A climate for contemporary evolution

A new study of divergence in freshwater fish provides strong evidence of rapid, temperature-mediated adaptation. This study is particularly important in the ongoing debate over the extent and significance of evolutionary response to climate change because divergence has occurred in relatively few generations in spite of ongoing gene flow and in the aftermath of a significant genetic bottleneck, factors that have previously been considered obstacles to evolution. Climate change may thus be more likely to foster contemporary evolutionary responses than has been anticipated, and I argue here for the importance of investigating their possible occurrence.     

The merging of community ecology and phylogenetic biology

The increasing availability of phylogenetic data, computing power and informatics tools has facilitated a rapid expansion of studies that apply phylogenetic data and methods to community ecology. Several key areas are reviewed in which phylogenetic information helps to resolve long-standing controversies in community ecology, challenges previous assumptions, and opens new areas of investigation. In particular, studies in phylogenetic community ecology have helped to reveal the multitude of processes driving community assembly and have demonstrated the importance of evolution in the assembly process. Phylogenetic approaches have also increased understanding of the consequences of community interactions for speciation, adaptation and extinction. Finally, phylogenetic community structure and composition holds promise for predicting ecosystem processes and impacts of global change. Major challenges to advancing these areas remain. In particular, determining the extent to which ecologically relevant traits are phylogenetically conserved or convergent, and over what temporal scale, is critical to understanding the causes of community phylogenetic structure and its evolutionary and ecosystem consequences. Harnessing phylogenetic information to understand and forecast changes in diversity and dynamics of communities is a critical step in managing and restoring the Earth's biota in a time of rapid global change.     

Interplay between global patterns of environmental temperature and variation in nonshivering thermogenesis of rodent species across large spatial scales

The purpose of this study was to test for correlations of mass-independent nonshivering thermogenesis (NST) in rodent species with climatic factors such as maximum and minimum geographic temperature. We first analyzed whether the responses of rodents show a phylogenetic signal. If so, and if the NST over a broad geographical range is similar, then such responses probably reflect physiological evolutionary adaptation. Our results show that NST did not show phylogenetic signal, appears to be evolutionary labile and is negatively correlated with environmental temperature. We predicted that species evolved in cold climates will exhibit higher mass-independent NST than species from warmer habitats. Indeed, we observed that the relationships between mass-independent NST and minimum temperature ( r _s=−0.411, P =0.009) as well as between NST and maximum temperature ( r _s=−0.443, P =0.004) were both negatively and significantly correlated, thus supporting our predictions. Thus, thermal physiology may be a significant factor underlying the ecological and evolutionary success of animals. Finally we suggest that due to the pressing need to explain and predict the likely biological impact of climatic change, advances in this field are necessary.     

Macroecology, global change and the shadow of forgotten ancestors

Many recent studies have evaluated how global changes will affect biodiversity, and have mainly focused on how to develop conservation strategies to avoid, or at least minimize, extinctions due to shifts in suitable habitats for the species. However, these complex potential responses might be in part structured in phylogeny, because of the macroecological traits underlying them. In this comment, we review recent analytical developments in phylogenetic comparative methods that can be used to understand patterns of trait changes under environmental change. We focus on a partial regression approach that allows for partitioning the variance of traits into a fraction attributed to a pure ecological component, a fraction attributed to phylogenetically structured environmental variation (niche conservatism) and a fraction that may be attributed to phylogenetic effects only. We then develop a novel interpretation for linking these components for multiple traits with potential responses of species to global environmental change (i.e. adaptation, range shifts or extinctions). We hope that this interpretation will stimulate further research linking evolutionary components of multiple traits with broad-scale environmental changes.     

A phylogenetic approach to cultural evolution

There has been a rapid increase in the use of phylogenetic methods to study the evolution of languages and culture. Languages fit a tree model of evolution well, at least in their basic vocabulary, challenging the view that blending, or admixture among neighbouring groups, was predominant in cultural history. Here, we argue that we can use language trees to test hypotheses about not only cultural history and diversification, but also bio-cultural adaptation. Phylogenetic comparative methods take account of the non-independence of cultures (Galton's problem), which can cause spurious statistical associations in comparative analyses. Advances in phylogenetic methods offer new possibilities for the analysis of cultural evolution, including estimating the rate of evolution and the direction of coevolutionary change of traits on the tree. They also enable phylogenetic uncertainty to be incorporated into the analyses, so that one does not have to treat phylogenetic trees as if they were known without error.     

