Parallel gene expression evolution in natural and laboratory evolved populations

The Potential for Experimental Evolution to Uncover Trade-Offs Associated With Anthropogenic and Climate Change Adaptation

Evolutionary responses to climate change may incur trade-offs due to energetic constraints and mechanistic limitations, which are both influenced by environmental context. Adaptation to one stressor may result in life history trade-offs, canalization of phenotypic plasticity, and the inability to tolerate other stressors, among other potential costs. While trade-offs incurred during adaptation are difficult to detect in natural populations, experimental evolution can provide important insights by measuring correlated responses to selection as populations adapt to changing environments. However, studies testing for trade-offs have generally lagged behind the growth in the use of experimental evolution in climate change studies. We argue that the important insights generated by the few studies that have tested for trade-offs make a strong case for including these types of measurements in future studies of climate adaptation. For example, there is emerging consensus from experimental evolution studies that tolerance and tolerance plasticity trade-offs are an often-observed outcome of adaptation to anthropogenic change. In recent years, these types of studies have been strengthened by the use of sequencing of experimental populations, which provides promising new avenues for understanding the molecular mechanisms underlying observed phenotypic trade-offs.

Life stage-specific effects of heat stress on spermatogenesis and oogenesis in Drosophila melanogaster

Biodiversity is increasingly threatened by unpredictable, frequent, and intense climatic events like heatwaves that pose harmful impacts on ectotherms. Beyond the health and survival of organisms, reduced reproductive performance has emerged as a critical fitness consequence of thermal stress induced by high temperatures. Many studies on these effects expose organisms to heat stress during the adult stage or throughout development, often focusing on cumulative effects across life stages, and they tend to examine one or the other sex. This approach may not reflect the short-term nature of many extreme heat events and limits our understanding of stage- and sex-specific fitness consequences in short-lived organisms. To address this gap, we used Drosophila melanogaster to investigate the sex-specific reproductive performance following short heat stress of varying intensity at different developmental stages. We found the thermal sensitivity to be higher in males than females, and to increase toward adult emergence, leading to nearly complete reproductive failure and substantially slowed recovery. These results highlight how even brief bouts of heat stress during a sensitive phase could affect population dynamics and persistence. Our findings also underscore that incorporating both sex and life stage could improve predictions of species persistence.

Alternative splicing in parallel evolution and the evolutionary potential in sticklebacks

Repeatability of adaptation to similar environments provides opportunity to evaluate the predictability of natural selection. While many studies have investigated gene expression differences between populations adapted to contrasting environments, the role of post-transcriptional processes such as alternative splicing has rarely been evaluated in the context of parallel adaptation. To address the aforementioned knowledge gap, we reanalysed transcriptomic data from three pairs of threespine stickleback (Gasterosteus aculeatus) ecotypes adapted to marine or freshwater environment. First, we identified genes with repeated expression or splicing divergence across ecotype pairs, and compared the genetic architecture and biological processes between parallelly expressed and parallelly spliced loci. Second, we analysed the extent to which parallel adaptation was reflected at gene expression and alternative splicing levels. Finally, we tested how the two axes of transcriptional variation differed in their potential for evolutionary change. Although both repeated differential splicing and differential expression across ecotype pairs showed tendency for parallel divergence, the degree of parallelism was lower for splicing than expression. Furthermore, parallel divergences in splicing and expression were likely to be associated with distinct cis-regulatory genetic variants and functionally unique set of genes. Finally, we found that parallelly spliced genes showed higher nucleotide diversity than parallelly expressed genes, indicating splicing is less susceptible to genetic variation erosion during parallel adaptation. Our results provide novel insight into the role of splicing in parallel adaptation, and underscore the contribution of splicing to the evolutionary potential of wild populations under environmental change.

Experimental Evolution in a Warming World: The Omics Era

A comprehensive understanding of the genetic mechanisms that shape species responses to thermal variation is essential for more accurate predictions of the impacts of climate change on biodiversity. Experimental evolution with high-throughput resequencing approaches (evolve and resequence) is a highly effective tool that has been increasingly employed to elucidate the genetic basis of adaptation. The number of thermal evolve and resequence studies is rising, yet there is a dearth of efforts to integrate this new wealth of knowledge. Here, we review this literature showing how these studies have contributed to increase our understanding on the genetic basis of thermal adaptation. We identify two major trends: highly polygenic basis of thermal adaptation and general lack of consistency in candidate targets of selection between studies. These findings indicate that the adaptive responses to specific environments are rather independent. A review of the literature reveals several gaps in the existing research. Firstly, there is a paucity of studies done with organisms of diverse taxa. Secondly, there is a need to apply more dynamic and ecologically relevant thermal environments. Thirdly, there is a lack of studies that integrate genomic changes with changes in life history and behavioral traits. Addressing these issues would allow a more in-depth understanding of the relationship between genotype and phenotype. We highlight key methodological aspects that can address some of the limitations and omissions identified. These include the need for greater standardization of methodologies and the utilization of new technologies focusing on the integration of genomic and phenotypic variation in the context of thermal adaptation.

