Contrasting gene expression programs correspond with predator‐induced phenotypic plasticity within and across generations in Daphnia

Research has shown that a change in environmental conditions can alter the expression of traits during development (i.e., “within‐generation phenotypic plasticity”) as well as induce heritable phenotypic responses that persist for multiple generations (i.e., “transgenerational plasticity”, TGP). It has long been assumed that shifts in gene expression are tightly linked to observed trait responses at the phenotypic level. Yet, the manner in which organisms couple within‐ and TGP at the molecular level is unclear. Here we tested the influence of fish predator chemical cues on patterns of gene expression within‐ and across generations using a clone of Daphnia ambigua that is known to exhibit strong TGP but weak within‐generation plasticity. Daphnia were reared in the presence of predator cues in generation 1, and shifts in gene expression were tracked across two additional asexual experimental generations that lacked exposure to predator cues. Initial exposure to predator cues in generation 1 was linked to ~50 responsive genes, but such shifts were 3–4× larger in later generations. Differentially expressed genes included those involved in reproduction, exoskeleton structure and digestion; major shifts in expression of genes encoding ribosomal proteins were also identified. Furthermore, shifts within the first‐generation and transgenerational shifts in gene expression were largely distinct in terms of the genes that were differentially expressed. Such results argue that the gene expression programmes involved in within‐ vs. transgeneration plasticity are fundamentally different. Our study provides new key insights into the plasticity of gene expression and how it relates to phenotypic plasticity in nature.     

DEVELOPMENTAL DECOUPLING OF ALTERNATIVE PHENOTYPES: INSIGHTS FROM THE TRANSCRIPTOMES OF HORN‐POLYPHENIC BEETLES

Developmental mechanisms play an important role in determining the costs, limits, and evolutionary consequences of phenotypic plasticity. One issue central to these claims is the hypothesis of developmental decoupling, where alternate morphs result from evolutionarily independent developmental pathways. We address this assumption through a microarray study that tests whether differences in gene expression between alternate morphs are as divergent as those between sexes, a classic example of developmental decoupling. We then examine whether genes with morph‐biased expression are less conserved than genes with shared expression between morphs, as predicted if developmental decoupling relaxes pleiotropic constraints on divergence. We focus on the developing horns and brains of two species of horned beetles with impressive sexual‐ and morph‐dimorphism in the expression of horns and fighting behavior. We find that patterns of gene expression were as divergent between morphs as they were between sexes. However, overall patterns of gene expression were also highly correlated across morphs and sexes. Morph‐biased genes were more evolutionarily divergent, suggesting a role of relaxed pleiotropic constraints or relaxed selection. Together these results suggest that alternate morphs are to some extent developmentally decoupled, and that this decoupling has significant evolutionary consequences. However, alternative morphs may not be as developmentally decoupled as sometimes assumed and such hypotheses of development should be revisited and refined.     

Mechanical vibrations from tadpoles' flapping tails transform salamander's carnivorous morphology

Some prey or predator organisms exhibit striking rapid morphological plastic changes with distinct morphology under the condition of predator or prey presence. Remote chemicals propagating from the inducing agents are the prevalent induction cues for most examples of induction of distinct morphs. Sonic and visual cues, as well as chemical cues, are known as triggers for induction of behavioural plasticity. Here we show that hydraulic vibration originating from flapping tails of anuran tadpoles is a key cue in relation to induction of a distinct carnivorous morphology, a broad-headed morph, in larval salamander Hynobius retardatus, which is able to efficiently capture and handle prey. This result was further supported by the fact that simple mechanical vibrations of tail-like vinyl fins were able to induce the morph without any biological cues. Induction of the morph triggered by hydraulic vibration provides a novel concept for understanding the proximate mechanisms of induction of morphological changes.     

