and physiological traits associated with salinity avoidance and tolerance. Saline-origin populations had greater biomass and reproduction under saline conditions than non-saline populations, consistent with local adaptation to saline soils. Additionally, parental environmental exposure to salt increased this difference in performance. In terms of environmental effects on mechanisms of salinity adaptation, parental exposure to salt spurred phenological differences that facilitated salt avoidance, while offspring exposure to salt resulted in traits associated with greater salt tolerance. Non-saline origin populations expressed traits associated with greater growth in the absence of salt while, for saline adapted populations, the ability to maintain greater performance in saline environments was also associated with lower growth potential in the absence of salt. Plastic responses induced by parental and offspring environments in phenology, leaf traits, and gas exchange contribute to salinity adaptation in M. truncatula. The ability of plants to tolerate environmental stress, such as high soil salinity, is likely modulated by a combination of parental effects and within-generation phenotypic plasticity, which are likely to vary in populations from contrasting environments.     

Robust dynamical pattern formation from a multifunctional minimal genetic circuit

Background  

A practical problem during the analysis of natural networks is their complexity, thus the use of synthetic circuits would allow to unveil the natural mechanisms of operation. Autocatalytic gene regulatory networks play an important role in shaping the development of multicellular organisms, whereas oscillatory circuits are used to control gene expression under variable environments such as the light-dark cycle.     

On the track of natural transformation in soil

Abstract The understanding of microbial gene transfer including how bacteria acquire and disseminate genes in natural environments will provide data on the role of horizontal transfer in evolution. This understanding has been stimulated in recent years by concern about the impact of genetically engineered microorganisms on natural environments. This prospect has increased interest in determining the regulatory mechanisms of indigenous microbial populations as well as detecting genetic interactions between bacteria introduced into soil and the indigenous microflora. This paper will review the strategies developed to demonstrate whether the different steps required by natural bacterial transformation (the uptake of naked DNA by competent bacteria) could actually occur in soil. This will include a review on the release of DNA from microbial cells by passive or active mechanisms, its persistence by adsorption of extracellular DNA onto major soil components such as sand or clay minerals and the uptake of DNA by competent bacteria.     

Genetic and epigenetic regulation of stress responses in natural plant populations

Plants have developed intricate mechanisms involving gene regulatory systems to adjust to stresses. Phenotypic variation in plants under stress is classically attributed to DNA sequence variants. More recently, it was found that epigenetic modifications - DNA methylation-, chromatin- and small RNA-based mechanisms - can contribute separately or together to phenotypes by regulating gene expression in response to the stress effect. These epigenetic modifications constitute an additional layer of complexity to heritable phenotypic variation and the evolutionary potential of natural plant populations because they can affect fitness. Natural populations can show differences in performance when they are exposed to changes in environmental conditions, partly because of their genetic variation but also because of their epigenetic variation. The line between these two components is blurred because little is known about the contribution of genotypes and epigenotypes to stress tolerance in natural populations. Recent insights in this field have just begun to shed light on the behavior of genetic and epigenetic variation in natural plant populations under biotic and abiotic stresses. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.     

Geographic variation in diapause incidence, life-history traits, and climatic adaptation in Drosophila melanogaster

In Drosophila melanogaster, exposure of females to low temperature and shortened photoperiod can induce the expression of reproductive quiescence or diapause. Diapause expression is highly variable within and among natural populations and has significant effects on life-history profiles, including patterns of longevity, fecundity, and stress resistance. We hypothesized that if diapause expression is associated with overwintering mechanisms and adaptation to temperate environments, the frequency of diapause incidence would exhibit a latitudinal cline among natural populations. Because stress resistance and reproductive traits are also clinal in this species, we also examined how patterns of fecundity and longevity varied with geography and how stress resistance and associated traits differed constitutively between diapause and nondiapause lines. Diapause incidence was shown to vary predictably with latitude, ranging from 35% to 90% among natural populations in the eastern United States Survivorship under starvation stress differed between diapause and nondiapause lines; diapause phenotypes were also distinct for total body triglyceride content and the developmental distribution of oocytes in the ovary following stress exposure. Patterns of longevity, fecundity, and ovariole number also varied with geography. The data suggest that, for North American populations, diapause expression is functionally associated with overwintering mechanisms and may be an integral life-history component in natural populations.     

