The pace of modern life, revisited

Fluctuating selection maintains distinct species phenotypes in an ecological community in the wild

Species' phenotypic characteristics often remain unchanged over long stretches of geological time. Stabilizing selection-in which fitness is highest for intermediate phenotypes and lowest for the extremes-has been widely invoked as responsible for this pattern. At the community level, such stabilizing selection acting individually on co-occurring species is expected to produce a rugged fitness landscape on which different species occupy distinct fitness peaks. However, even with an explosion of microevolutionary field studies over the past four decades, evidence for persistent stabilizing selection driving long-term stasis is lacking. Nonetheless, biologists continue to invoke stabilizing selection as a major factor explaining macroevolutionary patterns. Here, by directly measuring natural selection in the wild, we identified a complex community-wide fitness surface in which four Anolis lizard species each occupy a distinct fitness peak close to their mean phenotype. The presence of local fitness optima within species, and fitness valleys between species, presents a barrier to adaptive evolutionary change and acts to maintain species differences through time. However, instead of continuously operating stabilizing selection, we found that species were maintained on these peaks by the combination of many independent periods among which selection fluctuated in form, strength, direction, or existence and in which stabilizing selection rarely occurred. Our results suggest that lack of substantial phenotypic evolutionary change through time may be the result of selection, but not persistent stabilizing selection as classically envisioned.

Contemporary changes in phenotypic variation, and the potential consequences for eco-evolutionary dynamics

Most studies assessing rates of phenotypic change focus on population mean trait values, whereas a largely overlooked additional component is changes in population trait variation. Theoretically, eco-evolutionary dynamics mediated by such changes in trait variation could be as important as those mediated by changes in trait means. To date, however, no study has comprehensively summarised how phenotypic variation is changing in contemporary populations. Here, we explore four questions using a large database: How do changes in trait variances compare to changes in trait means? Do different human disturbances have different effects on trait variance? Do different trait types have different effects on changes in trait variance? Do studies that established a genetic basis for trait change show different patterns from those that did not? We find that changes in variation are typically small; yet we also see some very large changes associated with particular disturbances or trait types. We close by interpreting and discussing the implications of our findings in the context of eco-evolutionary studies.

SEED: A framework for integrating ecological stoichiometry and eco-evolutionary dynamics

Characterising the extent and sources of intraspecific variation and their ecological consequences is a central challenge in the study of eco-evolutionary dynamics. Ecological stoichiometry, which uses elemental variation of organisms and their environment to understand ecosystem patterns and processes, can be a powerful framework for characterising eco-evolutionary dynamics. However, the current emphasis on the relative content of elements in the body (i.e. organismal stoichiometry) has constrained its application. Intraspecific variation in the rates at which elements are acquired, assimilated, allocated or lost is often greater than the variation in organismal stoichiometry. There is much to gain from studying these traits together as components of an 'elemental phenotype'. Furthermore, each of these traits can have distinct ecological effects that are underappreciated in the current literature. We propose a conceptual framework that explores how microevolutionary change in the elemental phenotype occurs, how its components interact with each other and with other traits, and how its changes can affect a wide range of ecological processes. We demonstrate how the framework can be used to generate novel hypotheses and outline pathways for future research that enhance our ability to explain, analyse and predict eco-evolutionary dynamics.

Ammonium effects on oxidative stress, telomere length, and locomotion across life stages of an anuran from habitats with contrasting land-use histories

Understanding the mechanistic implications behind wildlife responses to global changes is a central topic in eco-evolutionary research. In particular, anthropic pollution is known to impact wild populations across the globe, which may have even stronger consequences for species with complex life cycles. Among vertebrates, amphibians represent a paradigmatic example of metamorphosis, and their characteristics make them highly vulnerable to pollution. Here, we tested for differences in the redox status, telomere length, and locomotor performance across life stages of green frogs (Pelophylax perezi) from agrosystem and natural habitats, both constitutively and in response to an experimental ammonium exposure (10 mg/L). We found that larvae from the agrosystem constitutively showed an enhanced redox status (better antioxidant balance against H₂O₂, lower lipid peroxidation) but shorter telomeres as compared to larvae from the natural environment. The larval redox response to ammonium was, overall, similar in both habitats. In contrast, after metamorphosis, the redox status of individuals from the natural habitat seemed to cope better with ammonium exposure (denoted by lower lipid peroxidation), and differences between habitats in telomere length were no longer present. Intriguingly, while the swimming performance of larvae did not correlate with individual's physiology, metamorphs with lower glutathione reductase activity and longer telomeres had a better jumping performance. This may suggest that locomotor performance is both traded off with the production of reactive oxygen species and potentiated directly by longer telomeres or indirectly by the mechanisms that buffer their shortening. Overall, our study suggests that contrasting land-use histories can drive divergence in physiological pathways linked to individual health and lifespan. Since this pattern was life-stage dependent, divergent habitat conditions can have contrasting implications across the ontogenetic development of species with complex life cycles.