基因芯片技术在环境微生物群落研究中的应用

基因芯片技术作为一种快速、敏感、高通量的检测技术,近几年来在环境微生物群落研究中的应用越来越广泛并且得到充分的发展.它不仅可以研究环境微生物群落的微生物分布、种类、功能、动力学变化,还能分析环境污染等环境因素改变对其微生物生态的影响.本文按照基因芯片探针的设计方法,将环境样品群落研究基因芯片分为系统寡核苷酸芯片、功能基因芯片、群落基因组芯片、宏基因组芯片,并简要综述了该技术在活性污泥、土壤、水等环境样品微生物群落研究上的应用,最后,本文展望了该技术的研究方向和在寻找不同环境微生物群落之间差异微生物、差异基因或差异表达基因研究中的应用前景.     

Rapid differentiation of plasticity in life history and morphology during invasive range expansion and concurrent local adaptation in the horned beetle Onthophagus taurus

Understanding the interplay between genetic differentiation, ancestral plasticity, and the evolution of plasticity during adaptation to environmental variation is critical to predict populations’ responses to environmental change. However, the role of plasticity in rapid adaptation in nature remains poorly understood. We here use the invasion of the horned beetle Onthophagus taurus in the United States during the last half century to study the contribution of ancestral plasticity and post-invasion evolution of plastic responses in rapid population differentiation. We document latitudinal variation in life history and morphology, including genetic compensation in development time and body size, likely adaptive responses to seasonal constraints in the North. However, clinal variation in development time and size was strongly dependent on rearing temperature, suggesting that population differentiation in plasticity played a critical role in successful adaptation on ecological timescales. Clinal variation in wing shape was independent of ancestral plasticity, but correlated with derived plasticity, consistent with evolutionary interdependence. In contrast, clinal variation in tibia shape aligned poorly with thermal plasticity. Overall, this study suggests that post-invasion evolution of plasticity contributed to range expansions and concurrent adaptation to novel climatic conditions.     

PHYLOGENETIC CONSTRAINTS IN KEY FUNCTIONAL TRAITS BEHIND SPECIES’ CLIMATE NICHES: PATTERNS OF DESICCATION AND COLD RESISTANCE ACROSS 95 DROSOPHILA SPECIES

Species distributions are often constrained by climatic tolerances that are ultimately determined by evolutionary history and/or adaptive capacity, but these factors have rarely been partitioned. Here, we experimentally determined two key climatic niche traits (desiccation and cold resistance) for 92–95 Drosophila species and assessed their importance for geographic distributions, while controlling for acclimation, phylogeny, and spatial autocorrelation. Employing an array of phylogenetic analyses, we documented moderate‐to‐strong phylogenetic signal in both desiccation and cold resistance. Desiccation and cold resistance were clearly linked to species distributions because significant associations between traits and climatic variables persisted even after controlling for phylogeny. We used different methods to untangle whether phylogenetic signal reflected phylogenetically related species adapted to similar environments or alternatively phylogenetic inertia. For desiccation resistance, weak phylogenetic inertia was detected; ancestral trait reconstruction, however, revealed a deep divergence that could be traced back to the genus level. Despite drosophilids’ high evolutionary potential related to short generation times and high population sizes, cold resistance was found to have a moderate‐to‐high level of phylogenetic inertia, suggesting that evolutionary responses are likely to be slow. Together these findings suggest species distributions are governed by evolutionarily conservative climate responses, with limited scope for rapid adaptive responses to future climate change.     

Stimulus change detection in phasic auditory units in the frog midbrain: frequency and ear specific adaptation

Neural adaptation, a reduction in the response to a maintained stimulus, is an important mechanism for detecting stimulus change. Contributing to change detection is the fact that adaptation is often stimulus specific: adaptation to a particular stimulus reduces excitability to a specific subset of stimuli, while the ability to respond to other stimuli is unaffected. Phasic cells (e.g., cells responding to stimulus onset) are good candidates for detecting the most rapid changes in natural auditory scenes, as they exhibit fast and complete adaptation to an initial stimulus presentation. We made recordings of single phasic auditory units in the frog midbrain to determine if adaptation was specific to stimulus frequency and ear of input. In response to an instantaneous frequency step in a tone, 28 % of phasic cells exhibited frequency specific adaptation based on a relative frequency change (delta-f = ±16 %). Frequency specific adaptation was not limited to frequency steps, however, as adaptation was also overcome during continuous frequency modulated stimuli and in response to spectral transients interrupting tones. The results suggest that adaptation is separated for peripheral (e.g., frequency) channels. This was tested directly using dichotic stimuli. In 45 % of binaural phasic units, adaptation was ear specific: adaptation to stimulation of one ear did not affect responses to stimulation of the other ear. Thus, adaptation exhibited specificity for stimulus frequency and lateralization at the level of the midbrain. This mechanism could be employed to detect rapid stimulus change within and between sound sources in complex acoustic environments.     

