Contrasting effects of environment and genetics generate a continuum of parallel evolution

Parallel evolution in an island archipelago revealed by genomic sequencing of Hipposideros leaf-nosed bats

Body size is a key morphological attribute, often used to delimit species boundaries among closely related taxa. But body size can evolve in parallel, reaching similar final states despite independent evolutionary and geographic origins, leading to faulty assumptions of evolutionary history. Here, we document parallel evolution in body size in the widely distributed leaf-nosed bat genus Hipposideros, which has misled both taxonomic and evolutionary inference. We sequenced reduced representation genomic loci and measured external morphological characters from three closely related species from the Solomon Islands archipelago, delimited by body size. Species tree reconstruction confirms the paraphyly of two morphologically designated species. The nonsister relationship between large-bodied H. dinops lineages found on different islands indicates that large-bodied ecomorphs have evolved independently at least twice in the history of this radiation. A lack of evidence for gene flow between sympatric, closely related taxa suggests the rapid evolution of strong reproductive isolating barriers between morphologically distinct populations. Our results position Solomon Islands Hipposideros as a novel vertebrate system for studying the repeatability of parallel evolution under natural conditions. We conclude by offering testable hypotheses for how geography and ecology could be mediating the repeated evolution of large-bodied Hipposideros lineages in the Solomon Islands.

Inferring the evolution of reproductive isolation in a lineage of fossil threespine stickleback, Gasterosteus doryssus

Darwin attributed the absence of species transitions in the fossil record to his hypothesis that speciation occurs within isolated habitat patches too geographically restricted to be captured by fossil sequences. Mayr's peripatric speciation model added that such speciation would be rapid, further explaining missing evidence of diversification. Indeed, Eldredge and Gould's original punctuated equilibrium model combined Darwin's conjecture, Mayr's model and 124 years of unsuccessfully sampling the fossil record for transitions. Observing such divergence, however, could illustrate the tempo and mode of evolution during early speciation. Here, we investigate peripatric divergence in a Miocene stickleback fish, Gasterosteus doryssus. This lineage appeared and, over approximately 8000 generations, evolved significant reduction of 12 of 16 traits related to armour, swimming and diet, relative to its ancestral population. This was greater morphological divergence than we observed between reproductively isolated, benthic-limnetic ecotypes of extant Gasterosteus aculeatus. Therefore, we infer that reproductive isolation was evolving. However, local extinction of G. doryssus lineages shows how young, isolated, speciating populations often disappear, supporting Darwin's explanation for missing evidence and revealing a mechanism behind morphological stasis. Extinction may also account for limited sustained divergence within the stickleback species complex and help reconcile speciation rate variation observed across time scales.

Parallel evolution despite low genetic diversity in three-spined sticklebacks

When populations repeatedly adapt to similar environments they can evolve similar phenotypes based on shared genetic mechanisms (parallel evolution). The likelihood of parallel evolution is affected by demographic history, as it depends on the standing genetic variation of the source population. The three-spined stickleback (Gasterosteus aculeatus) repeatedly colonized and adapted to brackish and freshwater. Most parallel evolution studies in G. aculeatus were conducted at high latitudes, where freshwater populations maintain connectivity to the source marine populations. Here, we analysed southern and northern European marine and freshwater populations to test two hypotheses. First, that southern European freshwater populations (which currently lack connection to marine populations) lost genetic diversity due to bottlenecks and inbreeding compared to their northern counterparts. Second, that the degree of genetic parallelism is higher among northern than southern European freshwater populations, as the latter have been subjected to strong drift due to isolation. The results show that southern populations exhibit lower genetic diversity but a higher degree of genetic parallelism than northern populations. Hence, they confirm the hypothesis that southern populations have lost genetic diversity, but this loss probably happened after they had already adapted to freshwater conditions, explaining the high degree of genetic parallelism in the south.

Divergence time shapes gene reuse during repeated adaptation

When diverse lineages repeatedly adapt to similar environmental challenges, the extent to which the same genes are involved (gene reuse) varies across systems. We propose that divergence time among lineages is a key factor driving this variability: as lineages diverge, the extent of gene reuse should decrease due to reductions in allele sharing, functional differentiation among genes, and restructuring of genome architecture. Indeed, we show that many genomic studies of repeated adaptation find that more recently diverged lineages exhibit higher gene reuse during repeated adaptation, but the relationship becomes less clear at older divergence time scales. Thus, future research should explore the factors shaping gene reuse and their interplay across broad divergence time scales for a deeper understanding of evolutionary repeatability.

The effects of host ecology and phylogeny on gut microbiota (non)parallelism across birds and mammals

IMPORTANCE

What are the roles of determinism and contingency in evolution? The paleontologist and evolutionary biologist Stephen J. Gould raised this question in his famous thought experiment of "replaying life's tape." Settings where independent lineages have repeatedly adapted to similar ecological niches (i.e., parallel evolution) are well suited to address this question. Here, we quantified whether repeated ecological shifts across 53 mammalian and 50 avian host species are associated with parallel gut microbiota changes. Our results indicate that parallel shifts in host diet are associated with greater gut microbiota parallelism (i.e., more deterministic). While further research will be necessary to obtain a comprehensive picture of the circumstances under which deterministic gut microbiota changes might be expected, our study can be instrumental in motivating the use of more quantitative methods in microbiota research. This, in turn, can help us better understand microbiota dynamics during adaptive evolution of their hosts.

Adaptive and non-adaptive convergent evolution in feather reflectance of California Channel Islands songbirds

Convergent evolution is widely regarded as a signature of adaptation. However, testing the adaptive consequences of convergent phenotypes is challenging, making it difficult to exclude non-adaptive explanations for convergence. Here, we combined feather reflectance spectra and phenotypic trajectory analyses with visual and thermoregulatory modelling to test the adaptive significance of dark plumage in songbirds of the California Channel Islands. By evolving dark dorsal plumage, island birds are generally less conspicuous to visual-hunting raptors in the island environment than mainland birds. Dark dorsal plumage also reduces the energetic demands associated with maintaining homeothermy in the cool island climate. We also found an unexpected pattern of convergence, wherein the most divergent island populations evolved greater reflectance of near-infrared radiation. However, our heat flux models indicate that elevated near-infrared reflectance is not adaptive. Analysis of feather microstructure suggests that mainland-island differences are related to coloration of feather barbs and barbules rather than their structure. Our results indicate that adaptive and non-adaptive mechanisms interact to drive plumage evolution in this system. This study sheds light on the mechanisms driving the association between dark colour and wet, cold environments across the tree of life, especially in island birds.