Genomics for monitoring and understanding species responses to global climate change

All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species' potential to adapt to future environments. Understanding and monitoring how organisms respond to human-driven climate change is therefore a major priority for the conservation of biodiversity in a rapidly changing environment. Recent developments in genomic, transcriptomic and epigenomic technologies are enabling unprecedented insights into the evolutionary processes and molecular bases of adaptation. This Review summarizes methods that apply and integrate omics tools to experimentally investigate, monitor and predict how species and communities in the wild cope with global climate change, which is by genetically adapting to new environmental conditions, through range shifts or through phenotypic plasticity. We identify advantages and limitations of each method and discuss future research avenues that would improve our understanding of species' evolutionary responses to global climate change, highlighting the need for holistic, multi-omics approaches to ecosystem monitoring during global climate change.

From perplexing to predictive: are we ready to forecast insect disease susceptibility in a warming world?

Insects are critical to our ecosystems, but we do not fully understand their future in our warming world. Rising temperatures are affecting insect physiology in myriad ways, including changes to their immune systems and the ability to fight infection. Whether predicted changes in temperature will contribute to insect mortality or success, and the role of disease in their future survival, remains unclear. Although heat can enhance immunity by activating the integrated defense system (e.g. via the production of protective molecules such as heat-shock proteins) and accelerating enzyme activity, heat can also compromise the immune system through energetic-resource trade-offs and damage. The responses to heat are highly variable among species. The reasons for this variability are poorly known, and we are lagging in our understanding of how and why the immune system responds to changes in temperature. In this Commentary, we highlight the variation in insect immune responses to heat and the likely underlying mechanisms. We suggest that we are currently limited in our ability to predict the effects of rising temperatures on insect immunity and disease susceptibility, largely owing to incomplete information, coupled with a lack of tools for data integration. Moreover, existing data are concentrated on a relatively small number of insect Orders. We provide suggestions for a path towards making more accurate predictions, which will require studies with realistic temperature exposures and housing design, and a greater understanding of both the thermal biology of the immune system and connections between immunity and the physiological responses to heat.

Genome-wide selection signatures reveal widespread synergistic effects of two different stressors in Drosophila melanogaster

Experimental evolution combined with whole-genome sequencing (evolve and resequence (E&R)) is a powerful approach to study the adaptive architecture of selected traits. Nevertheless, so far the focus has been on the selective response triggered by a single stressor. Building on the highly parallel selection response of founder populations with reduced variation, we evaluated how the presence of a second stressor affects the genomic selection response. After 20 generations of adaptation to laboratory conditions at either 18°C or 29°C, strong genome-wide selection signatures were observed. Only 38% of the selection signatures can be attributed to laboratory adaptation (no difference between temperature regimes). The remaining selection responses are either caused by temperature-specific effects, or reflect the joint effects of temperature and laboratory adaptation (same direction, but the magnitude differs between temperatures). The allele frequency changes resulting from the combined effects of temperature and laboratory adaptation were more extreme in the hot environment for 83% of the affected genomic regions-indicating widespread synergistic effects of the two stressors. We conclude that E&R with reduced genetic variation is a powerful approach to study genome-wide fitness consequences driven by the combined effects of multiple environmental factors.

Genome-wide signatures of synergistic epistasis during parallel adaptation in a Baltic Sea copepod

The role of epistasis in driving adaptation has remained an unresolved problem dating back to the Evolutionary Synthesis. In particular, whether epistatic interactions among genes could promote parallel evolution remains unexplored. To address this problem, we employ an Evolve and Resequence (E&R) experiment, using the copepod Eurytemora affinis, to elucidate the evolutionary genomic response to rapid salinity decline. Rapid declines in coastal salinity at high latitudes are a predicted consequence of global climate change. Based on time-resolved pooled whole-genome sequencing, we uncover a remarkably parallel, polygenic response across ten replicate selection lines, with 79.4% of selected alleles shared between lines by the tenth generation of natural selection. Using extensive computer simulations of our experiment conditions, we find that this polygenic parallelism is consistent with positive synergistic epistasis among alleles, far more so than other mechanisms tested. Our study provides experimental and theoretical support for a novel mechanism promoting repeatable polygenic adaptation, a phenomenon that may be common for selection on complex physiological traits.