Differential predation on the two colour morphs of Nicaraguan Crater lake Midas cichlid fish: implications for the maintenance of its gold‐dark polymorphism

Predation can play an important role in the evolution and maintenance of prey colour polymorphisms. Several factors are known to affect predator choice, including the prey's relative abundance and conspicuousness. In polymorphic prey species, predators often target the most common or most visible morphs. To test if predator choice can explain why in Midas cichlid fish the more visible (gold) morph is also more rare than the inconspicuous dark morph, we conducted predation experiments using two differently coloured wax models in Nicaraguan crater lakes. Contrary to expectations, we observed an overall higher attack rate on the much more abundant, yet less conspicuous dark models, and propose frequency‐dependent predation as a potential explanation for this result. Interestingly, the attack rate differed between different types of predators. While avian predators were biased towards the abundant and less colourful dark morphs, fish predators did not show a strong bias. However, the relative attack rate of fish predators seemed to vary with the clarity of the water, as attack rates on gold models went up as water clarity decreased. The relative differential predation rates on different morphs might impact the relative abundance of both colour morphs and thus explain the maintenance of the colour polymorphism. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 123–131.     

Evidence of weaker phenotypic plasticity by prey to novel cues from non‐native predators

A central question in evolutionary biology is how coevolutionary history between predator and prey influences their interactions. Contemporary global change and range expansion of exotic organisms impose a great challenge for prey species, which are increasingly exposed to invading non‐native predators, with which they share no evolutionary history. Here, we complete a comprehensive survey of empirical studies of coevolved and naive predator?prey interactions to assess whether a shared evolutionary history with predators influences the magnitude of predator‐induced defenses mounted by prey. Using marine bivalves and gastropods as model prey, we found that coevolved prey and predator‐naive prey showed large discrepancies in magnitude of predator‐induced phenotypic plasticity. Although naive prey, predominantly among bivalve species, did exhibit some level of plasticity – prey exposed to native predators showed significantly larger amounts of phenotypic plasticity. We discuss these results and the implications they may have for native communities and ecosystems.     

An interaction‐driven cannibalistic reaction norm

Cannibalism is induced in larval‐stage populations of the Hokkaido salamander, Hynobius retardatus, under the control of a cannibalism reaction norm. Here, I examined phenotypic expression under the cannibalism reaction norm, and how the induction of a cannibalistic morph under the norm leads to populational morphological diversification. I conducted a set of experiments in which density was manipulated to be either low or high. In the high‐density treatment, the populations become dimorphic with some individuals developing into the cannibal morph type. I performed an exploratory analysis based on geometric morphometrics and showed that shape characteristics differed between not only cannibal and noncannibal morph types in the high‐density treatment but also between those morph types and the solitary morph type in the low‐density treatment. Size and shape of cannibal and noncannibal individuals were found to be located at either end of a continuum of expression following a unique size–shape integration rule that was different from the rule governing the size and shape variations of the solitary morph type. This result implies that the high‐density‐driven inducible morphology of an individual is governed by a common integration rule during the development of dimorphism under the control of the cannibalism reaction norm. Phenotypic expression under the cannibalism reaction norm is driven not only by population density but also by social interactions among the members of a population: variation in the populational expression of dimorphism is associated with contingent social interaction events among population members. The induced cannibalistic morph thus reflects not only by contest‐type exploitative competition but also interference competition.     

Not attackable or not crackable—How pre‐ and post‐attack defenses with different competition costs affect prey coexistence and population dynamics

It is well‐known that prey species often face trade‐offs between defense against predation and competitiveness, enabling predator‐mediated coexistence. However, we lack an understanding of how the large variety of different defense traits with different competition costs affects coexistence and population dynamics. Our study focusses on two general defense mechanisms, that is, pre‐attack (e.g., camouflage) and post‐attack defenses (e.g., weaponry) that act at different phases of the predator—prey interaction. We consider a food web model with one predator, two prey types and one resource. One prey type is undefended, while the other one is pre‐ or post‐attack defended paying costs either by a higher half‐saturation constant for resource uptake or a lower maximum growth rate. We show that post‐attack defenses promote prey coexistence and stabilize the population dynamics more strongly than pre‐attack defenses by interfering with the predator's functional response: Because the predator spends time handling “noncrackable” prey, the undefended prey is indirectly facilitated. A high half‐saturation constant as defense costs promotes coexistence more and stabilizes the dynamics less than a low maximum growth rate. The former imposes high costs at low resource concentrations but allows for temporally high growth rates at predator‐induced resource peaks preventing the extinction of the defended prey. We evaluate the effects of the different defense mechanisms and costs on coexistence under different enrichment levels in order to vary the importance of bottom‐up and top‐down control of the prey community.     