Rapid Parallel Adaptation to Anthropogenic Heavy Metal Pollution

The impact of human-mediated environmental change on the evolutionary trajectories of wild organisms is poorly understood. In particular, capacity of species to adapt rapidly (in hundreds of generations or less), reproducibly and predictably to extreme environmental change is unclear. Silene uniflora is predominantly a coastal species, but it has also colonized isolated, disused mines with phytotoxic, zinc-contaminated soils. To test whether rapid, parallel adaptation to anthropogenic pollution has taken place, we used reduced representation sequencing (ddRAD) to reconstruct the evolutionary history of geographically proximate mine and coastal population pairs and found largely independent colonization of mines from different coastal sites. Furthermore, our results show that parallel evolution of zinc tolerance has occurred without gene flow spreading adaptive alleles between mine populations. In genomic regions where signatures of selection were detected across multiple mine-coast pairs, we identified genes with functions linked to physiological differences between the putative ecotypes, although genetic differentiation at specific loci is only partially shared between mine populations. Our results are consistent with a complex, polygenic genetic architecture underpinning rapid adaptation. This shows that even under a scenario of strong selection and rapid adaptation, evolutionary responses to human activities (and other environmental challenges) may be idiosyncratic at the genetic level and, therefore, difficult to predict from genomic data.     

Adapting with Microbial Help: Microbiome Flexibility Facilitates Rapid Responses to Environmental Change

Animals and plants are metaorganisms and associate with microbes that affect their physiology, stress tolerance, and fitness. Here the hypothesis that alteration of the microbiome may constitute a fast-response mechanism to environmental change is examined. This is supported by recent reciprocal transplant experiments with reef corals, which have shown that their microbiome adapts to thermally variable habitats and changes over time when transplanted into different environments. Further, inoculation of corals with beneficial bacteria increases their stress tolerance. But corals differ in their ability to flexibly associate with different bacteria. How scales of microbiome flexibility may reflect different metaorganism adaptation mechanisms is discussed and future directions for research are pinpointed. It is posited that microbiome flexibility is a broad phenomenon that contributes to the ability of organisms to respond to environmental change. Importantly, adapting with microbial help may provide an alternate route to organismal adaptation that facilitates rapid responses.     

Evolutionary history underlies plant physiological responses to global change since the last glacial maximum

Assessing family‐ and species‐level variation in physiological responses to global change across geologic time is critical for understanding factors that underlie changes in species distributions and community composition. Here, we used stable carbon isotopes, leaf nitrogen content and stomatal measurements to assess changes in leaf‐level physiology in a mixed conifer community that underwent significant changes in composition since the last glacial maximum (LGM) (21 kyr BP). Our results indicate that most plant taxa decreased stomatal conductance and/or maximum photosynthetic capacity in response to changing conditions since the LGM. However, plant families and species differed in the timing and magnitude of these physiological responses, and responses were more similar within families than within co‐occurring species assemblages. This suggests that adaptation at the level of leaf physiology may not be the main determinant of shifts in community composition, and that plant evolutionary history may drive physiological adaptation to global change over recent geologic time.     

Phylogenetic conservatism and climate factors shape flowering phenology in alpine meadows

The study of phylogenetic conservatism in alpine plant phenology is critical for predicting climate change impacts; currently we have a poor understanding of how phylogeny and climate factors interactively influence plant phenology. Therefore, we explored the influence of phylogeny and climate factors on flowering phenology in alpine meadows. For two different types of alpine plant communities, we recorded phenological data, including flowering peak, first flower budding, first flowering, first fruiting and the flowering end for 62 species over the course of 5 years (2008–2012). From sequences in two plastid regions, we constructed phylogenetic trees. We used Blomberg’s K and Pagel’s lambda to assess the phylogenetic signal in phenological traits and species’ phenological responses to climate factors. We found a significant phylogenetic signal in the date of all reproductive phenological events and in species’ phenological responses to weekly day length and temperature. The number of species in flower was strongly associated with the weekly day lengths and followed by the weekly temperature prior to phenological activity. Based on phylogenetic eigenvector regression (PVR) analysis, we found a highly shared influence of phylogeny and climate factors on alpine species flowering phenology. Our results suggest the phylogenetic conservatism in both flowering and fruiting phenology may depend on the similarity of responses to external environmental cues among close relatives.     