Cross-disciplinary information for understanding macroevolution

Many different macroevolutionary models can produce the same observations. Despite efforts in building more complex and realistic models, it may still be difficult to distinguish the processes that have generated the biodiversity we observe. In this opinion we argue that we can make new progress by reaching out across disciplines, relying on independent data and theory to constrain macroevolutionary inference. Using mainly paleontological insights and data, we illustrate how we can eliminate less plausible or implausible models, and/or parts of parameter space, while applying comparative phylogenetic approaches. We emphasize that such cross-disciplinary insights and data can be drawn between many other disciplines relevant to macroevolution. We urge cross-disciplinary training, and collaboration using common-use databases as a platform for increasing our understanding.

Human impacts outpace natural processes in the Amazon

Amazonian environments are being degraded by modern industrial and agricultural activities at a pace far above anything previously known, imperiling its vast biodiversity reserves and globally important ecosystem services. The most substantial threats come from regional deforestation, because of export market demands, and global climate change. The Amazon is currently perched to transition rapidly from a largely forested to a nonforested landscape. These changes are happening much too rapidly for Amazonian species, peoples, and ecosystems to respond adaptively. Policies to prevent the worst outcomes are known and must be enacted immediately. We now need political will and leadership to act on this information. To fail the Amazon is to fail the biosphere, and we fail to act at our peril.

The challenge of demonstrating contemporary natural selection on polygenic quantitative traits in the wild

In a From the Cover article in this issue of Molecular Ecology, Ashraf et al. (2022) apply genomic prediction methods, devised by breeders to inform artificial selection, to understand the genetic component of variation in highly polygenic quantitative traits in Soay sheep (Figure 1). These methods have allowed them to investigate the effects of contemporary natural selection on genetic variation underlying these traits in the wild (Hunter et al., 2022). Genomic prediction approaches promise to enhance our understanding of the evolution of highly polygenic quantitative traits in the wild and may allow us to document concrete examples of their natural selection in real time in systems that would otherwise be intractable.

Large-effect loci mediate rapid adaptation of salmon body size after river regulation

Understanding the potential of natural populations to adapt to altered environments is becoming increasingly relevant in evolutionary research. Currently, our understanding of adaptation to human alteration of the environment is hampered by lack of knowledge on the genetic basis of traits, lack of time series, and little or no information on changes in optimal trait values. Here, we used time series data spanning nearly a century to investigate how the body mass of Atlantic salmon (Salmo salar) adapts to river regulation. We found that the change in body mass followed the change in waterflow, both decreasing to ∼1/3 of their original values. Allele frequency changes at two loci in the regions of vgll3 and six6 predicted more than 80% of the observed body mass reduction. Modeling the adaptive dynamics revealed that the population mean lagged behind its optimum before catching up approximately six salmon generations after the initial waterflow reduction. Our results demonstrate rapid adaptation mediated by large-effect loci and provide insight into the temporal dynamics of evolutionary rescue following human disturbance.

Pollution gradient leads to local adaptation and small-scale spatial variability of communities and functions in an urban marine environment

Urbanization of coastal habitats, of which harbors and marinas are the paragon, has led to various ecological paradigms about their functioning. Harbor infrastructures offer new hard substrata that are colonized by a wide variety of organisms (biofouling) including many introduced species. These structures also modify hydrodynamism and contaminant dispersal, leading to strong disturbance gradients within them. Differences in sessile community structure have previously been correlated to these gradients at small spatial scale (<100 m). Local adaptation might be involved to explain such results, but as correlation is not causation, the present study aims to understand the causal link between the environmental gradients and community structure through a reciprocal transplant experiment among three sites of a marina (inner, middle, entrance). Our results highlighted strong small-scale spatial variations of contaminants (trace metals, PCB, pesticides, and PAH) in sediments and animal samples which have been causally linked to changes in community composition after transplant. But historical contingency and colonization succession also play an important role. Our results provided strong evidence for local adaptation since community structure, respiration, and pollutant uptake in Bugula neritina, as well as the metabolomes of B. neritina and Ciona intestinalis were impacted by the transplant with a disadvantage for individuals transplanted from the entrance to the inner location. The here observed results may thus indicate that the disturbance gradient in marinas might constitute a staple for selecting pollutant-resistant species and populations, causing local adaptation. This highlights the importance of conducting further studies into small scale local adaptation.