Uncovering the genetic architecture of parallel evolution

Identifying the genetic architecture underlying adaptive traits is exceptionally challenging in natural populations. This is because associations between traits not only mask the targets of selection but also create correlated patterns of genomic divergence that hinder our ability to isolate causal genetic effects. Here, we examine the repeated evolution of components of the auxin pathway that have contributed to the replicated loss of gravitropism (i.e. the ability of a plant to bend in response to gravity) in multiple populations of the Senecio lautus species complex in Australia. We use a powerful approach which combines parallel population genomics with association mapping in a Multiparent Advanced Generation Inter-Cross (MAGIC) population to break down genetic and trait correlations to reveal how adaptive traits evolve during replicated evolution. We sequenced auxin and shoot gravitropism-related gene regions in 80 individuals from six natural populations (three parallel divergence events) and 133 individuals from a MAGIC population derived from two of the recently diverged natural populations. We show that artificial tail selection on gravitropism in the MAGIC population recreates patterns of parallel divergence in the auxin pathway in the natural populations. We reveal a set of 55 auxin gene regions that have evolved repeatedly during the evolution of the species, of which 50 are directly associated with gravitropism divergence in the MAGIC population. Our work creates a strong link between patterns of genomic divergence and trait variation contributing to replicated evolution by natural selection, paving the way to understand the origin and maintenance of adaptations in natural populations.

On the Origins of Phenotypic Parallelism in Benthic and Limnetic Stickleback

Rapid evolution of similar phenotypes in similar environments, giving rise to in situ parallel adaptation, is an important hallmark of ecological speciation. However, what appears to be in situ adaptation can also arise by dispersal of divergent lineages from elsewhere. We test whether two contrasting phenotypes repeatedly evolved in parallel, or have a single origin, in an archetypal example of ecological adaptive radiation: benthic-limnetic three-spined stickleback (Gasterosteus aculeatus) across species pair and solitary lakes in British Columbia. We identify two genomic clusters across freshwater populations, which differ in benthic-limnetic divergent phenotypic traits and separate benthic from limnetic individuals in species pair lakes. Phylogenetic reconstruction and niche evolution modeling both suggest a single evolutionary origin for each of these clusters. We detected strong phylogenetic signal in benthic-limnetic divergent traits, suggesting that they are ancestrally retained. Accounting for ancestral state retention, we identify local adaptation of body armor due to the presence of an intraguild predator, the sculpin (Cottus asper), and environmental effects of lake depth and pH on body size. Taken together, our results imply a predominant role for retention of ancestral characteristics in driving trait distribution, with further selection imposed on some traits by environmental factors.

Environmental and climatic drivers of phenotypic evolution and distribution changes in a widely distributed subfamily of subterranean mammals

How environmental factors shape species morphology and distributions is a key issue in ecology, especially in similar environments. Species of Myospalacinae exhibit widespread distribution spanning the eastern Eurasian steppe and the extreme adaptation to the subterranean environment, providing an excellent opportunity for investigating species responses to environmental changes. At the national scale, we here use geometric morphometric and distributional data to assess the environmental and climatic drivers of morphological evolution and distribution of Myospalacinae species in China. Based on phylogenetic relationships of Myospalacinae species constructed using genomic data in China, we integrate geometric morphometrics and ecological niche models to reveal the interspecific variation of skull morphology, trace the ancestral state, and assess factors influencing interspecific variation. Our approach further allows us to project future distributions of Myospalacinae species throughout China. We found that the interspecific morphology variations were mainly concentrated in the temporal ridge, premaxillary-frontal suture, premaxillary-maxillary suture, and molars, and the skull morphology of the two current species in Myospalacinae followed the ancestral state; temperature and precipitation were important environmental variables influencing skull morphology. Elevation, temperature annual range, and precipitation of warmest quarter were identified as dominant factors affecting the distribution of Myospalacinae species in China, and their suitable habitat area will decrease in the future. Collectively, environmental and climate changes have an effect on skull phenotypes of subterranean mammals, highlighting the contribution of phenotypic differentiation in similar environments in the formation of species phenotypes. Climate change will further shrink their habitats under future climate assumptions in the short-term. Our findings provide new insights into effects of environmental and climate change on the morphological evolution and distribution of species as well as a reference for biodiversity conservation and species management.

Polygenic routes lead to parallel altitudinal adaptation in Heliosperma pusillum (Caryophyllaceae)

Understanding how organisms adapt to the environment is a major goal of modern biology. Parallel evolution-the independent evolution of similar phenotypes in different populations-provides a powerful framework to investigate the evolutionary potential of populations, the constraints of evolution, its repeatability and therefore its predictability. Here, we quantified the degree of gene expression and functional parallelism across replicated ecotype formation in Heliosperma pusillum (Caryophyllaceae), and gained insights into the architecture of adaptive traits. Population structure analyses and demographic modelling support a previously formulated hypothesis of parallel polytopic divergence of montane and alpine ecotypes. We detect a large proportion of differentially expressed genes (DEGs) underlying divergence within each replicate ecotype pair, with a strikingly low number of shared DEGs across pairs. Functional enrichment of DEGs reveals that the traits affected by significant expression divergence are largely consistent across ecotype pairs, in strong contrast to the nonshared genetic basis. The remarkable redundancy of differential gene expression indicates a polygenic architecture for the diverged adaptive traits. We conclude that polygenic traits appear key to opening multiple routes for adaptation, widening the adaptive potential of organisms.

Dimensionality and Modularity of Adaptive Variation: Divergence in Threespine Stickleback from Diverse Environments

AbstractPopulations are subjected to diverse environmental conditions that affect fitness and induce evolutionary or plastic responses, resulting in phenotypic divergence. Some authors contend that such divergence is concentrated along a single major axis of trait covariance even if that axis does not lead populations directly toward a fitness optimum. Other authors argue that divergence can occur readily along many phenotype axes at the same time. We use populations of threespine stickleback (Gasterosteus aculeatus) from 14 lakes with contrasting ecological conditions to find some resolution along the continuum between these two extremes. Unlike many previous studies, we included several functional suites of traits (defensive, swimming, trophic) potentially subject to different sources of selection. We find that populations exhibit dimensionality of divergence that is high enough to preclude a history of constraint along a single axis-both for divergence in multivariate mean trait values and for the structure of trait covariances. Dimensionality varied among trait suites and were strongly influenced by the inclusion of specific traits, and integration of trait suites varied between populations. We leverage this variation into new insights about the process of divergence and suggest that similar analyses could increase understanding of other adaptive radiations.