Inheritance patterns of photoperiodic diapause induction in Leptinotarsa decemlineata

Photoperiod is a reliable indicator of season and an important cue that many insects use for phenological synchronization. Undergoing range expansion insects can face a change in the local photoperiod to which they need to resynchronize. Rapid range expansion can be associated with rapid photoperiodic adaptation, which can be associated with intense selection on strongly heritable polygenic traits. Alternatively, it is proposed that, in insects with an XO sex‐determination system, genes with large effect residing on the sex chromosome could drive photoperiodic adaptation because the gene or genes are exposed to selection in the sex carrying only a single X‐chromosome. The present study seeks to understand which of these alternatives more likely explains the rapid photoperiodic adaptation in European Colorado potato beetles Leptinotarsa decemlineata Say. Diapause induction is assessed in beetles from a northern and a southern population, as well as from reciprocal hybrid crosses between the northern and southern population, when reared at an intermediate length photoperiod. The crosses within population display the expected responses, with the northern and southern populations showing high and low diapause propensity, respectively. The hybrids show intermediate responses in all studied traits. No clear difference in the responses in hybrids depending on the latitudinal origin of their father or mother is detected, even though partial paternal line dominance is seen in the responses of male beetles in one hybrid cross. These results therefore indicate that, in L. decemlineata, photoperiodic diapause induction is strongly heritable, and has an additive polygenic autosomal background.     

Similarities in butterfly emergence dates among populations suggest local adaptation to climate

Phenology shifts are the most widely cited examples of the biological impact of climate change, yet there are few assessments of potential effects on the fitness of individual organisms or the persistence of populations. Despite extensive evidence of climate‐driven advances in phenological events over recent decades, comparable patterns across species' geographic ranges have seldom been described. Even fewer studies have quantified concurrent spatial gradients and temporal trends between phenology and climate. Here we analyse a large data set (~129 000 phenology measures) over 37 years across the UK to provide the first phylogenetic comparative analysis of the relative roles of plasticity and local adaptation in generating spatial and temporal patterns in butterfly mean flight dates. Although populations of all species exhibit a plastic response to temperature, with adult emergence dates earlier in warmer years by an average of 6.4 days per °C, among‐population differences are significantly lower on average, at 4.3 days per °C. Emergence dates of most species are more synchronised over their geographic range than is predicted by their relationship between mean flight date and temperature over time, suggesting local adaptation. Biological traits of species only weakly explained the variation in differences between space‐temperature and time‐temperature phenological responses, suggesting that multiple mechanisms may operate to maintain local adaptation. As niche models assume constant relationships between occurrence and environmental conditions across a species' entire range, an important implication of the temperature‐mediated local adaptation detected here is that populations of insects are much more sensitive to future climate changes than current projections suggest.     

Rapid responses to a strong experimental selection for heat hardening in the invasive whitefly Bemisia tabaci MEAM 1

Adaptation to new environments is an important issue for invasive species as colonization depends on evolvability in their new distribution range. Here, we considered the case of the whitefly Bemisia tabaci MEAM 1 (Gennadius) (Hemiptera: Aleyrodidae), a pest that has recently invaded Colombia and where thermal adaptation has been proposed to explain its colonizing ability. An experimental evolution study was conducted to assess the evolutionary potential of B. tabaci in relation to its upper thermal limits, to explain its rapid adaptation during post‐invasion periods. Selection for hardening capacity was conducted in four whitefly populations. We measured thermal responses in relation to fitness components (survival, fecundity, and viability) for 5–7 generations under a strong selection regime. Heat hardening responded rapidly in both sexes. This was expressed as an increase in survival, but not in fecundity or viability. These results suggest that thermal responses for heat hardening are not correlated and evolve independently. Increased survival after few generations of selection points to high adaptive potential in this insect, which leads to rapid post‐invasion adaptation. Our study can help to predict population responses to environmental change and explain the colonizing ability of this pest.     

Rapid loss of stress resistance in Drosophila melanogaster under adaptation to laboratory culture

We investigate changes in resistance to desiccation and starvation during adaptation of Drosophila melanogaster to laboratory culture. We test the hypothesis that resistance to environmental stresses is lost under laboratory adaptation. For both traits, there was a rapid loss of resistance over a three-year period. The rapidity of the response suggested that mutation accumulation could not account for it. Rather, resistance to environmental stresses appeared to be lost as a correlated response to selection on another trait, such as early fertility, with which stress resistance is negatively genetically correlated. These results suggest that caution is needed when extrapolating from evolution of stress resistance in long-established laboratory stocks to patterns of responses and correlated responses in natural populations.     