Ionizing radiation and melanism in Chornobyl tree frogs

Human actions are altering ecosystems worldwide. Among human‐released pollutants, ionizing radiation arises as a rare but potentially devastating threat to natural systems. The Chornobyl accident (1986) represents the largest release of radioactive material to the environment. Our aim was to examine how exposure to radiation from the Chornobyl accident influences dorsal skin coloration of Eastern tree frog (Hyla orientalis) males sampled across a wide gradient of radioactive contamination in northern Ukraine. We assessed the relationship between skin frog coloration (which can act as a protective mechanism against ionizing radiation), radiation conditions and oxidative stress levels. Skin coloration was darker in localities closest to areas with high radiation levels at the time of the accident, whereas current radiation levels seemed not to influence skin coloration in Chornobyl tree frogs. Tree frogs living within the Chornobyl Exclusion Zone had a remarkably darker dorsal skin coloration than frogs from outside the Zone. The maintenance of dark skin coloration was not linked to physiological costs in terms of frog body condition or oxidative status, and we did not detect short‐term changes in frog coloration. Dark coloration is known to protect against different sources of radiation by neutralizing free radicals and reducing DNA damage, and, particularly melanin pigmentation has been proposed as a buffering mechanism against ionizing radiation. Our results suggest that exposure to high levels of ionizing radiation, likely at the time of the accident, may have been selected for darker coloration in Chornobyl tree frogs. Further studies are needed to determine the underlying mechanisms and evolutionary consequences of the patterns found here.

Freshwater Colonization, Adaptation, and Genomic Divergence in Threespine Stickleback

The Threespine Stickleback is ancestrally a marine fish, but many marine populations breed in fresh water (i.e., are anadromous), facilitating their colonization of isolated freshwater habitats a few years after they form. Repeated adaptation to fresh water during at least 10 My and continuing today has led to Threespine Stickleback becoming a premier system to study rapid adaptation. Anadromous and freshwater stickleback breed in sympatry and may hybridize, resulting in introgression of freshwater-adaptive alleles into anadromous populations, where they are maintained at low frequencies as ancient standing genetic variation. Anadromous stickleback have accumulated hundreds of freshwater-adaptive alleles that are disbursed as few loci per marine individual and provide the basis for adaptation when they colonize fresh water. Recent whole-lake experiments in lakes around Cook Inlet, Alaska have revealed how astonishingly rapid and repeatable this process is, with the frequency of 40% of the identified freshwater-adaptive alleles increasing from negligible (∼1%) in the marine founder to ≥50% within ten generations in fresh water, and freshwater phenotypes evolving accordingly. These high rates of genomic and phenotypic evolution imply very intense directional selection on phenotypes of heterozygotes. Sexual recombination rapidly assembles freshwater-adaptive alleles that originated in different founders into multilocus freshwater haplotypes, and regions important for adaptation to freshwater have suppressed recombination that keeps advantageous alleles linked within large haploblocks. These large haploblocks are also older and appear to have accumulated linked advantageous mutations. The contemporary evolution of Threespine Stickleback has provided broadly applicable insights into the mechanisms that facilitate rapid adaptation.

How does genetic architecture affect eco-evolutionary dynamics? A theoretical perspective

Recent studies have revealed the importance of feedbacks between contemporary rapid evolution (i.e. evolution that occurs through changes in allele frequencies) and ecological dynamics. Despite its inherent interdisciplinary nature, however, studies on eco-evolutionary feedbacks have been mostly ecological and tended to focus on adaptation at the phenotypic level without considering the genetic architecture of evolutionary processes. In empirical studies, researchers have often compared ecological dynamics when the focal species under selection has a single genotype with dynamics when it has multiple genotypes. In theoretical studies, common approaches are models of quantitative traits where mean trait values change adaptively along the fitness gradient and Mendelian traits with two alleles at a single locus. On the other hand, it is well known that genetic architecture can affect short-term evolutionary dynamics in population genetics. Indeed, recent theoretical studies have demonstrated that genetic architecture (e.g. the number of loci, linkage disequilibrium and ploidy) matters in eco-evolutionary dynamics (e.g. evolutionary rescue where rapid evolution prevents extinction and population cycles driven by (co)evolution). I propose that theoretical approaches will promote the synthesis of functional genomics and eco-evolutionary dynamics through models that combine population genetics and ecology as well as nonlinear time-series analyses using emerging big data.

