Environmental adaptations as windows on molecular evolution

Changes in gene regulation may play an important role in adaptive evolution, particularly during adaptation to a changing environment. However, little is known about the molecular mechanisms underlying adaptively significant variation in gene regulation. To address this question, we are using environmental adaptations in populations of a fish, Fundulus heteroclitus as a window into the molecular evolution of gene regulation. F. heteroclitus are found along the East Coast of North America, with populations distributed along a steep thermal gradient. At the extremes of the species range, populations have undergone local adaptation to their habitat temperatures. A variety of genes differ in their regulation between these populations. We have determined the mechanism responsible for changes in lactate dehydrogenase-B (Ldh-B) gene regulation. A limited number of mutations in the regulatory sequence of this gene result in changes in its expression. Both the phenotypic (increased LDH activity) and genotypic (changes in Ldh-B regulatory sequences) differences between populations have been shown to be affected by natural selection, rather than genetic drift. Therefore, even a small number of mutations within important regulatory sequences can provide evolutionarily significant variation and have an impact on environmental adaptation.     

Evidence of current impact of climate change on life: a walk from genes to the biosphere

We review the evidence of how organisms and populations are currently responding to climate change through phenotypic plasticity, genotypic evolution, changes in distribution and, in some cases, local extinction. Organisms alter their gene expression and metabolism to increase the concentrations of several antistress compounds and to change their physiology, phenology, growth and reproduction in response to climate change. Rapid adaptation and microevolution occur at the population level. Together with these phenotypic and genotypic adaptations, the movement of organisms and the turnover of populations can lead to migration toward habitats with better conditions unless hindered by barriers. Both migration and local extinction of populations have occurred. However, many unknowns for all these processes remain. The roles of phenotypic plasticity and genotypic evolution and their possible trade‐offs and links with population structure warrant further research. The application of omic techniques to ecological studies will greatly favor this research. It remains poorly understood how climate change will result in asymmetrical responses of species and how it will interact with other increasing global impacts, such as N eutrophication, changes in environmental N : P ratios and species invasion, among many others. The biogeochemical and biophysical feedbacks on climate of all these changes in vegetation are also poorly understood. We here review the evidence of responses to climate change and discuss the perspectives for increasing our knowledge of the interactions between climate change and life.     

The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast

The experimental evolution of laboratory populations of microbes provides an opportunity to observe the evolutionary dynamics of adaptation in real time. Until very recently, however, such studies have been limited by our inability to systematically find mutations in evolved organisms. We overcome this limitation by using a variety of DNA microarray-based techniques to characterize genetic changes—including point mutations, structural changes, and insertion variation—that resulted from the experimental adaptation of 24 haploid and diploid cultures of Saccharomyces cerevisiae to growth in either glucose, sulfate, or phosphate-limited chemostats for ∼200 generations. We identified frequent genomic amplifications and rearrangements as well as novel retrotransposition events associated with adaptation. Global nucleotide variation detection in ten clonal isolates identified 32 point mutations. On the basis of mutation frequencies, we infer that these mutations and the subsequent dynamics of adaptation are determined by the batch phase of growth prior to initiation of the continuous phase in the chemostat. We relate these genotypic changes to phenotypic outcomes, namely global patterns of gene expression, and to increases in fitness by 5–50%. We found that the spectrum of available mutations in glucose- or phosphate-limited environments combined with the batch phase population dynamics early in our experiments allowed several distinct genotypic and phenotypic evolutionary pathways in response to these nutrient limitations. By contrast, sulfate-limited populations were much more constrained in both genotypic and phenotypic outcomes. Thus, the reproducibility of evolution varies with specific selective pressures, reflecting the constraints inherent in the system-level organization of metabolic processes in the cell. We were able to relate some of the observed adaptive mutations (e.g., transporter gene amplifications) to known features of the relevant metabolic pathways, but many of the mutations pointed to genes not previously associated with the relevant physiology. Thus, in addition to answering basic mechanistic questions about evolutionary mechanisms, our work suggests that experimental evolution can also shed light on the function and regulation of individual metabolic pathways.     

Systematic detection of polygenic cis-regulatory evolution

The idea that most morphological adaptations can be attributed to changes in the cis-regulation of gene expression levels has been gaining increasing acceptance, despite the fact that only a handful of such cases have so far been demonstrated. Moreover, because each of these cases involves only one gene, we lack any understanding of how natural selection may act on cis-regulation across entire pathways or networks. Here we apply a genome-wide test for selection on cis-regulation to two subspecies of the mouse Mus musculus. We find evidence for lineage-specific selection at over 100 genes involved in diverse processes such as growth, locomotion, and memory. These gene sets implicate candidate genes that are supported by both quantitative trait loci and a validated causality-testing framework, and they predict a number of phenotypic differences, which we confirm in all four cases tested. Our results suggest that gene expression adaptation is widespread and that these adaptations can be highly polygenic, involving cis-regulatory changes at numerous functionally related genes. These coordinated adaptations may contribute to divergence in a wide range of morphological, physiological, and behavioral phenotypes.     