Repeated genetic divergence plays a minor role in repeated phenotypic divergence of lake-stream stickleback

Recent studies have shown that the repeated evolution of similar phenotypes in response to similar ecological conditions (here "parallel evolution") often occurs through mutations in the same genes. However, many previous studies have focused on known candidate genes in a limited number of systems. Thus, the question of how often parallel phenotypic evolution is due to parallel genetic changes remains open. Here, we used quantitative trait locus (QTL) mapping in F2 intercrosses between lake and stream threespine stickleback (Gasterosteus aculeatus) from four independent watersheds on Vancouver Island, Canada to determine whether the same QTL underlie divergence in the same phenotypes across, between, and within watersheds. We find few parallel QTL, even in independent crosses from the same watershed or for phenotypes that have diverged in parallel. These findings suggest that different mutations can lead to similar phenotypes. The low genetic repeatability observed in these lake-stream systems contrasts with the higher genetic repeatability observed in other stickleback systems. We speculate that differences in evolutionary history, gene flow, and/or the strength and direction of selection might explain these differences in genetic parallelism and emphasize that more work is needed to move beyond documenting genetic parallelism to identifying the underlying causes.

Towards evolutionary predictions: Current promises and challenges

Evolution has traditionally been a historical and descriptive science, and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purposes, such as to prepare for the future, to try and change the course of evolution or to determine how well we understand evolutionary processes. Similarly, the exact aspect of the evolved population that we want to predict may also differ. For example, we could try to predict which genotype will dominate, the fitness of the population or the extinction probability of a population. In addition, there are many uses of evolutionary predictions that may not always be recognized as such. The main goal of this review is to increase awareness of methods and data in different research fields by showing the breadth of situations in which evolutionary predictions are made. We describe how diverse evolutionary predictions share a common structure described by the predictive scope, time scale and precision. Then, by using examples ranging from SARS-CoV2 and influenza to CRISPR-based gene drives and sustainable product formation in biotechnology, we discuss the methods for predicting evolution, the factors that affect predictability and how predictions can be used to prevent evolution in undesirable directions or to promote beneficial evolution (i.e. evolutionary control). We hope that this review will stimulate collaboration between fields by establishing a common language for evolutionary predictions.

Quantifying (non)parallelism of gut microbial community change using multivariate vector analysis

Parallel evolution of phenotypic traits is regarded as strong evidence for natural selection and has been studied extensively in a variety of taxa. However, we have limited knowledge of whether parallel evolution of host organisms is accompanied by parallel changes of their associated microbial communities (i.e., microbiotas), which are crucial for their hosts' ecology and evolution. Determining the extent of microbiota parallelism in nature can improve our ability to identify the factors that are associated with (putatively adaptive) shifts in microbial communities. While it has been emphasized that (non)parallel evolution is better considered as a quantitative continuum rather than a binary phenomenon, quantitative approaches have rarely been used to study microbiota parallelism. We advocate using multivariate vector analysis (i.e., phenotypic change vector analysis) to quantify direction and magnitude of microbiota changes and discuss the applicability of this approach for studying parallelism, and we compiled an R package for multivariate vector analysis of microbial communities ('multivarvector'). We exemplify its use by reanalyzing gut microbiota data from multiple fish species that exhibit parallel shifts in trophic ecology. We found that multivariate vector analysis results were largely consistent with other statistical methods, parallelism estimates were not affected by the taxonomic level at which the microbiota is studied, and parallelism might be stronger for gut microbiota function compared to taxonomic composition. This approach provides an analytical framework for quantitative comparisons across host lineages, thereby providing the potential to advance our capacity to predict microbiota changes. Hence, we emphasize that the development and application of quantitative measures, such as multivariate vector analysis, should be further explored in microbiota research in order to better understand the role of microbiota dynamics during their hosts' adaptive evolution, particularly in settings of parallel evolution.

The role of plastic and evolved DNA methylation in parallel adaptation of threespine stickleback (Gasterosteus aculeatus)

Repeated phenotypic patterns among populations undergoing parallel evolution in similar environments provide support for the deterministic role of natural selection. Epigenetic modifications can mediate plastic and evolved phenotypic responses to environmental change and might make important contributions to parallel adaptation. While many studies have explored the genetic basis of repeated phenotypic divergence, the role of epigenetic processes during parallel adaptation remains unclear. The parallel evolution of freshwater ecotypes of threespine stickleback fish (Gasterosteus aculeatus) following colonization of thousands of lakes and streams from the ocean is a classic example of parallel phenotypic and genotypic adaptation. To investigate epigenetic modifications during parallel adaptation of threespine stickleback, we reanalysed three independent data sets that investigated DNA methylation variation between marine and freshwater ecotypes. Although we found widespread methylation differentiation between ecotypes, there was no significant tendency for CpG sites associated with repeated methylation differentiation across studies to be parallel versus nonparallel. To next investigate the role of plastic versus evolved changes in methylation during freshwater adaptation, we explored if CpG sites exhibiting methylation plasticity during salinity change were more likely to also show evolutionary divergence in methylation between ecotypes. The directions of divergence between ecotypes were generally in the opposite direction to those observed for plasticity when ecotypes were challenged with non-native salinity conditions, suggesting that most plastic responses are likely to be maladaptive during colonization of new environments. Finally, we found a greater number of CpG sites showing evolved changes when ancestral marine ecotypes are acclimated to freshwater environments, whereas plastic changes predominate when derived freshwater ecotypes transition back to their ancestral marine environments. These findings provide evidence for an epigenetic contribution to parallel adaptation and demonstrate the contrasting roles of plastic and evolved methylation differences during adaptation to new environments.

Climatic similarity and genomic background shape the extent of parallel adaptation in Timema stick insects

Evolution can repeat itself, resulting in parallel adaptations in independent lineages occupying similar environments. Moreover, parallel evolution sometimes, but not always, uses the same genes. Two main hypotheses have been put forth to explain the probability and extent of parallel evolution. First, parallel evolution is more likely when shared ecologies result in similar patterns of natural selection in different taxa. Second, parallelism is more likely when genomes are similar because of shared standing variation and similar mutational effects in closely related genomes. Here we combine ecological, genomic, experimental and phenotypic data with Bayesian modelling and randomization tests to quantify the degree of parallelism and its relationship with ecology and genetics. Our results show that the extent to which genomic regions associated with climate are parallel among species of Timema stick insects is shaped collectively by shared ecology and genomic background. Specifically, the extent of genomic parallelism decays with divergence in climatic conditions (that is, habitat or ecological similarity) and genomic similarity. Moreover, we find that climate-associated loci are likely subject to selection in a field experiment, overlap with genetic regions associated with cuticular hydrocarbon traits and are not strongly shaped by introgression between species. Our findings shed light on when evolution is most expected to repeat itself.