This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.

Using genomic prediction to detect microevolutionary change of a quantitative trait

Detecting microevolutionary responses to natural selection by observing temporal changes in individual breeding values is challenging. The collection of suitable datasets can take many years and disentangling the contributions of the environment and genetics to phenotypic change is not trivial. Furthermore, pedigree-based methods of obtaining individual breeding values have known biases. Here, we apply a genomic prediction approach to estimate breeding values of adult weight in a 35-year dataset of Soay sheep (Ovis aries). Comparisons are made with a traditional pedigree-based approach. During the study period, adult body weight decreased, but the underlying genetic component of body weight increased, at a rate that is unlikely to be attributable to genetic drift. Thus cryptic microevolution of greater adult body weight has probably occurred. Genomic and pedigree-based approaches gave largely consistent results. Thus, using genomic prediction to study microevolution in wild populations can remove the requirement for pedigree data, potentially opening up new study systems for similar research.

Effects of insularity on genetic diversity within and among natural populations

We conducted a quantitative literature review of genetic diversity (GD) within and among populations in relation to categorical population size and isolation (together referred to as “insularity”). Using populations from within the same studies, we were able to control for between‐study variation in methodology, as well as demographic and life histories of focal species. Contrary to typical expectations, insularity had relatively minor effects on GD within and among populations, which points to the more important role of other factors in shaping evolutionary processes. Such effects of insularity were sometimes seen—particularly in study systems where GD was already high overall. That is, insularity influenced GD in a study system when GD was high even in non‐insular populations of the same study system—suggesting an important role for the “scope” of influences on GD. These conclusions were more robust for within population GD versus among population GD, although several biases might underlie this difference. Overall, our findings indicate that population‐level genetic assumptions need to be tested rather than assumed in nature, particularly for topics underlying current conservation management practices.

On the genetic architecture of rapidly adapting and convergent life history traits in guppies

The genetic basis of traits shapes and constrains how adaptation proceeds in nature; rapid adaptation can proceed using stores of polygenic standing genetic variation or hard selective sweeps, and increasing polygenicity fuels genetic redundancy, reducing gene re-use (genetic convergence). Guppy life history traits evolve rapidly and convergently among natural high- and low-predation environments in northern Trinidad. This system has been studied extensively at the phenotypic level, but little is known about the underlying genetic architecture. Here, we use four independent F2 QTL crosses to examine the genetic basis of seven (five female, two male) guppy life history phenotypes and discuss how these genetic architectures may facilitate or constrain rapid adaptation and convergence. We use RAD-sequencing data (16,539 SNPs) from 370 male and 267 female F2 individuals. We perform linkage mapping, estimates of genome-wide and per-chromosome heritability (multi-locus associations), and QTL mapping (single-locus associations). Our results are consistent with architectures of many loci of small-effect for male age and size at maturity and female interbrood period. Male trait associations are clustered on specific chromosomes, but female interbrood period exhibits a weak genome-wide signal suggesting a potentially highly polygenic component. Offspring weight and female size at maturity are also associated with a single significant QTL each. These results suggest rapid, repeatable phenotypic evolution of guppies may be facilitated by polygenic trait architectures, but subsequent genetic redundancy may limit gene re-use across populations, in agreement with an absence of strong signatures of genetic convergence from recent analyses of wild guppies.

Evolution of thermal physiology alters the projected range of threespine stickleback under climate change

Species distribution models (SDMs) are widely used to predict range shifts but could be unreliable under climate change scenarios because they do not account for evolution. The thermal physiology of a species is a key determinant of its range and thus incorporating thermal trait evolution into SDMs might be expected to alter projected ranges. We identified a genetic basis for physiological and behavioural traits that evolve in response to temperature change in natural populations of threespine stickleback (Gasterosteus aculeatus). Using these data, we created geographical range projections using a mechanistic niche area approach under two climate change scenarios. Under both scenarios, trait data were either static ("no evolution" models), allowed to evolve at observed evolutionary rates ("evolution" models) or allowed to evolve at a rate of evolution scaled by the trait variance that is explained by quantitative trait loci (QTL; "scaled evolution" models). We show that incorporating these traits and their evolution substantially altered the projected ranges for a widespread panmictic marine population, with over 7-fold increases in area under climate change projections when traits are allowed to evolve. Evolution-informed SDMs should improve the precision of forecasting range dynamics under climate change, and aid in their application to management and the protection of biodiversity.