Does Genetic Variation Maintained by Environmental Heterogeneity Facilitate Adaptation to Novel Selection?

Laboratory-adapted and wild-type black soldier flies express differential plasticity in bioconversion and nutrition when reared on urban food waste streams

BACKGROUND

The black soldier fly (BSF) offers a potential solution to address shortages of feed and food sources; however, selecting effective rearing substrates remains a major hurdle in BSF farming. In an urban area like Singapore, current practice is based on rearing BSF on homogeneous waste streams (e.g., spent brewery grains or okara) because heterogeneous food wastes (e.g., mixed kitchen/canteen waste or surplus cooked food) present several operational challenges with respect to the standardization of development, nutritional content, and harvesting.

RESULTS

In this study, we compared two genetic strains of BSF larvae (wild-type and laboratory-adapted line) in a bioconversion experiment with diverse types of food waste (homogeneous/heterogeneous; plant/meat) and we quantified the phenotypic plasticity. Our results demonstrate different plasticity in bioconversion performance, larval growth and larval nutrition between the two BSF lines. This difference may be attributed to the selective breeding the laboratory-adapted line has experienced. Notably, larval lipid content displayed little to no genetic variation for plasticity compared with larval protein and carbohydrate content. Despite variation in larval development, heterogeneous food wastes can produce better performance in bioconversion, larval growth, and larval nutrient content than homogeneous food waste. All-meat diets result in high larvae mortality but larval survival could be rescued by mixing meat with plant-based food wastes.

CONCLUSION

Overall, we suggest using mixed meals for BSF larvae feeding. Targeted breeding may be a promising strategy for the BSF industry but it is important to consider the selection effects on plasticity in larval nutrition carefully. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Facilitated Adaptation as A Conservation Tool in the Present Climate Change Context: A Methodological Guide

Climate change poses a novel threat to biodiversity that urgently requires the development of adequate conservation strategies. Living organisms respond to environmental change by migrating to locations where their ecological niche is preserved or by adapting to the new environment. While the first response has been used to develop, discuss and implement the strategy of assisted migration, facilitated adaptation is only beginning to be considered as a potential approach. Here, we present a review of the conceptual framework for facilitated adaptation, integrating advances and methodologies from different disciplines. Briefly, facilitated adaptation involves a population reinforcement that introduces beneficial alleles to enable the evolutionary adaptation of a focal population to pressing environmental conditions. To this purpose, we propose two methodological approaches. The first one (called pre-existing adaptation approach) is based on using pre-adapted genotypes existing in the focal population, in other populations, or even in closely related species. The second approach (called de novo adaptation approach) aims to generate new pre-adapted genotypes from the diversity present in the species through artificial selection. For each approach, we present a stage-by-stage procedure, with some techniques that can be used for its implementation. The associated risks and difficulties of each approach are also discussed.

Rapid evolution generates synergism between multiple stressors: Linking theory and an evolution experiment

Global change encompasses many co-occurring anthropogenic stressors. Understanding the interactions between these multiple stressors, whether they be additive, antagonistic or synergistic, is critical for ecosystem managers when prioritizing which stressors to mitigate in the face of global change. While such interactions between stressors appear prevalent, it remains unclear if and how these interactions change over time, as the majority of multiple-stressor studies rarely span multiple generations of study organisms. Although meta-analyses have reported some intriguing temporal trends in stressor interactions, for example that synergism may take time to emerge, the mechanistic basis for such observations is unknown. In this study, by analysing data from an evolution experiment with the rotifer Brachionus calyciflorus (~35 generations and 31,320 observations), we show that adaptation to multiple stressors shifts stressor interactions towards synergism. We show that trade-offs, where populations cannot optimally perform multiple tasks (i.e. adapting to multiple stressors), generate this bias towards synergism. We also show that removal of stressors from evolved populations does not necessarily increase fitness and that there is variation in the evolutionary trajectories of populations that experienced the same stressor regimes. Our results highlight outstanding questions at the interface between evolution and global change biology, and illustrate the importance of considering rapid adaptation when managing or restoring ecosystems subjected to multiple stressors under global change.