Gross Karyotypic and Phenotypic Alterations among Different Progenies of the Candida glabrata CBS138/ATCC2001 Reference Strain

Genomic plasticity is a mechanism for adaptation to environmental cues such as host responses and antifungal drug pressure in many fungi including the human pathogenic yeast Candida glabrata. In this study we evaluated the phenotypic and genotypic stability of the world-wide used C. glabrata reference strain CBS138/ATCC2001 under laboratory conditions. A set of ten lineages of this wild type strain and genetically modified progenies were obtained from different scientific laboratories, and analyzed for genotypic and phenotypic alterations. Even though the derivates were indistinguishable by multi locus sequence typing, different phenotypic groups that correlated with specific karyotypic changes were observed. In addition, modifications in the adherence capacity to plastic surface emerged that were shown to correlate with quantitative changes in adhesin gene expression rather than subtelomeric gene loss or differences in the number of macrosatellite repeats within adhesin genes. These results confirm the genomic plasticity of C. glabrata and show that chromosomal aberrations and functional adaptations may occur not only during infection and under antimicrobial therapy, but also under laboratory conditions without extreme selective pressures. These alterations can significantly affect phenotypic properties such as cell surface attributes including adhesion and the cell wall carbohydrate composition and therefore, if unnoticed, may adulterate the outcome of genetic studies.     

环境因素所致印迹基因改变与子代器官发育

印迹基因是由大约100个基因组成的一类特殊子集,主要以亲本单等位基因的方式表达,对胚胎的生长发育具有重要作用.近年来发现,环境因素所引起的印迹基因表观遗传修饰改变可造成胎儿多脏器发育不良甚至成年后多疾病易感,且存在多代遗传效应.本文基于国内外最新研究进展,总结了印迹基因表达改变对个体发育阶段以及生命后期器官功能的影响,...     

TEMPERATURE‐DEPENDENT TURNOVERS IN SEX‐DETERMINATION MECHANISMS: A QUANTITATIVE MODEL

Sex determination is often seen as a dichotomous process: individual sex is assumed to be determined either by genetic (genotypic sex determination, GSD) or by environmental factors (environmental sex determination, ESD), most often temperature (temperature sex determination, TSD). We endorse an alternative view, which sees GSD and TSD as the ends of a continuum. Both effects interact a priori, because temperature can affect gene expression at any step along the sex‐determination cascade. We propose to define sex‐determination systems at the population‐ (rather than individual) level, via the proportion of variance in phenotypic sex stemming from genetic versus environmental factors, and we formalize this concept in a quantitative‐genetics framework. Sex is seen as a threshold trait underlain by a liability factor, and reaction norms allow modeling interactions between genotypic and temperature effects (seen as the necessary consequences of thermodynamic constraints on the underlying physiological processes). As this formalization shows, temperature changes (due to e.g., climatic changes or range expansions) are expected to provoke turnovers in sex‐ determination mechanisms, by inducing large‐scale sex reversal and thereby sex‐ratio selection for alternative sex‐determining genes. The frequency of turnovers and prevalence of homomorphic sex chromosomes in cold‐blooded vertebrates might thus directly relate to the temperature dependence in sex‐determination mechanisms.     

The genetic basis of adaptation: lessons from concealing coloration in pocket mice

Recent studies on the genetics of adaptive coat-color variation in pocket mice (Chaetodipus intermedius) are reviewed in the context of several on-going debates about the genetics of adaptation. Association mapping with candidate genes was used to identify mutations responsible for melanism in four different populations of C. intermedius. Here, I review four main results (i) a single gene, the melanocortin-1-receptor (Mc1r), appears to be responsible for most of the phenotypic variation in color in one population, the Pinacate site; (ii) four or fewer nucleotide changes at Mc1r appear to be responsible for the difference in receptor function; (iii) studies of migration-selection balance suggest that the selection coefficient associated with the dark Mc1r allele at the Pinacate site is large; and (iv) different (unknown) genes underlie the evolution of melanism on three other lava flows. These findings are discussed in light of the evolution of convergent phenotypes, the average size of phenotypic effects underlying adaptation, the evolution of dominance, and the distinction between adaptations caused by changes in gene dosage versus gene structure.     

