Identification of candidate loci for adaptive phenotypic plasticity in natural populations of spadefoot toads

Phenotypic plasticity allows organisms to alter their phenotype in direct response to changes in the environment. Despite growing recognition of plasticity's role in ecology and evolution, few studies have probed plasticity's molecular bases—especially using natural populations. We investigated the genetic basis of phenotypic plasticity in natural populations of spadefoot toads (Spea multiplicata). Spea tadpoles normally develop into an “omnivore” morph that is favored in long‐lasting, low‐density ponds. However, if tadpoles consume freshwater shrimp or other tadpoles, they can alternatively develop (via plasticity) into a “carnivore” morph that is favored in ephemeral, high‐density ponds. By combining natural variation in pond ecology and morph production with population genetic approaches, we identified candidate loci associated with each morph (carnivores vs. omnivores) and loci associated with adaptive phenotypic plasticity (adaptive vs. maladaptive morph choice). Our candidate morph loci mapped to two genes, whereas our candidate plasticity loci mapped to 14 genes. In both cases, the identified genes tended to have functions related to their putative role in spadefoot tadpole biology. Our results thereby form the basis for future studies into the molecular mechanisms that mediate plasticity in spadefoots. More generally, these results illustrate how diverse loci might mediate adaptive plasticity.     

Variation in body size and metamorphic traits of Iberian spadefoot toads over a short geographic distance

Determinants of geographic variation in body size are often poorly understood, especially in organisms with complex life cycles. We examined patterns of adult body size and metamorphic traits variation in Iberian spadefoot toad ( Pelobates cultripes ) populations, which exhibit an extreme reduction in adult body size, 71.6% reduction in body mass, within just about 30 km at south-western Spain. We hypothesized that size at and time to metamorphosis would be predictive of the spatial pattern observed in adult body size. Larvae from eight populations were raised in a common garden experiment at two different larval densities that allow to differentiate whether population divergence was genetically based or was simply a reflection of environmental variation and, in addition, whether this population divergence was modulated by differing crowding larval environments. Larger adult size populations had higher larval growth rates, attaining larger sizes at metamorphosis, and exhibited higher survival than smaller-sized populations at both densities, although accentuated at a low larval density. These population differences appeared to be consistent once embryo size variation was controlled for, suggesting that this phenotypic divergence is not due to maternal effects. Our results suggest considerable genetic differentiation in metamorphic traits that parallels and may be a causal determinant of geographic variation in adult body size.     

Variation in the degree and costs of adaptive phenotypic plasticity among Rana temporaria populations

Adaptive phenotypic plasticity in the form of capacity to accelerate development as a response to pond drying risk is known from many amphibian species. However, very little is known about factors that might constrain the evolution of this type of plasticity, and few studies have explored to what degree plasticity might be constrained by trade-offs dictated by adaptation to different environmental conditions. We compared the ability of southern and northern Scandinavian common frog (Rana temporaria) larvae originating from 10 different populations to accelerate their development in response to simulated pond drying risk and the resulting costs in metamorphic size in a factorial laboratory experiment. We found that (i) northern larvae developed faster than the southern larvae in all treatments, (ii) a capacity to accelerate the response was present in all five southern and all five northern populations tested, but that the magnitude of the response was much larger (and less variable) in the southern than in the northern populations, and that (iii) significant plasticity costs in metamorphic size were present in the southern populations, the plastic genotypes having smaller metamorphic size in the absence of desiccation risk, but no evidence for plasticity costs was found in the northern populations. We suggest that the weaker response to pond drying risk in the northern populations is due to stronger selection on large metamorphic size as compared with southern populations. In other words, seasonal time constraints that have selected the northern larvae to be fast growing and developing, may also constrain their innate ability for adaptive phenotypic plasticity.     