Mutation in phcA Enhanced the Adaptation of Ralstonia solanacearum to Long-Term Acid Stress

Bacterial wilt, caused by the plant pathogen Ralstonia solanacearum, occurs more severely in acidified soil according to previous reports. However, R. solanacearum cannot grow well in acidic environments under barren nutrient culture conditions, especially when the pH is lower than 5. With the worsening acidification of farmland, further determination of how R. solanacearum adapts to the long-term acidic environment is worthwhile. In this study, experimental evolution was applied to evaluate the adaptability and mechanism of the R. solanacearum experimental population responding to long-term acid stress. We chose the CQPS-1 strain as the ancestor, and minimal medium (MM medium) with different pH values as the culture environment to simulate poor soil. After 1500 generations of serial passage experiments in pH 4.9 MM, acid-adapted experimental strains (denoted as C49 strains) were obtained, showing significantly higher growth rates than the growth rates of control experimental strains (serial passage experiment in pH 6.5 MM, denoted as C65 strains). Competition experiments showed that the competitive indices (CIs) of all selected clones from C49 strains were superior to the ancestor in acidic environment competitiveness. Based on the genome variation analysis and functional verification, we confirmed that loss of function in the phcA gene was associated with the acid fitness gain of R. solanacearum, which meant that the inactivation of the PhcA regulator caused by gene mutation mediated the population expansion of R. solanacearum when growing in an acidic stress environment. Moreover, the swimming motility of acid evolution strains and the phcA deletion mutant was significantly enhanced compared to CQPS-1. This work provided evidence for understanding the adaptive strategy of R. solanacearum to the long-term acidic environment.

Population genomics provides insights into lineage divergence and local adaptation within the cotton bollworm

The cotton bollworm Helicoverpa armigera is a cosmopolitan pest and its diverse habitats plausibly contribute to the formation of diverse lineages. Despite the significant threat it poses to economic crops worldwide, its evolutionary history and genetic basis of local adaptation are poorly understood. In this study, we de novo assembled a high-quality chromosome-level reference genome of H. a. armigera (contig N50 = 7.34 Mb), with 99.13% of the HaSCD2 assembly assigned into 31 chromosomes (Z-chromosome + 30 autosomes). We constructed an ultra-dense variation map across 14 cotton bollworm populations and identified a novel lineage in northwestern China. Historical inference showed that effective population size changes coincided with global temperature fluctuation. We identified nine differentiated genes in the three H. armigera lineages (H. a. armigera, H. a. conferta, and the new northwestern Chinese lineage), of which per and clk genes are involved in circadian rhythm. Selective sweep analyses identified a series of GO categories related to climate adaptation, feeding behavior and insecticide tolerance. Our findings reveal fundamental knowledge of the local adaptation of different cotton bollworm lineages and will guide the formulation of cotton bollworm management measures at different scales.

Evolution, Chance, and Aging

Aging has provided fruitful challenges for evolutionary theory, and evolutionary theory has deepened our understanding of aging. A great deal of genetic and molecular data now exists concerning mortality regulation and there is a growing body of knowledge concerning the life histories of diverse species. Assimilating all relevant data into a framework for the evolution of aging promises to significantly advance the field. We propose extensions of some key concepts to provide greater precision when applying these concepts to age-structured contexts. Secondary or byproduct effects of mutations are proposed as an important factor affecting survival patterns, including effects that may operate in small populations subject to genetic drift, widening the possibilities for mutation accumulation and pleiotropy. Molecular and genetic studies have indicated a diverse array of mechanisms that can modify aging and mortality rates, while transcriptome data indicate a high level of tissue and species specificity for genes affected by aging. The diversity of mechanisms and gene effects that can contribute to the pattern of aging in different organisms may mirror the complex evolutionary processes behind aging.