Habitat heterogeneity favors asexual reproduction in natural populations of grassthrips

Explaining the overwhelming success of sex among eukaryotes is difficult given the obvious costs of sex relative to asexuality. Different studies have shown that sex can provide benefits in spatially heterogeneous environments under specific conditions, but whether spatial heterogeneity commonly contributes to the maintenance of sex in natural populations remains unknown. We experimentally manipulated habitat heterogeneity for sexual and asexual thrips lineages in natural populations and under seminatural mesocosm conditions by varying the number of hostplants available to these herbivorous insects. Asexual lineages rapidly replaced the sexual ones, independently of the level of habitat heterogeneity in mesocosms. In natural populations, the success of sexual thrips decreased with increasing habitat heterogeneity, with sexual thrips apparently only persisting in certain types of hostplant communities. Our results illustrate how genetic diversity‐based mechanisms can favor asexuality instead of sex when sexual lineages co‐occur with genetically variable asexual lineages.     

Experimental evolution of Pseudomonas fluorescens in simple and complex environments

In complex environments that contain several substitutable resources, lineages may become specialized to consume only one or a few of them. Here we investigate the importance of environmental complexity in determining the evolution of niche width over approximately 900 generations in a chemically defined experimental system. We propagated 120 replicate lines of the bacterium Pseudomonas fluorescens in environments of different complexity by using between one and eight carbon substrates in each environment. Genotypes from populations selected in complex environments evolved greater mean and variance in fitness than those from populations selected in simple environments. Thus, lineages were able to adapt to several substrates simultaneously without any appreciable loss of function with respect to other substrates present in the media. There was greater genetic and genotype-by-environment interaction variance for fitness within populations selected in complex environments. It is likely that genetic variance in populations grown on complex media was maintained because the identity of the fittest genotype varied among carbon substrates. Our results suggest that evolution in complex environments will result neither in narrow specialists nor in complete generalists but instead in overlapping imperfect generalists, each of which has become adapted to a certain range of substrates but not to all.     

The genetic covariance among clinal environments after adaptation to an environmental gradient in Drosophila serrata

We examined the genetic basis of clinal adaptation by determining the evolutionary response of life-history traits to laboratory natural selection along a gradient of thermal stress in Drosophila serrata. A gradient of heat stress was created by exposing larvae to a heat stress of 36 degrees for 4 hr for 0, 1, 2, 3, 4, or 5 days of larval development, with the remainder of development taking place at 25 degrees. Replicated lines were exposed to each level of this stress every second generation for 30 generations. At the end of selection, we conducted a complete reciprocal transfer experiment where all populations were raised in all environments, to estimate the realized additive genetic covariance matrix among clinal environments in three life-history traits. Visualization of the genetic covariance functions of the life-history traits revealed that the genetic correlation between environments generally declined as environments became more different and even became negative between the most different environments in some cases. One exception to this general pattern was a life-history trait representing the classic trade-off between development time and body size, which responded to selection in a similar genetic fashion across all environments. Adaptation to clinal environments may involve a number of distinct genetic effects along the length of the cline, the complexity of which may not be fully revealed by focusing primarily on populations at the ends of the cline.     

Quantitative Genetics of Response to Competitors in Nemophila Menziesii: A Field Experiment

Recent investigations of evolution in heterogeneous environments have begun to accommodate genetic and environmental complexity typical of natural populations. Theoretical studies demonstrate that evolution of polygenic characters depends heavily on the genetic interdependence of the expression of traits in the different environments in which selection occurs, but information concerning this issue is scarce. We conducted a field experiment to assess the genetic variability of the annual plant Nemophila menziesii in five biotic regimes differing in plant density and composition. Significant, though modest, additive genetic variance in plant size was expressed in particular treatments. Evidence of additive genetic tradeoffs between interspecific and intraspecific competitive performance was found, but this result was not consistent throughout the experiment. Two aspects of experimental design may tend to obscure genetically based tradeoffs across environments in many previously published experiments: (1) inability to isolate additive genetic from other sources of variation and (2) use of novel (e.g., laboratory) environments.     