Genes that determine flower color: the role of regulatory changes in the evolution of phenotypic adaptations

A central goal of evolutionary genetics is to trace the causal pathway between mutations at particular genes and adaptation at the phenotypic level. The proximate objective is to identify adaptations through the analysis of molecular sequence data from specific candidate genes or their regulatory elements. In this paper, we consider the molecular evolution of floral color in the morning glory genus (Ipomoea) as a model for relating molecular and phenotypic evolution. To begin, flower color variation usually conforms to simple Mendelian transmission, thus facilitating genetic and molecular analyses. Population genetic studies of flower color polymorphisms in the common morning glory (Ipomoea purpurea) have shown that some morphs are subject to complex patterns of selection. Striking differences in floral color and morphology are also associated with speciation in the genus Ipomoea. The molecular bases for these adaptive shifts can be dissected because the biosynthetic pathways that determine floral pigmentation are well understood and many of the genes of flavonoid biosynthesis have been isolated and extensively studied. We present a comparative analysis of the level of gene expression in Ipomoea for several key genes in flavonoid biosynthesis. Specifically we ask: how frequently are adaptive shifts in flower color phenotypes associated with changes in regulation of gene expression versus mutations in structural genes? The results of this study show that most species differences in this crucial phenotype are associated with changes in the regulation of gene expression.     

Role of AP2/EREBP transcription factors in gene regulation during abiotic stress.

Crop plants are exposed to many types of abiotic stress during their life cycle. Water deficit derived from drought, low temperature or high salt concentration in the soil, is one of the most common environmental stresses that affects growth and development of plants through alterations in metabolism and gene expression. Adaptation to these conditions may involve passive tolerance or active homeostatic mechanisms for maintaining water balance. Active responses occur at different levels in the plant and may represent a concomitant protection against other types of stress such as pathogen attack. Many morphological and physiological adaptations to water stress are under the control of the plant hormone abscisic acid and involve specific activation of target genes that in one way or another protect cells against water deficit or participate in the regulation of the drought response. Here, we discuss recent advances in our understanding of drought adaptation mediated by specific changes in gene expression and the role of AP2/EREBP nuclear factors in these processes.     

Environmentally induced phenotypes and DNA methylation: how to deal with unpredictable conditions until the next generation and after

Organisms often respond to environmental changes by producing alternative phenotypes. Epigenetic processes such as DNA methylation may contribute to environmentally induced phenotypic variation by modifying gene expression. Changes in DNA methylation, unlike DNA mutations, can be influenced by the environment; they are stable at the time scale of an individual and present different levels of heritability. These characteristics make DNA methylation a potentially important molecular process to respond to environmental change. The aim of this review is to present the implications of DNA methylation on phenotypic variations driven by environmental changes. More specifically, we explore epigenetic concepts concerning phenotypic change in response to the environment and heritability of DNA methylation, namely the Baldwin effect and genetic accommodation. Before addressing this point, we report major differences in DNA methylation across taxa and the role of this modification in producing and maintaining environmentally induced phenotypic variation. We also present the different methods allowing the detection of methylation polymorphism. We believe this review will be helpful to molecular ecologists, in that it highlights the importance of epigenetic processes in ecological and evolutionary studies.     

Phenotypic plasticity: Eco-Devo and evolution

Phenotypic plasticity refers to the ability of an organism to alter its physiology/morphology/behavior in response to changes in environmental conditions. Although encompassing various phenomena spanning multi-ple levels of organization, most plastic responses seem to take place by altering gene expression and eventually altering ontogenetic trajectory in response to environmental variation. Epigenetic modifications provide a plausi-ble link between the environment and alterations in gene expression, and the alterations in phenotype based on environmentally induced epigenetic modifications can be inherited transgenerationally. Even closely related species and populations with different genotypes may exhibit differences in the patterns and the extents of plastic responses, indicating the wide existence of plasticity genes which are independent of trait means and directly respond to environmental stimuli by triggering phenotypic changes. The ability of plasticity is not only able to affect the adaptive evolution of species significantly, but is also an outcome of evolutionary processes. Therefore, phenotypic plasticity is a potentially important molder of adaptation and evolution.     

High-Altitude Adaptation: Mechanistic Insights from Integrated Genomics and Physiology

Population genomic analyses of high-altitude humans and other vertebrates have identified numerous candidate genes for hypoxia adaptation, and the physiological pathways implicated by such analyses suggest testable hypotheses about underlying mechanisms. Studies of highland natives that integrate genomic data with experimental measures of physiological performance capacities and subordinate traits are revealing associations between genotypes (e.g., hypoxia-inducible factor gene variants) and hypoxia-responsive phenotypes. The subsequent search for causal mechanisms is complicated by the fact that observed genotypic associations with hypoxia-induced phenotypes may reflect second-order consequences of selection-mediated changes in other (unmeasured) traits that are coupled with the focal trait via feedback regulation. Manipulative experiments to decipher circuits of feedback control and patterns of phenotypic integration can help identify causal relationships that underlie observed genotype–phenotype associations. Such experiments are critical for correct inferences about phenotypic targets of selection and mechanisms of adaptation.