Evidence of adaptive divergence in plasticity: density- and site-dependent selection on shade-avoidance responses in Impatiens capensis

We investigated the conditions under which plastic responses to density are adaptive in natural populations of Impatiens capensis and determined whether plasticity has evolved differently in different selective environments. Previous studies showed that a population that evolved in a sunny site exhibited greater plasticity in response to density than did a population that evolved in a woodland site. Using replicate inbred lines in a reciprocal transplant that included a density manipulation, we asked whether such population differentiation was consistent with the hypothesis of adaptive divergence. We hypothesized that plasticity would be more strongly favored in the sunny site than in the woodland site; consequently, we predicted that selection would be more strongly density dependent in the sunny site, favoring the phenotype that was expressed at each density. Selection on internode length and flowering date was consistent with the hypothesis of adaptive divergence in plasticity. Few costs or benefits of plasticity were detected independently from the expressed phenotype, so plasticity was selected primarily through selection on the phenotype. Correlations between phenotypes and their plasticity varied with the environment and would cause indirect selection on plasticity to be environment dependent. We showed that an appropriate plastic response even to a rare environment can greatly increase genotypic fitness when that environment is favorable. Selection on the measured characters contributed to local adaptation and fully accounted for fitness differences between populations in all treatments except the woodland site at natural density.     

The shape of things to come: linking developmental plasticity to post‐metamorphic morphology in anurans

Development consists of growth and differentiation, which can be partially decoupled and can be affected by environmental factors to different extents. In amphibians, variation in the larval environment influences development and causes changes in post‐metamorphic shape. We examined post‐metamorphic consequences, both morphological and locomotory, of alterations in growth and development. We reared tadpoles of two phylogenetically and ecologically distant frog species (the red‐eyed treefrog Agalychnis callidryas and the African clawed frog Xenopus laevis) under different temperatures with ad libitum food supply and under different food levels at a constant temperature. Low temperature and low food levels both resulted in similarly extended larval periods. However, low temperature yielded relatively long‐legged frogs with a lower degree of ossification than warm temperature, whereas low food yielded relatively short‐legged frogs with a higher degree of ossification than high food levels. Such allometric differences had no effect on locomotor performance of juveniles. Our results provide a basis for understanding the relationship between growth, differentiation and post‐metamorphic shape in anurans and help explain many of the discrepancies reported in previous studies.     

The fitness costs of developmental canalization and plasticity

Organisms are capable of an astonishing repertoire of phenotypic responses to the environment, and these often define important adaptive solutions to heterogeneous and unpredictable conditions. The terms ‘phenotypic plasticity’ and ‘canalization’ indicate whether environmental variation has a large or small effect on the phenotype. The evolution of canalization and plasticity is influenced by optimizing selection‐targeting traits within environments, but inherent fitness costs of plasticity may also be important. We present a meta‐analysis of 27 studies (of 16 species of plant and 7 animals) that have measured selection on the degree of plasticity independent of the characters expressed within environments. Costs of plasticity and canalization were equally frequent and usually mild; large costs were observed only in studies with low sample size. We tested the importance of several covariates, but only the degree of environmental stress was marginally positively related to the cost of plasticity. These findings suggest that costs of plasticity are often weak, and may influence phenotypic evolution only under stressful conditions.     

Heterochronic developmental shift caused by thyroid hormone in larval sand dollars and its implications for phenotypic plasticity and the evolution of nonfeeding development

Recent work on a diverse array of echinoderm species has demonstrated, as is true in amphibians, that thyroid hormone (TH) accelerates development to metamorphosis. Interestingly, the feeding larvae of several species of sea urchins seem to obtain TH through their diet of planktonic algae (exogenous source), whereas nonfeeding larvae of the sand dollar Peronella japonica produce TH themselves (endogenous source). Here we examine the effects of TH (thyroxine) and a TH synthesis inhibitor (thiourea) on the development of Dendraster excentricus, a sand dollar with a feeding larva. We report reduced larval skeleton lengths and more rapid development of the juvenile rudiment in the exogenous TH treatments when compared to controls. Also, larvae treated with exogenous TH reached metamorphic competence faster at a significantly reduced juvenile size, representing the greatest reduction in juvenile size ever reported for an echinoid species with feeding larvae. These effects of TH on D. excentricus larval development are strikingly similar to the phenotypically plastic response of D. excentricus larvae reared under high food conditions. We hypothesize that exogenous (algae-derived) TH is the plasticity cue in echinoid larvae, and that the larvae use ingested TH levels as an indicator for larval nutrition, ultimately signaling the attainment of metamorphic competence. Furthermore, our experiments with the TH synthesis inhibitor thiourea indicate that D. excentricus larvae can produce some TH endogenously. Endogenous TH production might, therefore, be a shared feature among sand dollars, facilitating the evolution of nonfeeding larval development in that group. Mounting evidence on the effects of thyroid hormones in echinoderm development suggests life-history models need to incorporate metamorphic hormone effects and the evolution of metamorphic hormone production.     