Facilitation alters climate change risk on rocky shores

A huge fraction of global biodiversity resides within biogenic habitats that ameliorate physical stresses. In most cases, details of how physical conditions within facilitative habitats respond to external climate forcing remain unknown, hampering climate change predictions for many of the world's species. Using intertidal mussel beds as a model system, we characterize relationships among external climate conditions and within-microhabitat heat and desiccation conditions. We use these data, along with physiological tolerances of two common inhabitant taxa (the isopod Cirolana harfordi and the porcelain crab Petrolisthes cinctipes), to examine the magnitude of climate risk inside and outside biogenic habitat, applying an empirically derived model of evaporation to simulate mortality risk under a high-emissions climate-warming scenario. We found that biogenic microhabitat conditions responded so weakly to external climate parameters that mortality risk was largely unaffected by climate warming. In contrast, outside the biogenic habitat, desiccation drove substantial mortality in both species, even at temperatures 4.4-8.6°C below their hydrated thermal tolerances. These findings emphasize the importance of warming-exacerbated desiccation to climate-change risk and the role of biogenic habitats in buffering this less-appreciated stressor. Our results suggest that, when biogenic habitats remain intact, climate warming may have weak direct effects on organisms within them. Instead, risk to such taxa is likely to be indirect and tightly coupled with the fate of habitat-forming populations. Conserving and restoring biogenic habitats that offer climate refugia could therefore be crucial to supporting biodiversity in the face of climate warming.

Building a bridge between adaptive capacity and adaptive potential to understand responses to environmental change

Adaptive capacity is a topic at the forefront of environmental change research with roots in both social, ecological, and evolutionary science. It is closely related to the evolutionary biology concept of adaptive potential. In this systematic literature review, we: (1) summarize the history of these topics and related fields; (2) assess relationship(s) between the concepts among disciplines and the use of the terms in climate change research, and evaluate methodologies, metrics, taxa biases, and the geographic scale of studies; and (3) provide a synthetic conceptual framework to clarify concepts. Bibliometric analyses revealed the terms have been used most frequently in conservation and evolutionary biology journals, respectively. There has been a greater growth in studies of adaptive potential than adaptive capacity since 2001, but a greater geographical extent of adaptive capacity studies. Few studies include both, and use is often superficial. Our synthesis considers adaptive potential as one process contributing to adaptive capacity of complex systems, notes "sociological" adaptive capacity definitions include actions aimed at desired outcome (i.e., policies) as a system driver whereas "biological" definitions exclude such drivers, and suggests models of adaptive capacity require integration of evolutionary and social-ecological system components.

The molecular mechanisms that determine different degrees of polyphagy in the Bemisia tabaci species complex

The whitefly Bemisia tabaci is a closely related group of >35 cryptic species that feed on the phloem sap of a broad range of host plants. Species in the complex differ in their host-range breadth, but the mechanisms involved remain poorly understood. We investigated, therefore, how six different B. tabaci species cope with the environmental unpredictability presented by a set of four common and novel host plants. Behavioral studies indicated large differences in performances on the four hosts and putative specialization of one of the species to cassava plants. Transcriptomic analyses revealed two main insights. First, a large set of genes involved in metabolism (>85%) showed differences in expression between the six species, and each species could be characterized by its own unique expression pattern of metabolic genes. However, within species, these genes were constitutively expressed, with a low level of environmental responsiveness (i.e., to host change). Second, within each species, sets of genes mainly associated with the super-pathways "environmental information processing" and "organismal systems" responded to the host switching events. These included genes encoding for proteins involved in sugar homeostasis, signal transduction, membrane transport, and immune, endocrine, sensory and digestive responses. Our findings suggested that the six B. tabaci species can be divided into four performance/transcriptomic "Types" and that polyphagy can be achieved in multiple ways. However, polyphagy level is determined by the specific identity of the metabolic genes/pathways that are enriched and overexpressed in each species (the species' individual metabolic "tool kit").