Water balance in desert Drosophila: lessons from non-charismatic microfauna

Water stress is a particularly important problem for insects and other small organisms in arid environments. Cactophilic fruit flies in the genus Drosophila have invaded deserts on numerous occasions, including multiple independent invasions of North American deserts. Because the evolutionary history of this genus is so well studied, we can investigate the mechanisms of adaptation in a rigorous phylogenetic context. As expected, desert fruit flies lose water less rapidly than their mesic congeners. They are also able to tolerate the loss of a greater percentage of body water, but this difference is mainly due to phylogenetic history, and does not represent an adaptation specifically to desert habitats. A laboratory analogue of desert Drosophila is provided by populations of D. melanogaster that have been subjected to selection for desiccation resistance. Selected populations resemble desert species in that they lose water slowly, relative to control populations, and are not more tolerant of dehydration stress. They differ, however, in having much higher water contents and different behavioral responses to desiccating conditions. Our comparisons of laboratory and natural populations reveal that not all possible adaptive mechanisms evolve in stressful environments. Different physiological and behavioral strategies may evolve depending upon the particular options available in the environment.     

Shifts in morphology and diet of non-native sticklebacks introduced into Japanese crater lakes

An increasing number of exotic animals are causing ecological problems. Therefore, for better ecosystem management, it is important to understand how exotic species colonize and adapt to novel environments. The threespine sticklebacks (Gasterosteus aculeatus) can be a good vertebrate model system to explore the ecological and genetic mechanisms of adaptation not only in natural populations, but also in non-native populations. Although morphological changes have been documented in several introduced populations of stickleback, little is known about the dietary changes during colonization into novel environments. Here, we investigated the morphological and dietary changes of exotic threespine stickleback populations introduced into three Japanese crater lakes (Lake Towada, Lake Kussharo, and Lake Shikotsu). Sticklebacks were introduced into the crater lakes likely along with salmonids transplanted for aquaculture. The stickleback population in Lake Kussharo had multiple mitochondrial haplotypes and had larger phenotypic variances than other crater lake stickleback populations that had only one mitochondrial haplotype. Compilation of historical data on the morphology and stomach contents of the Lake Towada stickleback population showed that substantial shifts in body size and stomach contents occurred after colonization. Some of these changes may be related to an outbreak of the Schistocephalus parasite. These results suggest that sticklebacks can change their morphology and trophic ecology when they colonize novel environments. Therefore, extreme care should be taken when salmonids are transported between watersheds for aquaculture and that long-term monitoring of exotic species is essential for ecosystem management. In addition, further genetic studies on phenotypic changes in crater lake sticklebacks would help elucidate the genetic mechanisms underlying the adaptation of exotic fishes to novel environments.     

Environmental Noise,Genetic Diversity and the Evolution of Evolvability and Robustness in Model Gene Networks

The ability of organisms to adapt and persist in the face of environmental change is accepted as a fundamental feature of natural systems. More contentious is whether the capacity of organisms to adapt (or “evolvability”) can itself evolve and the mechanisms underlying such responses. Using model gene networks, I provide evidence that evolvability emerges more readily when populations experience positively autocorrelated environmental noise (red noise) compared to populations in stable or randomly varying (white noise) environments. Evolvability was correlated with increasing genetic robustness to effects on network viability and decreasing robustness to effects on phenotypic expression; populations whose networks displayed greater viability robustness and lower phenotypic robustness produced more additive genetic variation and adapted more rapidly in novel environments. Patterns of selection for robustness varied antagonistically with epistatic effects of mutations on viability and phenotypic expression, suggesting that trade-offs between these properties may constrain their evolutionary responses. Evolution of evolvability and robustness was stronger in sexual populations compared to asexual populations indicating that enhanced genetic variation under fluctuating selection combined with recombination load is a primary driver of the emergence of evolvability. These results provide insight into the mechanisms potentially underlying rapid adaptation as well as the environmental conditions that drive the evolution of genetic interactions.     

The evolutionary dynamics of evolvability in a gene network model

Evolvability, the ability of populations to adapt, has recently emerged as a major unifying concept in biology. Although the study of evolvability offers new insights into many important biological questions, the conceptual bases of evolvability, and the mechanisms of its evolution, remain controversial. We used simulated evolution of a model of gene network dynamics to test the contentious hypothesis that natural selection can favour high evolvability, in particular in sexual populations. Our results conclusively demonstrate that fluctuating natural selection can increase the capacity of model gene networks to adapt to new environments. Detailed studies of the evolutionary dynamics of these networks establish a broad range of validity for this result and quantify the evolutionary forces responsible for changes in evolvability. Analysis of the genotype–phenotype map of these networks also reveals mechanisms connecting evolvability, genetic architecture and robustness. Our results suggest that the evolution of evolvability can have a pervasive influence on many aspects of organisms.