Promising directions in plant phenotypic plasticity

A research agenda for the next phase of plasticity studies calls for contributions from a diverse group of biologists, working both independently and collaboratively, to pursue four promising directions: examining dynamic, anatomical/architectural, and cross-generational plasticity along with simpler growth traits; carefully assessing the adaptive significance of those plasticity patterns; investigating the intricate transduction pathways that lead from environmental signal to phenotypic response; and considering the rich environmental context of natural systems. Progress in these areas will allow us to address broad and timely questions regarding the ecological and evolutionary significance of plasticity and the nature of phenotypic determination.     

Phenotypic plasticity and divergence in gene expression

The extent to which phenotypic plasticity, or the ability of a single genotype to produce different phenotypes in different environments, impedes or promotes genetic divergence has been a matter of debate within evolutionary biology for many decades (see, for example, Ghalambor et al. 2007 ; Pfennig et al. 2010 ). Similarly, the role of evolution in shaping phenotypic plasticity remains poorly understood (Pigliucci 2005 ). In this issue of Molecular Ecology, Dayan et al. ( 2015 ) provide empirical data relevant to these questions by assessing the extent of plasticity and divergence in the expression levels of 2272 genes in muscle tissue from killifish (genus Fundulus) exposed to different temperatures. F. heteroclitus (Fig.  1 A) and F. grandis are minnows that inhabit estuarine marshes (Fig.  1 B) along the coasts of the Atlantic Ocean and Gulf of Mexico in North America. These habitats undergo large variations in temperature both daily and seasonally, and these fish are known to demonstrate substantial phenotypic plasticity in response to temperature change (e.g. Fangue et al. 2006 ). Furthermore, the range of F. heteroclitus spans a large latitudinal gradient of temperatures, such that northern populations experience temperatures that are on average ~10°C colder than do southern populations (Schulte 2007 ). By comparing gene expression patterns between populations of these fish from different thermal habitats held in the laboratory at three different temperatures, Dayan et al. ( 2015 ) address two important questions regarding the interacting effects of plasticity and evolution: (i) How does phenotypic plasticity affect adaptive divergence? and (ii) How does adaptive divergence affect plasticity?     

Correlated evolution of phenotypic plasticity in metamorphic timing

Phenotypic plasticity has long been a focus of research, but the mechanisms of its evolution remain controversial. Many amphibian species exhibit a similar plastic response in metamorphic timing in response to multiple environmental factors; therefore, more than one environmental factor has likely influenced the evolution of plasticity. However, it is unclear whether the plastic responses to different factors have evolved independently. In this study, we examined the relationship between the plastic responses to two experimental factors (water level and food type) in larvae of the salamander Hynobius retardatus, using a cause-specific Cox proportional hazards model on the time to completion of metamorphosis. Larvae from ephemeral ponds metamorphosed earlier than those from permanent ponds when kept at a low water level or fed conspecific larvae instead of larval Chironomidae. This acceleration of metamorphosis depended only on the permanency of the larvae's pond of origin, but not on the conspecific larval density (an indicator of the frequency of cannibalism) in the ponds. The two plastic responses were significantly correlated, indicating that they may evolve correlatively. Once plasticity evolved as an adaptation to habitat desiccation, it might have relatively easily become a response to other ecological factors, such as food type via the pre-existing developmental pathway.     