Toxicity, Physiological, and Ultrastructural Effects of Arsenic and Cadmium on the Extremophilic Microalga Chlamydomonas acidophila

The cytotoxicity of cadmium (Cd), arsenate (As(V)), and arsenite (As(III)) on a strain of Chlamydomonas acidophila, isolated from the Rio Tinto, an acidic environment containing high metal(l)oid concentrations, was analyzed. We used a broad array of methods to produce complementary information: cell viability and reactive oxygen species (ROS) generation measures, ultrastructural observations, transmission electron microscopy energy dispersive x-ray microanalysis (TEM-XEDS), and gene expression. This acidophilic microorganism was affected differently by the tested metal/metalloid: It showed high resistance to arsenic while Cd was the most toxic heavy metal, showing an LC₅₀ = 1.94 µM. Arsenite was almost four-fold more toxic (LC₅₀= 10.91 mM) than arsenate (LC₅₀ = 41.63 mM). Assessment of ROS generation indicated that both arsenic oxidation states generate superoxide anions. Ultrastructural analysis of exposed cells revealed that stigma, chloroplast, nucleus, and mitochondria were the main toxicity targets. Intense vacuolization and accumulation of energy reserves (starch deposits and lipid droplets) were observed after treatments. Electron-dense intracellular nanoparticle-like formation appeared in two cellular locations: inside cytoplasmic vacuoles and entrapped into the capsule, around each cell. The chemical nature (Cd or As) of these intracellular deposits was confirmed by TEM-XEDS. Additionally, they also contained an unexpected high content in phosphorous, which might support an essential role of poly-phosphates in metal resistance.

The combined use of raw and phylogenetically independent methods of outlier detection uncovers genome-wide dynamics of local adaptation in a lizard

Local adaptation is a dynamic process by which different allele combinations are selected in different populations at different times, and whose genetic signature can be inferred by genome-wide outlier analyses. We combined gene flow estimates with two methods of outlier detection, one of them independent of population coancestry (CIOA) and the other one not (ROA), to identify genetic variants favored when ecology promotes phenotypic convergence. We analyzed genotyping-by-sequencing data from five populations of a lizard distributed over an environmentally heterogeneous range that has been changing since the split of eastern and western lineages ca. 3 mya. Overall, western lizards inhabit forest habitat and are unstriped, whereas eastern ones inhabit shrublands and are striped. However, one population (Lerma) has unstriped phenotype despite its eastern ancestry. The analysis of 73,291 SNPs confirmed the east-west division and identified nonoverlapping sets of outliers (12 identified by ROA and 9 by CIOA). ROA revealed ancestral adaptive variation in the uncovered outliers that were subject to divergent selection and differently fixed for eastern and western populations at the extremes of the environmental gradient. Interestingly, such variation was maintained in Lerma, where we found high levels of heterozygosity for ROA outliers, whereas CIOA uncovered innovative variants that were selected only there. Overall, it seems that both the maintenance of ancestral variation and asymmetric migration have counterbalanced adaptive lineage splitting in our model species. This scenario, which is likely promoted by a changing and heterogeneous environment, could hamper ecological speciation of locally adapted populations despite strong genetic structure between lineages.

Species interactions mediate thermal evolution

Understanding whether populations and communities can evolve fast enough to keep up with ongoing climate change is one of the most pressing issues in biology today. A growing number of studies have documented rapid evolutionary responses to warming, suggesting that populations may be able to persist despite temperature increases. The challenge now is to better understand how species interactions, which are ubiquitous in nature, mediate these population responses to warming. Here, we use laboratory natural selection experiments in a freshwater community to test hypotheses related to how thermal evolution of Daphnia pulex to two selection temperatures (12 and 18°C) is mediated by rapid thermal evolution of its algal resource (Scenedesmus obliquus) or by the presence of the zooplankton predator Chaoborus americanus. We found that cold-evolved algae (a high-quality resource) facilitated the evolution of increased thermal plasticity in Daphnia populations selected at 12°C, for both body size and per capita growth rates (r). Conversely, warm-evolved algae facilitated the evolution of increased r thermal plasticity for Daphnia selected at 18°C. Lastly, we found that the effect of selection temperature on evolved Daphnia body size was more pronounced when Daphnia were also reared with predators. These data demonstrate that trait evolution of a focal population to the thermal environment can be affected by both bottom-up and top-down species interactions and that rapid temperature evolution of a resource can have cascading effects on consumer thermal evolution. Our study highlights the importance of incorporating species interactions when estimating ecological and evolutionary responses of populations and communities to ongoing temperature warming.