Temperature-dependent effects of house fly proto-Y chromosomes on gene expression could be responsible for fitness differences that maintain polygenic sex determination

Sex determination, the developmental process by which sexually dimorphic phenotypes are established, evolves fast. Evolutionary turnover in a sex determination pathway may occur via selection on alleles that are genetically linked to a new master sex determining locus on a newly formed proto-sex chromosome. Species with polygenic sex determination, in which master regulatory genes are found on multiple different proto-sex chromosomes, are informative models to study the evolution of sex determination and sex chromosomes. House flies are such a model system, with male determining loci possible on all six chromosomes and a female-determiner on one of the chromosomes as well. The two most common male-determining proto-Y chromosomes form latitudinal clines on multiple continents, suggesting that temperature variation is an important selection pressure responsible for maintaining polygenic sex determination in this species. Temperature-dependent fitness effects could be manifested through temperature-dependent gene expression differences across proto-Y chromosome genotypes. These gene expression differences may be the result of cis regulatory variants that affect the expression of genes on the proto-sex chromosomes, or trans effects of the proto-Y chromosomes on genes elswhere in the genome. We used RNA-seq to identify genes whose expression depends on proto-Y chromosome genotype and temperature in adult male house flies. We found no evidence for ecologically meaningful temperature-dependent expression differences of sex determining genes between male genotypes, but we were probably not sampling an appropriate developmental time-point to identify such effects. In contrast, we identified many other genes whose expression depends on the interaction between proto-Y chromosome genotype and temperature, including genes that encode proteins involved in reproduction, metabolism, lifespan, stress response, and immunity. Notably, genes with genotype-by-temperature interactions on expression were not enriched on the proto-sex chromosomes. Moreover, there was no evidence that temperature-dependent expression is driven by chromosome-wide cis-regulatory divergence between the proto-Y and proto-X alleles. Therefore, if temperature-dependent gene expression is responsible for differences in phenotypes and fitness of proto-Y genotypes across house fly populations, these effects are driven by a small number of temperature-dependent alleles on the proto-Y chromosomes that may have trans effects on the expression of genes on other chromosomes.

Functional biology in its natural context: A search for emergent simplicity

The immeasurable complexity at every level of biological organization creates a daunting task for understanding biological function. Here, we highlight the risks of stripping it away at the outset and discuss a possible path toward arriving at emergent simplicity of understanding while still embracing the ever-changing complexity of biotic interactions that we see in nature.

Parallel gene expression evolution in natural and laboratory evolved populations

Ecological adaptation is frequently inferred by the comparison of natural populations from different environments. Nevertheless, inference of the selective forces suffers the challenge that many environmental factors covary. With well-controlled environmental conditions, experimental evolution provides a powerful approach to complement the analysis of natural populations. On the other hand, it is apparent that laboratory conditions differ in many ways from natural environments, which raises the question as to what extent selection responses in experimental evolution studies can inform us about adaptation processes in the wild. In this study, we compared the expression profiles of replicated Drosophila melanogaster populations which have been exposed to two distinct temperature regimes (18/28 and 10/20°C) in the laboratory for more than 80 generations. Using gene-wise differential expression analysis and co-expression network analysis, we identified 541 genes and three coregulated gene modules that evolved in the same direction in both temperature regimes, and most of these changes probably reflect an adaptation to the space constraint or diurnal temperature fluctuation that is common in both selection regimes. In total, 203 genes and seven modules evolved temperature-specific expression changes. Remarkably, we detected a significant overlap of these temperature-adaptive genes/modules from experimental evolution with temperature-adaptive genes inferred from natural Drosophila populations covering two different temperature clines. We conclude that well-designed experimental evolution studies are a powerful tool to dissect evolutionary responses.

Can laboratory evolution experiments teach us about natural populations?

The ability to predict how natural populations will evolve and adapt to major changes in environmental conditions has long been of interest to evolutionary biologists and ecologists alike. The reality of global climate change has also created a pressing need for advancement in this particular area of research, as species are increasingly faced with rapid shifts in abiotic and biotic conditions. Evolutionary genomics has the potential to be incredibly useful as we move forward in addressing this need and in particular, evolve and resequence (E&R) studies-where researchers combine experimental evolution with whole-genome sequencing-have an important role to play. However, while E&R studies have shown a great deal of promise in tackling fundamental questions regarding the genetics of adaptation (Long et al., 2015; Schlötterer et al., 2014), it is unclear whether results from laboratory experiments can be directly translated to natural populations. In a From the Cover article in this issue of Molecular Ecology, Hsu et al. (Mol Ecol, 29, 2020) explicitly contend with this issue by examining the overlap between genes implicated in thermal adaptation in a Drosophila melanogaster E&R study and genes identified by comparing natural populations from different latitudinal clines. They report significant correlations between the two sets of temperature-adaptive genes and ultimately conclude that E&R studies can indeed generate insights applicable to populations inhabiting complex natural environments. While more work is needed to assess the generality of these conclusions, Hsu and Belmouaden (Mol Ecol, 29, 2020) contribute an important precedent.