Crest evolution in newts: implications for reconstruction methods, sexual selection, phenotypic plasticity and the origin of novelties

The dorsal crest of newts (Salamandridae) is a novel, phenotypically plastic, sexually selected trait that may evolve in association with complex courtship behaviours. We estimated a near-comprehensive, time-calibrated phylogeny for salamandrids and analysed the evolution of their crests and display behaviour. Different models give conflicting reconstructions for crest evolution, showing that likelihood can estimate incorrect ancestral states with strong statistical support. The best-fitting model suggests that crests evolved once and were lost repeatedly, supporting the hypothesis that sexually selected traits may be frequently lost. We demonstrate the correlated evolution of crests and courtship behaviour and show that species with larger numbers of crest-related traits have larger repertoires of behaviours. We also show that phenotypically plastic morphological traits can be maintained over long macroevolutionary timescales (～25-48 Myr). Finally, we use salamandrids to address how novel structures may arise, and support a model involving the expansion and subdivision of pre-existing structures.     

Phenotypic plasticity in gene expression contributes to divergence of locally adapted populations of Fundulus heteroclitus

We examine the interaction between phenotypic plasticity and evolutionary adaptation using muscle gene expression levels among populations of the fish Fundulus heteroclitus acclimated to three temperatures. Our analysis reveals shared patterns of phenotypic plasticity due to thermal acclimation as well as non‐neutral patterns of variation among populations adapted to different thermal environments. For the majority of significant differences in gene expression levels, phenotypic plasticity and adaptation operate on different suites of genes. The subset of genes that demonstrate both adaptive differences and phenotypic plasticity, however, exhibit countergradient variation of expression. Thus, expression differences among populations counteract environmental effects, reducing the phenotypic differentiation between populations. Finally, gene‐by‐environment interactions among genes with non‐neutral patterns of expression suggest that the penetrance of adaptive variation depends on the environmental conditions experienced by the individual.     

Evolutionary implications of phenotypic plasticity in the hindlimb of the lizard Anolis sagrei

Abstract.— Species of Anolis lizards that use broad substrates have long legs, which provide enhanced maximal sprint speed, whereas species that use narrow surfaces have short legs, which permit careful movements. We raised hatchling A. sagrei in terraria provided with only broad or only narrow surfaces. At the end of the experiment, lizards in the broad treatment had relatively longer hindlimbs than lizards in the narrow treatment. These results indicate that not only is hindlimb length a plastic trait in these lizards, but that this plasticity leads to the production of phenotypes appropriate to particular environments. Comparison to hindlimb lengths of other Anolis species indicates that the range of plasticity is limited compared to the diversity shown throughout the anole radiation. Nonetheless, this plasticity potentially could have played an important role in the early stages of the Caribbean anole radiation.     

Evolution and molecular mechanisms of adaptive developmental plasticity

Aside from its selective role in filtering inter-individual variation during evolution by natural selection, the environment also plays an instructive role in producing variation during development. External environmental cues can influence developmental rates and/or trajectories and lead to the production of distinct phenotypes from the same genotype. This can result in a better match between adult phenotype and selective environment and thus represents a potential solution to problems posed by environmental fluctuation. The phenomenon is called adaptive developmental plasticity. The study of developmental plasticity integrates different disciplines (notably ecology and developmental biology) and analyses at all levels of biological organization, from the molecular regulation of changes in organismal development to variation in phenotypes and fitness in natural populations. Here, we focus on recent advances and examples from morphological traits in animals to provide a broad overview covering (i) the evolution of developmental plasticity, as well as its relevance to adaptive evolution, (ii) the ecological significance of alternative environmentally induced phenotypes, and the way the external environment can affect development to produce them, (iii) the molecular mechanisms underlying developmental plasticity, with emphasis on the contribution of genetic, physiological and epigenetic factors, and (iv) current challenges and trends, including the relevance of the environmental sensitivity of development to studies in ecological developmental biology, biomedicine and conservation biology.     