Thermal tolerance in the keystone species Daphnia magna—a candidate gene and an outlier analysis approach

Changes in temperature have occurred throughout Earth's history. However, current warming trends exacerbated by human activities impose severe and rapid loss of biodiversity. Although understanding the mechanisms orchestrating organismal response to climate change is important, remarkably few studies document their role in nature. This is because only few systems enable the combined analysis of genetic and plastic responses to environmental change over long time spans. Here, we characterize genetic and plastic responses to temperature increase in the aquatic keystone grazer Daphnia magna combining a candidate gene and an outlier analysis approach. We capitalize on the short generation time of our species, facilitating experimental evolution, and the production of dormant eggs enabling the analysis of long‐term response to environmental change through a resurrection ecology approach. We quantify plasticity in the expression of 35 candidate genes in D. magna populations resurrected from a lake that experienced changes in average temperature over the past century and from experimental populations differing in thermal tolerance isolated from a selection experiment. By measuring expression in multiple genotypes from each of these populations in control and heat treatments, we assess plastic responses to extreme temperature events. By measuring evolutionary changes in gene expression between warm‐ and cold‐adapted populations, we assess evolutionary response to temperature changes. Evolutionary response to temperature increase is also assessed via an outlier analysis using EST‐linked microsatellite loci. This study provides the first insights into the role of plasticity and genetic adaptation in orchestrating adaptive responses to environmental change in D. magna.     

Behavioural responses to human‐induced environmental change

The initial response of individuals to human‐induced environmental change is often behavioural. This can improve the performance of individuals under sudden, large‐scale perturbations and maintain viable populations. The response can also give additional time for genetic changes to arise and, hence, facilitate adaptation to new conditions. On the other hand, maladaptive responses, which reduce individual fitness, may occur when individuals encounter conditions that the population has not experienced during its evolutionary history, which can decrease population viability. A growing number of studies find human disturbances to induce behavioural responses, both directly and by altering factors that influence fitness. Common causes of behavioural responses are changes in the transmission of information, the concentration of endocrine disrupters, the availability of resources, the possibility of dispersal, and the abundance of interacting species. Frequent responses are alterations in habitat choice, movements, foraging, social behaviour and reproductive behaviour. Behavioural responses depend on the genetically determined reaction norm of the individuals, which evolves over generations. Populations first respond with individual behavioural plasticity, whereafter changes may arise through innovations and the social transmission of behavioural patterns within and across generations, and, finally, by evolution of the behavioural response over generations. Only a restricted number of species show behavioural adaptations that make them thrive in severely disturbed environments. Hence, rapid human‐induced disturbances often decrease the diversity of native species, while facilitating the spread of invasive species with highly plastic behaviours. Consequently, behavioural responses to human‐induced environmental change can have profound effects on the distribution, adaptation, speciation and extinction of populations and, hence, on biodiversity. A better understanding of the mechanisms of behavioural responses and their causes and consequences could improve our ability to predict the effects of human‐induced environmental change on individual species and on biodiversity.     

Shifts in coding properties and maintenance of information transmission during adaptation in barrel cortex

Neuronal responses to ongoing stimulation in many systems change over time, or “adapt.” Despite the ubiquity of adaptation, its effects on the stimulus information carried by neurons are often unknown. Here we examine how adaptation affects sensory coding in barrel cortex. We used spike-triggered covariance analysis of single-neuron responses to continuous, rapidly varying vibrissa motion stimuli, recorded in anesthetized rats. Changes in stimulus statistics induced spike rate adaptation over hundreds of milliseconds. Vibrissa motion encoding changed with adaptation as follows. In every neuron that showed rate adaptation, the input–output tuning function scaled with the changes in stimulus distribution, allowing the neurons to maintain the quantity of information conveyed about stimulus features. A single neuron that did not show rate adaptation also lacked input–output rescaling and did not maintain information across changes in stimulus statistics. Therefore, in barrel cortex, rate adaptation occurs on a slow timescale relative to the features driving spikes and is associated with gain rescaling matched to the stimulus distribution. Our results suggest that adaptation enhances tactile representations in primary somatosensory cortex, where they could directly influence perceptual decisions.