Genomic basis and phenotypic manifestation of (non-)parallel serpentine adaptation in Arabidopsis arenosa

Parallel evolution is common in nature and provides one of the most compelling examples of rapid environmental adaptation. In contrast to the recent burst of studies addressing genomic basis of parallel evolution, integrative studies linking genomic and phenotypic parallelism are scarce. Edaphic islands of toxic serpentine soils provide ideal systems for studying rapid parallel adaptation in plants, imposing strong, spatially replicated selection on recently diverged populations. We leveraged threefold independent serpentine adaptation of Arabidopsis arenosa and combined reciprocal transplants, ion uptake phenotyping, and available genome-wide polymorphisms to test if parallelism is manifested to a similar extent at both genomic and phenotypic levels. We found pervasive phenotypic parallelism in functional traits yet with varying magnitude of fitness differences that was congruent with neutral genetic differentiation between populations. Limited costs of serpentine adaptation suggest absence of soil-driven trade-offs. On the other hand, the genomic parallelism at the gene level was significant, although relatively minor. Therefore, the similarly modified phenotypes, for example, of ion uptake arose possibly by selection on different loci in similar functional pathways. In summary, we bring evidence for the important role of genetic redundancy in rapid adaptation involving traits with polygenic architecture.

Compiling forty years of guppy research to investigate the factors contributing to (non)parallel evolution

Examples of parallel evolution have been crucial for our understanding of adaptation via natural selection. However, strong parallelism is not always observed even in seemingly similar environments where natural selection is expected to favour similar phenotypes. Leveraging this variation in parallelism within well-researched study systems can provide insight into the factors that contribute to variation in adaptive responses. Here we analyse the results of 36 studies reporting 446 average trait values in Trinidadian guppies, Poecilia reticulata, from different predation regimes. We examine how the extent of predator-driven phenotypic parallelism is influenced by six factors: sex, trait type, rearing environment, ecological complexity, evolutionary history, and time since colonization. Analyses show that parallel evolution in guppies is highly variable and weak on average, with only 24.7% of the variation among populations being explained by predation regime. Levels of parallelism appeared to be especially weak for colour traits, and parallelism decreased with increasing complexity of evolutionary history (i.e., when estimates of parallelism from populations within a single drainage were compared to estimates of parallelism from populations pooled between two major drainages). Suggestive - but not significant - trends that warrant further research include interactions between the sexes and different trait categories. Quantifying and accounting for these and other sources of variation among evolutionary 'replicates' can be leveraged to better understand the extent to which seemingly similar environments drive parallel and nonparallel aspects of phenotypic divergence.

Evolutionary gain and loss of a pathological immune response to parasitism

Parasites impose fitness costs on their hosts. Biologists often assume that natural selection favors infection-resistant hosts. Yet, when the immune response itself is costly, theory suggests that selection may sometimes favor loss of resistance, which may result in alternative stable states where some populations are resistant and others are tolerant. Intraspecific variation in immune costs is rarely surveyed in a manner that tests evolutionary patterns, and there are few examples of adaptive loss of resistance. Here, we show that when marine threespine stickleback colonized freshwater lakes, they gained resistance to the freshwater-associated cestode Schistocephalus solidus. Extensive peritoneal fibrosis and inflammation are a commonly observed phenotype that contributes to suppression of cestode growth and viability but also imposes a substantial cost on fecundity. Combining genetic mapping and population genomics, we find that opposing selection generates immune system differences between tolerant and resistant populations, consistent with divergent optimization.

Inversions and parallel evolution

Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions.

This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.

Variation in the genomic basis of parallel phenotypic and ecological divergence in benthic and pelagic morphs of Icelandic Arctic charr (Salvelinus alpinus)

Sympatric adaptive phenotypic divergence should be underlain by genomic differentiation between sub-populations. When divergence drives similar patterns of phenotypic and ecological variation within species we expect evolution to draw on common allelic variation. We investigated divergence histories and genomic signatures of adaptive divergence between benthic and pelagic morphs of Icelandic Arctic charr. Divergence histories for each of four populations were reconstructed using coalescent modelling and 14,187 single nucleotide polymorphisms. Sympatric divergence with continuous gene flow was supported in two populations while allopatric divergence with secondary contact was supported in one population; we could not differentiate between demographic models in the fourth population. We detected parallel patterns of phenotypic divergence along benthic-pelagic evolutionary trajectories among populations. Patterns of genomic differentiation between benthic and pelagic morphs were characterized by outlier loci in many narrow peaks of differentiation throughout the genome, which may reflect the eroding effects of gene flow on nearby neutral loci. We then used genome-wide association analyses to relate both phenotypic (body shape and size) and ecological (carbon and nitrogen stable isotopes) variation to patterns of genomic differentiation. Many peaks of genomic differentiation were associated with phenotypic and ecological variation in the three highly divergent populations, suggesting a genomic basis for adaptive divergence. We detected little evidence for a parallel genomic basis of differentiation as most regions and outlier loci were not shared among populations. Our results show that adaptive divergence can have varied genomic consequences in populations with relatively recent common origins, similar divergence histories, and parallel phenotypic divergence.

Hybrid evolution repeats itself across environmental contexts in Texas sunflowers (Helianthus)

To what extent is evolution repeatable? Little is known about whether the evolution of hybrids is more (or less) repeatable than that of nonhybrids. We used field experimental evolution in annual sunflowers (Helianthus) in Texas to ask the extent to which hybrid evolution is repeatable across environments compared to nonhybrid controls. We created hybrids between Helianthus annuus (L.) and H. debilis (Nutt.) and grew plots of both hybrids and nonhybrid controls through eight generations at three sites in Texas. We collected seeds from each generation and grew each generation × treatment × home site combination at two final common gardens. We estimated the strength and direction of evolution in terms of fitness and 24 traits, tested for repeated versus nonrepeated evolution, and assessed overall phenotypic evolution across lineages and in relation to a locally adapted phenotype. Hybrids consistently evolved higher fitness over time, while controls did not, although trait evolution varied in strength across home sites. Repeated evolution was more evident in hybrids versus nonhybrid controls, and hybrid evolution was often in the direction of the locally adapted phenotype. Our findings have implications for both the nature of repeatability in evolution and the contribution of hybridization to evolution across environmental contexts.

Non-parallel morphological divergence following colonization of a new host plant

Adaptation to new ecological niches is known to spur population diversification and may lead to speciation if gene flow is ceased. While adaptation to the same ecological niche is expected to be parallel, it is more difficult to predict whether selection against maladaptive hybridization in secondary sympatry results in parallel divergence also in traits that are not directly related to the ecological niches. Such parallelisms in response to selection for reproductive isolation can be identified through estimating parallelism in reproductive character displacement across different zones of secondary contact. Here, we use a host shift in the phytophagous peacock fly Tephritis conura, with both host races represented in two geographically separate areas East and West of the Baltic Sea to investigate convergence in morphological adaptations. We asked (i) if there are consistent morphological adaptations to a host plant shift and (ii) if the response to secondary sympatry with the alternate host race is parallel across contact zones. We found surprisingly low and variable, albeit significant, divergence between host races. Only one trait, the length of the female ovipositor, which serves an important function in the interaction with the hosts, was consistently different between host races. Instead, co-existence with the other host race significantly affected the degree of morphological divergence, but the divergence was largely driven by different traits in different contact zones. Thus, local stochastic fixation or reinforcement could generate trait divergence, and additional evidence is needed to conclude whether divergence is locally adaptive.