Shedding light on the evolution of plasticity in natural populations

Plasticity allows for changes in phenotype in response to environmental cues, often facilitating local adaptation to seasonal environments. Phenotypic plasticity alone, however, may not always be sufficient to ensure adaptation to new localities. In particular, changing cues associated with shifting seasonal regimes may no longer induce appropriate phenotypic responses in new environments ( Nicotra et al. 2010 ). Plastic responses must thus evolve to avoid being maladaptive. To date, the extent to which plastic responses can change and the genetic mechanisms by which this can happen have remained elusive. In this issue of Molecular Ecology, Blackman et al. (2011a) harness natural variation in flowering time among populations of the wild sunflower, Helianthus annuus, to demonstrate that plasticity has indeed evolved in this species. Remarkably, they are able to detect changes in gene expression that are associated with both a loss of plasticity and a reversal of the plastic response. These changes occur in two separate, but integrated, regulatory pathways controlling the transition to flowering, suggesting that complex regulatory networks that incorporate multiple environmental and developmental cues may facilitate the evolution of plastic responses. This study leverages knowledge from plant genetic models to provide a surprising level of insight into the evolution of an adaptive trait in a non‐model species. Through discoveries of the roles of gene duplication and network modularity in the evolution of plastic responses, the study raises questions about the degree to which species‐specific network architectures may act as a constraint to the potential of adaptation.     

Temperature,size and developmental plasticity in birds

As temperatures increase, there is growing evidence that species across much of the tree of life are getting smaller. These climate change-driven size reductions are often interpreted as a temporal analogue of the observation that individuals within a species tend to be smaller in the warmer parts of the species'' range. For ectotherms, there has been a broad effort to understand the role of developmental plasticity in temperature–size relationships, but in endotherms, this mechanism has received relatively little attention in favour of selection-based explanations. We review the evidence for a role of developmental plasticity in warming-driven size reductions in birds and highlight insulin-like growth factors as a potential mechanism underlying plastic responses to temperature in endotherms. We find that, as with ectotherms, changes in temperature during development can result in shifts in body size in birds, with size reductions associated with warmer temperatures being the most frequent association. This suggests developmental plasticity may be an important, but largely overlooked, mechanism underlying warming-driven size reductions in endotherms. Plasticity and natural selection have very different constraining forces, thus understanding the mechanism linking temperature and body size in endotherms has broad implications for predicting future impacts of climate change on biodiversity.     

Evolutionary quantitative genetics of nonlinear developmental systems

In quantitative genetics, the effects of developmental relationships among traits on microevolution are generally represented by the contribution of pleiotropy to additive genetic covariances. Pleiotropic additive genetic covariances arise only from the average effects of alleles on multiple traits, and therefore the evolutionary importance of nonlinearities in development is generally neglected in quantitative genetic views on evolution. However, nonlinearities in relationships among traits at the level of whole organisms are undeniably important to biology in general, and therefore critical to understanding evolution. I outline a system for characterizing key quantitative parameters in nonlinear developmental systems, which yields expressions for quantities such as trait means and phenotypic and genetic covariance matrices. I then develop a system for quantitative prediction of evolution in nonlinear developmental systems. I apply the system to generating a new hypothesis for why direct stabilizing selection is rarely observed. Other uses will include separation of purely correlative from direct and indirect causal effects in studying mechanisms of selection, generation of predictions of medium‐term evolutionary trajectories rather than immediate predictions of evolutionary change over single generation time‐steps, and the development of efficient and biologically motivated models for separating additive from epistatic genetic variances and covariances.     

Selection experiments and the study of phenotypic plasticity1

Abstract Laboratory selection experiments are powerful tools for establishing evolutionary potentials. Such experiments provide two types of information, knowledge about genetic architecture and insight into evolutionary dynamics. They can be roughly classified into two types: (1) artificial selection in which the experimenter selects on a focal trait or trait index, and (2) quasi‐natural selection in which the experimenter establishes a set of environmental conditions and then allows the population to evolve. Both approaches have been used in the study of phenotypic plasticity. Artificial selection experiments have taken various forms including: selection directly on a reaction norm, selection on a trait in multiple environments, and selection on a trait in a single environment. In the latter experiments, evolution of phenotypic plasticity is investigated as a correlated response. Quasi‐natural selection experiments have examined the effects of both spatial and temporal variation. I describe how to carry out such experiments, summarize past efforts, and suggest further avenues of research.