Ecological specialization in populations adapted to constant versus heterogeneous environments

Populations vary in their degree of ecological specialization. An intuitive, but often untested, hypothesis is that populations evolving under greater environmental heterogeneity will evolve to be less specialized. How important is environmental heterogeneity in explaining among-population variation in specialization? We assessed juvenile viability of 20 Drosophila melanogaster populations evolving under one of four regimes: (1) a salt-enriched environment, (2) a cadmium-enriched environment, (3) a temporally varying environment, and (4) a spatially varying environment. Juvenile viability was tested in both the original selective environments and a set of novel environments. In both the original and novel environments, populations from the constant cadmium regime had the lowest average viability and the highest variance in viability across environments but populations from the other three regimes were similar. Our results suggest that variation in specialization among these populations is most simply explained as a pleiotropic by-product of adaptation to specific environments rather than resulting from a history of exposure to environmental heterogeneity.

Experimental evidence that density mediates negative frequency-dependent selection on aggression

Aggression can be beneficial in competitive environments if aggressive individuals are more likely to access resources than non-aggressive individuals. However, variation in aggressive behaviour persists within populations, suggesting that high levels of aggression might not always be favoured. The goal of this study was to experimentally assess the effects of population density and phenotypic frequency on selection on aggression in a competitive environment. We compared survival of two strains of Drosophila melanogaster that differ in aggression across three density treatments and five frequency treatments (single strain groups, equal numbers of each strain and strains mixed at 3:1 and 1:3 ratios) during a period of limited resources. While there was no difference in survival across single-strain treatments, survival was strongly density dependent, with declining survival as density increased. Furthermore, at medium and high densities, there was evidence of negative frequency-dependent selection, where rare strains experienced greater survival than common strains. However, there was no evidence of negative frequency-dependent selection at low density. Our results indicate that the benefits of aggression during periods of limited resources can depend on the interaction between the phenotypic composition of populations and population density, both of which are mechanisms that could maintain variation in aggressive behaviours within natural populations.

A fitness trade-off between seasons causes multigenerational cycles in phenotype and population size

Although seasonality is widespread and can cause fluctuations in the intensity and direction of natural selection, we have little information about the consequences of seasonal fitness trade-offs for population dynamics. Here we exposed populations of Drosophila melanogaster to repeated seasonal changes in resources across 58 generations and used experimental and mathematical approaches to investigate how viability selection on body size in the non-breeding season could affect demography. We show that opposing seasonal episodes of natural selection on body size interacted with both direct and delayed density dependence to cause populations to undergo predictable multigenerational density cycles. Our results provide evidence that seasonality can set the conditions for life-history trade-offs and density dependence, which can, in turn, interact to cause multigenerational population cycles.

Experimental Evolution of Gene Expression and Plasticity in Alternative Selective Regimes

Little is known of how gene expression and its plasticity evolves as populations adapt to different environmental regimes. Expression is expected to evolve adaptively in all populations but only those populations experiencing environmental heterogeneity are expected to show adaptive evolution of plasticity. We measured the transcriptome in a cadmium-enriched diet and a salt-enriched diet for experimental populations of Drosophila melanogaster that evolved for ~130 generations in one of four selective regimes: two constant regimes maintained in either cadmium or salt diets and two heterogeneous regimes that varied either temporally or spatially between the two diets. For populations evolving in constant regimes, we find a strong signature of counter-gradient evolution; the evolved expression differences between populations adapted to alternative diets is opposite to the plastic response of the ancestral population that is naïve to both diets. Based on expression patterns in the ancestral populations, we identify a set of genes for which we predict selection in heterogeneous regimes to result in increases in plasticity and we find the expected pattern. In contrast, a set of genes where we predicted reduced plasticity did not follow expectation. Nonetheless, both gene sets showed a pattern consistent with adaptive expression evolution in heterogeneous regimes, highlighting the difference between observing “optimal” plasticity and improvements in environment-specific expression. Looking across all genes, there is evidence in all regimes of differences in biased allele expression across environments (“allelic plasticity”) and this is more common among genes with plasticity in total expression.

Different developmental environments change how genes are expressed and what phenotypes are produced. Here we examine how the responsiveness of gene expression to different environments (“expression plasticity”) evolves in populations adapted to constant environments or heterogeneous ones (temporal or spatial heterogeneity) using experimental populations of D. melanogaster. We find the plastic response of the ancestral population that is naïve to both environments is generally opposed by the evolved differences between populations adapted to alternative environments. Populations that live in heterogeneous environments show evidence of adaptive expression evolution in genes predicted to evolve changes in plasticity.