Genomic changes underlying repeated niche shifts in an adaptive radiation

In adaptive radiations, single lineages rapidly diversify by adapting to many new niches. Little is known yet about the genomic mechanisms involved, that is, the source of genetic variation or genomic architecture facilitating or constraining adaptive radiation. Here, we investigate genomic changes associated with repeated invasion of many different freshwater niches by threespine stickleback in the Haida Gwaii archipelago, Canada, by resequencing single genomes from one marine and 28 freshwater populations. We find 89 likely targets of parallel selection in the genome that are enriched for old standing genetic variation. In contrast to theoretical expectations, their genomic architecture is highly dispersed with little clustering. Candidate genes and genotype-environment correlations match the three major environmental axes predation regime, light environment, and ecosystem size. In a niche space with these three dimensions, we find that the more divergent a new niche from the ancestral marine habitat, the more loci show signatures of parallel selection. Our findings suggest that the genomic architecture of parallel adaptation in adaptive radiation depends on the steepness of ecological gradients and the dimensionality of the niche space.

Age-dependent genetic architecture across ontogeny of body size in sticklebacks

Heritable variation in traits under natural selection is a prerequisite for evolutionary response. While it is recognized that trait heritability may vary spatially and temporally depending on which environmental conditions traits are expressed under, less is known about the possibility that genetic variance contributing to the expected selection response in a given trait may vary at different stages of ontogeny. Specifically, whether different loci underlie the expression of a trait throughout development and thus providing an additional source of variation for selection to act on in the wild, is unclear. Here we show that body size, an important life-history trait, is heritable throughout ontogeny in the nine-spined stickleback (Pungitius pungitius). Nevertheless, both analyses of quantitative trait loci and genetic correlations across ages show that different chromosomes/loci contribute to this heritability in different ontogenic time-points. This suggests that body size can respond to selection at different stages of ontogeny but that this response is determined by different loci at different points of development. Hence, our study provides important results regarding our understanding of the genetics of ontogeny and opens an interesting avenue of research for studying age-specific genetic architecture as a source of non-parallel evolution.

Population-level variation in parasite resistance due to differences in immune initiation and rate of response

Closely related populations often differ in resistance to a given parasite, as measured by infection success or failure. Yet, the immunological mechanisms of these evolved differences are rarely specified. Does resistance evolve via changes to the host's ability to recognize that an infection exists, actuate an effective immune response, or attenuate that response? We tested whether each of these phases of the host response contributed to threespine sticklebacks' recently evolved resistance to their tapeworm Schistocephalus solidus. Although marine stickleback and some susceptible lake fish permit fast-growing tapeworms, other lake populations are resistant and suppress tapeworm growth via a fibrosis response. We subjected lab-raised fish from three populations (susceptible marine "ancestors," a susceptible lake population, and a resistant lake population) to a novel immune challenge using an injection of (1) a saline control, (2) alum, a generalized pro-inflammatory adjuvant that causes fibrosis, (3) a tapeworm protein extract, or (4) a combination of alum and tapeworm protein. With enough time, all three populations generated a robust fibrosis response to the alum treatments. Yet, only the resistant population exhibited a fibrosis response to the tapeworm protein alone. Thus, these populations differed in their ability to respond to the tapeworm protein but shared an intact fibrosis pathway. The resistant population also initiated fibrosis faster in response to alum, and was able to attenuate fibrosis, unlike the susceptible populations' slow but longer lasting response to alum. As fibrosis has pathological side effects that reduce fecundity, the faster recovery by the resistant population may reflect an adaptation to mitigate the costs of immunity. Broadly, our results confirm that parasite detection and immune initiation, activation speed, and immune attenuation simultaneously contribute to the evolution of parasite resistance and adaptations to infection in natural populations.

Global urban environmental change drives adaptation in white clover

Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale.

Detecting (non)parallel evolution in multidimensional spaces: angles, correlations and eigenanalysis

Parallelism between evolutionary trajectories in a trait space is often seen as evidence for repeatability of phenotypic evolution, and angles between trajectories play a pivotal role in the analysis of parallelism. However, properties of angles in multidimensional spaces have not been widely appreciated by biologists. To remedy this situation, this study provides a brief overview on geometric and statistical aspects of angles in multidimensional spaces. Under the null hypothesis that trajectory vectors have no preferred directions (i.e. uniform distribution on hypersphere), the angle between two independent vectors is concentrated around the right angle, with a more pronounced peak in a higher-dimensional space. This probability distribution is closely related to t- and beta distributions, which can be used for testing the null hypothesis concerning a pair of trajectories. A recently proposed method with eigenanalysis of a vector correlation matrix can be connected to the test of no correlation or concentration of multiple vectors, for which simple test procedures are available in the statistical literature. Concentration of vectors can also be examined by tools of directional statistics such as the Rayleigh test. These frameworks provide biologists with baselines to make statistically justified inferences for (non)parallel evolution.

Rapid, parallel evolution of field mustard (Brassica rapa) under experimental drought

Climate change is driving evolutionary and plastic responses in populations, but predicting these responses remains challenging. Studies that combine experimental evolution with ancestor-descendant comparisons allow assessment of the causes, parallelism, and adaptive nature of evolutionary responses, although such studies remain rare, particularly in a climate change context. Here, we created experimental populations of Brassica rapa derived from the same natural population and exposed these replicated populations to experimental drought or watered conditions for four generations. We then grew ancestors and descendants concurrently, following the resurrection approach. Experimental populations under drought showed rapid evolution of earlier flowering time and increased specific leaf area, consistent with a drought escape strategy and observations in natural populations. Evolutionary shifts followed the direction of selection and increased fitness under drought, indicative of adaptive evolution. Evolution to drought also occurred largely in parallel among replicate populations. Further, traits showed phenotypic plasticity to drought, but the direction and effect size of plasticity varied. Our results demonstrate parallel evolution to experimental drought, suggesting that evolution to strong, consistent selection may be predictable. Broadly, our study demonstrates the utility of combining experimental evolution with the resurrection approach to investigate responses to climate change.