An offensive predator phenotype selects for an amplified defensive phenotype in its prey

Inducible defenses of prey and inducible offenses of predators are examples of adaptive phenotypic plasticity. Although evolutionary ecologists have paid considerable attention to the adaptive significances of these strategies, they have rarely focused on their evolutionary impacts on the interacting species. Because the functional phenotypes of predator and prey determine strength of interactions between the species, the inducible plasticity can modify selective pressure on trait distribution and, ultimately, trait evolution in the interacting species. We experimentally tested this hypothesis in a predator–prey system composed of salamander larvae (Hynobius retardatus) and frog tadpoles (Rana pirica) capable of expressing antagonistic inducible offensive or defensive traits, an enlarged gape in the salamander larvae and a bulgy body in the tadpoles, when predator–prey interactions are strong. We examined selection strength on the tadpole’s defensive trait by comparing survival rates of tadpoles with different defensive levels under predation pressure from offensive or non-offensive salamander larvae. Survival rates of more-defensive tadpoles were greater than those of less-defensive tadpoles only when the tadpoles were exposed to offensive salamander larvae; thus, the predator’s offensive phenotype could select for an amplified defensive phenotype in their prey. As the expression of inducible offenses by H. retardatus larvae depends greatly on the composition of its ecological community, the inducible defensive bulgy morph of R. pirica tadpoles might have evolved in response to the variable expression of the H. retardatus offensive larval phenotype.     

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.     

Prey responses to fine‐scale variation in predation risk from combined predators

While it is well documented that organisms can express phenotypic plasticity in response to single gradients of environmental variation, our understanding of how organisms integrate information along multiple environmental gradients is limited in many systems. Using the freshwater snail Helisoma trivolvis and two common predators (water bugs Belostoma flumineum and crayfish Orconectes rusticus), we explored how prey integrate information along multiple predation risk gradients (i.e. caged predators fed increasing amounts of prey biomass) that induce opposing phenotypes. When exposed to single predators fed increasing amounts of prey biomass, we detected threshold responses; intermediate amounts of consumed biomass induced phenotypic responses, but higher amounts induced little additional induction. This suggests that additional increases in predator‐induced traits with greater predator risk offer minimal increases in fitness or that a limit in the response magnitude was reached. Additionally, the response thresholds were contingent on the predator and focal trait. For shell width, responses were generally detected at a lower amount of consumed biomass by water bugs compared to crayfish. Within the crayfish treatments, we found that the shell thickness response threshold was lower than the shell width response threshold. When we combined gradients of consumed biomass from both predators, we found that the magnitude of response to one predator was often reduced when the other predator was present. Interestingly, these effects were often detected at consumed biomass levels that were lower than the threshold concentration necessary to elicit a response in the single‐predator treatments. Moreover, our combined predator treatments revealed that snails shifted from discrete responses to more continuous (i.e. graded) responses. Together, our results reveal that organisms experiencing multiple environmental gradients can integrate this information to make phenotypic decisions and demonstrate the novel result that an exposure to multiple species of predators can lower the response threshold of prey.     

Mouth dimorphism in scale‐eating cichlid fish from Lake Tanganyika advances individual fitness

Random asymmetry, that is the coexistence of left‐ and right‐sided (or ‐handed) individuals within a population, is a particular case of natural variation; what triggers and maintains such dimorphisms remains unknown in most cases. Here, we report a field‐based cage experiment in the scale‐eating Tanganyikan cichlid Perissodus microlepis, which occurs in two morphs in nature: left‐skewed and right‐skewed individuals with respect to mouth orientation. Using underwater cages stocked with scale‐eaters and natural prey fish, we first confirm that, under semi‐natural conditions, left‐skewed scale‐eaters preferentially attack the right flank of their prey, whereas right‐skewed individuals feed predominantly from the left side. We then demonstrate that scale‐eaters have a higher probability for successful attacks when kept in dimorphic experimental populations (left‐ and right‐skewed morphs together) as compared to monomorphic populations (left‐ or right‐skewed morphs), most likely because prey fishes fail to accustom to strikes from both sides. The significantly increased probability for attacks appears to be the selective agent responsible for the evolution and maintenance of mouth dimorphism in P. microlepis, lending further support to the hypothesis that negative frequency‐dependent selection is the stabilizing force balancing the mouth dimorphism at quasi‐equal ratios in scale‐eating cichlids.     