Cast away in the Adriatic: Low degree of parallel genetic differentiation in three-spined sticklebacks

The three-spined stickleback (Gasterosteus aculeatus) has repeatedly and independently adapted to freshwater habitats from standing genetic variation (SGV) following colonization from the sea. However, in the Mediterranean Sea G. aculeatus is believed to have gone extinct, and thus the spread of locally adapted alleles between different freshwater populations via the sea since then has been highly unlikely. This is expected to limit parallel evolution, that is the extent to which phylogenetically related alleles can be shared among independently colonized freshwater populations. Using whole genome and 2b-RAD sequencing data, we compared levels of genetic differentiation and genetic parallelism of 15 Adriatic stickleback populations to 19 Pacific, Atlantic and Caspian populations, where gene flow between freshwater populations across extant marine populations is still possible. Our findings support previous studies suggesting that Adriatic populations are highly differentiated (average F_ST  ≈ 0.45), of low genetic diversity and connectivity, and likely to stem from multiple independent colonizations during the Pleistocene. Linkage disequilibrium network analyses in combination with linear mixed models nevertheless revealed several parallel marine-freshwater differentiated genomic regions, although still not to the extent observed elsewhere in the world. We hypothesize that current levels of genetic parallelism in the Adriatic lineages are a relic of freshwater adaptation from SGV prior to the extinction of marine sticklebacks in the Mediterranean that has persisted despite substantial genetic drift experienced by the Adriatic stickleback isolates.

Parallel shape divergence between ecotypes of the limpet Nacella concinna along the Antarctic Peninsula: a new model species for parallel evolution?

Parallel phenotypic divergence is the independent differentiation between phenotypes of the same lineage or species occupying ecologically similar environments in different populations. We tested in the Antarctic limpet Nacella concinna the extent of parallel morphological divergence in littoral and sublittoral ecotypes throughout its distribution range. These ecotypes differ in morphological, behavioural and physiological characteristics. We studied the lateral and dorsal outlines of shells and the genetic variation of the mitochondrial gene Cytochrome Oxidase subunit I from both ecotypes in 17 sample sites along more than 2,000 km. The genetic data indicate that both ecotypes belong to a single evolutionary lineage. The magnitude and direction of phenotypic variation differ between ecotypes across sample sites; completely parallel ecotype-pairs (i.e., they diverge in the same magnitude and in the same direction) were detected in 84.85% of lateral and 65.15% in dorsal view comparisons. Besides, specific traits (relative shell height, position of shell apex, and elliptical/pear-shape outline variation) showed high parallelism. We observed weak morphological covariation between the two shape shell views, indicating that distinct evolutionary forces and environmental pressures could be acting on this limpet shell shape. Our results demonstrate there is a strong parallel morphological divergence pattern in N. concinna along its distribution, making this Antarctic species a suitable model for the study of different evolutionary forces shaping the shell evolution of this limpet.

Parallel shifts of visual sensitivity and body coloration in replicate populations of extremophile fish

Visual sensitivity and body pigmentation are often shaped by both natural selection from the environment and sexual selection from mate choice. One way of quantifying the impact of the environment is by measuring how traits have changed after colonization of a novel habitat. To do this, we studied Poecilia mexicana populations that have repeatedly adapted to extreme sulphidic (H₂ S-containing) environments. We measured visual sensitivity using opsin gene expression, as well as body pigmentation, for populations in four independent drainages. Both visual sensitivity and body pigmentation showed significant parallel shifts towards greater medium-wavelength sensitivity and reflectance in sulphidic populations. Altogether we found that sulphidic habitats select for differences in visual sensitivity and pigmentation. Shifts between habitats may be due to both differences in the water's spectral properties and correlated ecological changes.

Speciation dynamics and extent of parallel evolution along a lake-stream environmental contrast in African cichlid fishes

Understanding the dynamics of speciation is a central topic in evolutionary biology. Here, we investigated how morphological and genomic differentiation accumulated along the speciation continuum in the African cichlid fish Astatotilapia burtoni. While morphological differentiation was continuously distributed across different lake-stream population pairs, we found that there were two categories with respect to genomic differentiation, suggesting a “gray zone” of speciation at ~0.1% net nucleotide divergence. Genomic differentiation was increased in the presence of divergent selection and drift compared to drift alone. The quantification of phenotypic and genetic parallelism in four cichlid species occurring along a lake-stream environmental contrast revealed parallel and antiparallel components in rapid adaptive divergence, and morphological convergence in species replicates inhabiting the same environments. Furthermore, we show that the extent of parallelism was higher when ancestral populations were more similar. Our study highlights the complementary roles of divergent selection and drift on speciation and parallel evolution.

Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins

Studying repeated adaptation can provide insights into the mechanisms allowing species to adapt to novel environments. Here, we investigate repeated evolution driven by habitat specialization in the common bottlenose dolphin. Parapatric pelagic and coastal ecotypes of common bottlenose dolphins have repeatedly formed across the oceans. Analyzing whole genomes of 57 individuals, we find that ecotype evolution involved a complex reticulated evolutionary history. We find parallel linked selection acted upon ancient alleles in geographically distant coastal populations, which were present as standing genetic variation in the pelagic populations. Candidate loci evolving under parallel linked selection were found in ancient tracts, suggesting recurrent bouts of selection through time. Therefore, despite the constraints of small effective population size and long generation time on the efficacy of selection, repeated adaptation in long-lived social species can be driven by a combination of ecological opportunities and selection acting on ancestral standing genetic variation.

Phenotypic and genotypic parallel evolution in parapatric ecotypes of Senecio

The independent and repeated adaptation of populations to similar environments often results in the evolution of similar forms. This phenomenon creates a strong correlation between phenotype and environment and is referred to as parallel evolution. However, we are still largely unaware of the dynamics of parallel evolution, as well as the interplay between phenotype and genotype within natural systems. Here, we examined phenotypic and genotypic parallel evolution in multiple parapatric Dune‐Headland coastal ecotypes of an Australian wildflower, Senecio lautus. We observed a clear trait‐environment association in the system, with all replicate populations having evolved along the same phenotypic evolutionary trajectory. Similar phenotypes have arisen via mutational changes occurring in different genes, although many share the same biological functions. Our results shed light on how replicated adaptation manifests at the phenotypic and genotypic levels within populations, and highlight S. lautus as one of the most striking cases of phenotypic parallel evolution in nature.

Urbanization extends flight phenology and leads to local adaptation of seasonal plasticity in Lepidoptera

Cities represent novel environments with altered seasonality; they are warmer, which may accelerate growth, but light pollution can also lengthen days, misleading organisms that use daylength to predict seasonal change. Using long-term observational data, we show that urban populations of a butterfly and a moth have longer flight seasons than neighboring rural populations for six Nordic city regions. Next, using laboratory experiments, we show that the induction of diapause by daylength has evolved in urban populations in the direction predicted by urban warming. We thus show that the altered seasonality of urban environments can lead to corresponding evolutionary changes in the seasonal responses of urban populations, a pattern that may be repeated in other species.

Urbanization is gaining force globally, which challenges biodiversity, and it has recently also emerged as an agent of evolutionary change. Seasonal phenology and life cycle regulation are essential processes that urbanization is likely to alter through both the urban heat island effect (UHI) and artificial light at night (ALAN). However, how UHI and ALAN affect the evolution of seasonal adaptations has received little attention. Here, we test for the urban evolution of seasonal life-history plasticity, specifically changes in the photoperiodic induction of diapause in two lepidopterans, Pieris napi (Pieridae) and Chiasmia clathrata (Geometridae). We used long-term data from standardized monitoring and citizen science observation schemes to compare yearly phenological flight curves in six cities in Finland and Sweden to those of adjacent rural populations. This analysis showed for both species that flight seasons are longer and end later in most cities, suggesting a difference in the timing of diapause induction. Then, we used common garden experiments to test whether the evolution of the photoperiodic reaction norm for diapause could explain these phenological changes for a subset of these cities. These experiments demonstrated a genetic shift for both species in urban areas toward a lower daylength threshold for direct development, consistent with predictions based on the UHI but not ALAN. The correspondence of this genetic change to the results of our larger-scale observational analysis of in situ flight phenology indicates that it may be widespread. These findings suggest that seasonal life cycle regulation evolves in urban ectotherms and may contribute to ecoevolutionary dynamics in cities.

Bridging Tumorigenesis and Therapy Resistance With a Non-Darwinian and Non-Lamarckian Mechanism of Adaptive Evolution

Although neo-Darwinian (and less often Lamarckian) dynamics are regularly invoked to interpret cancer's multifarious molecular profiles, they shine little light on how tumorigenesis unfolds and often fail to fully capture the frequency and breadth of resistance mechanisms. This uncertainty frames one of the most problematic gaps between science and practice in modern times. Here, we offer a theory of adaptive cancer evolution, which builds on a molecular mechanism that lies outside neo-Darwinian and Lamarckian schemes. This mechanism coherently integrates non-genetic and genetic changes, ecological and evolutionary time scales, and shifts the spotlight away from positive selection towards purifying selection, genetic drift, and the creative-disruptive power of environmental change. The surprisingly simple use-it or lose-it rationale of the proposed theory can help predict molecular dynamics during tumorigenesis. It also provides simple rules of thumb that should help improve therapeutic approaches in cancer.

Threespine Stickleback: A Model System For Evolutionary Genomics

The repeated adaptation of oceanic threespine sticklebacks to fresh water has made it a premier organism to study parallel evolution. These small fish have multiple distinct ecotypes that display a wide range of diverse phenotypic traits. Ecotypes are easily crossed in the laboratory, and families are large and develop quickly enough for quantitative trait locus analyses, positioning the threespine stickleback as a versatile model organism to address a wide range of biological questions. Extensive genomic resources, including linkage maps, a high-quality reference genome, and developmental genetics tools have led to insights into the genomic basis of adaptation and the identification of genomic changes controlling traits in vertebrates. Recently, threespine sticklebacks have been used as a model system to identify the genomic basis of highly complex traits, such as behavior and host-microbiome and host-parasite interactions. We review the latest findings and new avenues of research that have led the threespine stickleback to be considered a supermodel of evolutionary genomics.

Copy number variation of a fatty acid desaturase gene Fads2 associated with ecological divergence in freshwater stickleback populations

Fitness of aquatic animals can be limited by the scarcity of nutrients such as long-chain polyunsaturated fatty acids, especially docosahexaenoic acid (DHA). DHA availability from diet varies among aquatic habitats, imposing different selective pressures on resident animals to optimize DHA acquisition and synthesis. For example, DHA is generally poor in freshwater ecosystems compared to marine ecosystems. Our previous work revealed that, relative to marine fishes, several freshwater fishes evolved higher copy numbers of the fatty acid desaturase2 (Fads2) gene, which encodes essential enzymes for DHA biosynthesis, likely compensating for the limited availability of DHA in freshwater. Here, we demonstrate that Fads2 copy number also varies between freshwater sticklebacks inhabiting lakes and streams with stream fish having higher Fads2 copy number. Additionally, populations with benthic-like morphology possessed higher Fads2 copy number than those with planktivore-like morphology. This may be because benthic-like fish mainly feed on DHA-deficient prey such as macroinvertebrates whereas planktivore-like fish forage more regularly on DHA-rich prey, like copepods. Our results suggest that Fads2 copy number variation arises from ecological divergence not only between organisms exploiting marine and freshwater habitats but also between freshwater organisms exploiting divergent resources.

Clinal genomic analysis reveals strong reproductive isolation across a steep habitat transition in stickleback fish

How ecological divergence causes strong reproductive isolation between populations in close geographic contact remains poorly understood at the genomic level. We here study this question in a stickleback fish population pair adapted to contiguous, ecologically different lake and stream habitats. Clinal whole-genome sequence data reveal numerous genome regions (nearly) fixed for alternative alleles over a distance of just a few hundred meters. This strong polygenic adaptive divergence must constitute a genome-wide barrier to gene flow because a steep cline in allele frequencies is observed across the entire genome, and because the cline center closely matches the habitat transition. Simulations confirm that such strong divergence can be maintained by polygenic selection despite high dispersal and small per-locus selection coefficients. Finally, comparing samples from near the habitat transition before and after an unusual ecological perturbation demonstrates the fragility of the balance between gene flow and selection. Overall, our study highlights the efficacy of divergent selection in maintaining reproductive isolation without physical isolation, and the analytical power of studying speciation at a fine eco-geographic and genomic scale.

How ecological divergence causes reproductive isolation between populations in close contact remains poorly understood at the genomic level. This study presents a clinal investigation based on whole-genome sequencing to characterize reproductive isolation between threespine stickleback adapted to contiguous but ecologically different lake and stream habitats.

Multidimensional divergent selection, local adaptation, and speciation

Divergent selection applied to one or more traits drives local adaptation and may lead to ecological speciation. Divergent selection on many traits might be termed "multidimensional" divergent selection. There is a commonly held view that multidimensional divergent selection is likely to promote local adaptation and speciation to a greater extent than unidimensional divergent selection. We disentangle the core concepts underlying dimensionality as a property of the environment, phenotypes, and genome. In particular, we identify a need to separate the overall strength of selection and the number of loci affected from dimensionality per se, and to distinguish divergence dimensionality from dimensionality of stabilizing selection. We then critically scrutinize this commonly held view that multidimensional selection promotes speciation, re-examining the evidence base from theory, experiments, and nature. We conclude that the evidence base is currently weak and generally suffers from confounding of possible causal effects. Finally, we propose several mechanisms by which multidimensional divergent selection and related processes might influence divergence, both as a driver and as a barrier.

Predicting population genetic change in an autocorrelated random environment: Insights from a large automated experiment

Most natural environments exhibit a substantial component of random variation, with a degree of temporal autocorrelation that defines the color of environmental noise. Such environmental fluctuations cause random fluctuations in natural selection, affecting the predictability of evolution. But despite long-standing theoretical interest in population genetics in stochastic environments, there is a dearth of empirical estimation of underlying parameters of this theory. More importantly, it is still an open question whether evolution in fluctuating environments can be predicted indirectly using simpler measures, which combine environmental time series with population estimates in constant environments. Here we address these questions by using an automated experimental evolution approach. We used a liquid-handling robot to expose over a hundred lines of the micro-alga Dunaliella salina to randomly fluctuating salinity over a continuous range, with controlled mean, variance, and autocorrelation. We then tracked the frequencies of two competing strains through amplicon sequencing of nuclear and choloroplastic barcode sequences. We show that the magnitude of environmental fluctuations (determined by their variance), but also their predictability (determined by their autocorrelation), had large impacts on the average selection coefficient. The variance in frequency change, which quantifies randomness in population genetics, was substantially higher in a fluctuating environment. The reaction norm of selection coefficients against constant salinity yielded accurate predictions for the mean selection coefficient in a fluctuating environment. This selection reaction norm was in turn well predicted by environmental tolerance curves, with population growth rate against salinity. However, both the selection reaction norm and tolerance curves underestimated the variance in selection caused by random environmental fluctuations. Overall, our results provide exceptional insights into the prospects for understanding and predicting genetic evolution in randomly fluctuating environments.

Being able to predict evolution under natural selection is important for many applied fields of biology, ranging from agriculture to medicine or conservation. However, this endeavor is complicated by factors that inherently limit our ability to predict the future, such as random fluctuations in the environment. Population genetic theory indicates that probabilistic predictions can still be made in this context, but the extent to which this holds empirically, and whether these predictions can be based on simple measurements, are still open questions. Making progress on answering these questions can be achieved by capitalizing on experiments where the environment is precisely controlled over many generations. Here, we used a pipetting robot to generate random time series of salinities with controlled patterns of fluctuations, which we imposed on a microalga, Dunaliella salina. Tracking the frequencies of two genotypes in a mixture by sequencing two short barcode sequences, we were able to show how patterns of fluctuating selection relate to the fluctuating environment. Interestingly, parts of these responses, but not all, could be predicted by simpler measurements in constant environments, allowing precise characterization the limits and prospects for predicting evolution in fluctuating environments.

Phenotypic stability in scalar calcium of freshwater fish across a wide range of aqueous calcium availability in nature

Spatial environmental gradients can promote adaptive differences among conspecific populations as a result of local adaptation or phenotypic plasticity. Such divergence can be opposed by various constraints, including gene flow, limited genetic variation, temporal fluctuations, or developmental constraints. We focus on the constraint that can be imposed when some populations are found in locations characterized by low levels of an essential nutrient. We use scales of wild fish to investigate phenotypic effects of spatial variation in a potentially limiting nutrient-calcium. If scale calcium (we use "scalar" calcium for consistency with the physiology literature) simply reflects environmental calcium availability, we expect higher levels of scalar calcium in fish from calcium-rich water, compared to fish from calcium-poor water. To consider this "passive response" scenario, we analyzed scalar calcium concentrations from three native fish species (Lepomis gibbosus, Percina caprodes, and Perca flavescens) collected at multiple sites across a dissolved calcium gradient in the Upper St. Lawrence River. Contradicting the "passive response" scenario, we did not detect strong or consistent relationships between scalar calcium and water calcium. Instead, for a given proportional increase in water calcium across the wide environmental gradient, the corresponding proportional change in scalar calcium was much smaller. We thus favor the alternative "active homeostasis" scenario, wherein fish from calcium-poor water are better able to uptake, mobilize, and deposit calcium than are fish from calcium-rich water. We further highlight the importance of studying functional traits, such as scales, in their natural setting as opposed to only laboratory studies.

Continent-wide genomic signatures of adaptation to urbanisation in a songbird across Europe

Urbanisation is increasing worldwide, and there is now ample evidence of phenotypic changes in wild organisms in response to this novel environment. Yet, the genetic changes and genomic architecture underlying these adaptations are poorly understood. Here, we genotype 192 great tits (Parus major) from nine European cities, each paired with an adjacent rural site, to address this major knowledge gap in our understanding of wildlife urban adaptation. We find that a combination of polygenic allele frequency shifts and recurrent selective sweeps are associated with the adaptation of great tits to urban environments. While haplotypes under selection are rarely shared across urban populations, selective sweeps occur within the same genes, mostly linked to neural function and development. Collectively, we show that urban adaptation in a widespread songbird occurs through unique and shared selective sweeps in a core-set of behaviour-linked genes.

Repeatability of Adaptive Radiation Depends on Spatial Scale: Regional Versus Global Replicates of Stickleback in Lake Versus Stream Habitats

The repeatability of adaptive radiation is expected to be scale-dependent, with determinism decreasing as greater spatial separation among "replicates" leads to their increased genetic and ecological independence. Threespine stickleback (Gasterosteus aculeatus) provide an opportunity to test whether this expectation holds for the early stages of adaptive radiation-their diversification in freshwater ecosystems has been replicated many times. To better understand the repeatability of that adaptive radiation, we examined the influence of geographic scale on levels of parallel evolution by quantifying phenotypic and genetic divergence between lake and stream stickleback pairs sampled at regional (Vancouver Island) and global (North America and Europe) scales. We measured phenotypes known to show lake-stream divergence and used reduced representation genome-wide sequencing to estimate genetic divergence. We assessed the scale dependence of parallel evolution by comparing effect sizes from multivariate models and also the direction and magnitude of lake-stream divergence vectors. At the phenotypic level, parallelism was greater at the regional than the global scale. At the genetic level, putative selected loci showed greater lake-stream parallelism at the regional than the global scale. Generally, the level of parallel evolution was low at both scales, except for some key univariate traits. Divergence vectors were often orthogonal, highlighting possible ecological and genetic constraints on parallel evolution at both scales. Overall, our results confirm that the repeatability of adaptive radiation decreases at increasing spatial scales. We suggest that greater environmental heterogeneity at larger scales imposes different selection regimes, thus generating lower repeatability of adaptive radiation at larger spatial scales.