Sexual reproduction of the pentaploid,short‐styled Oxalis pes‐caprae allows the production of viable offspring

Reproduction is a key factor for the successful establishment and spread of introduced species. Oxalis pes‐caprae is a tristylous species with a self‐ and morph‐incompatibility sexual system that, in the invaded range of the western Mediterranean Basin, has been found to reproduce asexually because only the pentaploid, short‐styled morph (5x S‐morph) was introduced. The objective of this study was to test the ability of the 5x S‐morph of O. pes‐caprae to produce viable offspring in the absence of compatible mates, exploring the hypothesis that new morphs could have emerged by sexual reproduction events of the initially introduced morph. Pollen germination, pollen tube development, fruit and seed production, seed germination and offspring ploidy levels were analysed after controlled hand‐pollinations to assess self‐ and morph‐incompatibility and production of viable gametes by the 5x S‐morph. The self‐incompatibility system is still operating, but a partial breakdown in the morph‐incompatibility system combined with the production of viable gametes was observed, allowing sexual reproduction of the 5x S‐morph in the invaded range. The ability of the 5x S‐morph to reproduce sexually may have major consequences for the dynamics of invasive populations of O. pes‐caprae and could be one of the factors involved in the occurrence of new floral morphs in this invaded range.     

Having the guts to compete: how intestinal plasticity explains costs of inducible defences

Predators commonly induce phenotypic changes that make prey better at surviving predation at the cost of reduced growth. While we have a good understanding of how trait changes affect predation risk, we lack a mechanistic understanding of why predator‐induced phenotypes differ in growth. Using two mesocosm experiments, we combined phenotypic plasticity theory with predictions from optimal digestion theory to demonstrate that intra‐ and interspecific competition induced relatively long guts while predators induced relatively short guts. The longer guts induced by competition appear to be an adaptive response that allows more efficient digestion and more rapid growth whereas the shorter guts induced by predators appear to result from a tradeoff of building larger tails in predator environments at the cost of smaller bodies. By combining these two bodies of theory, we now have a much better understanding of the mechanisms that cause the phenotypic trade‐offs that select for inducible defences.     

Pro‐opiomelanocortin gene and melanin‐based colour polymorphism in a reptile

Colour polymorphism is widespread among vertebrates and plays important roles in prey–predator interactions, thermoregulation, social competition, and sexual selection. However, the genetic mechanisms involved in colour variation have been studied mainly in domestic mammals and birds, whereas information on wild animals remains scarce. Interestingly, the pro‐opiomelanocortin gene (POMC) gives rise to melanocortin hormones that trigger melanogenesis (by binding the melanocortin‐1‐receptor; Mc1r) and other physiological and behavioural functions (by binding the melanocortin receptors Mc1‐5rs). Owing to its pleiotropic effect, the POMC gene could therefore account for the numerous covariations between pigmentation and other phenotypic traits. We screened the POMC and Mc1r genes in 107 wild asp vipers (Vipera aspis) that can exhibit four discrete colour morphs (two unpatterned morphs: concolor or melanistic; two patterned morphs: blotched or lined) in a single population. Our study revealed a correlation between a single nucleotide polymorphism situated within the 3′‐untranslated region of the POMC gene and colour variation, whereas Mc1r was not found to be polymorphic. To the best of our knowledge, we disclose for the first time a relationship between a mutation at the POMC gene and coloration in a wild animal, as well as a correlation between a genetic marker and coloration in a snake species. Interestingly, similar mutations within the POMC 3′‐untranslated region are linked to human obesity and alcohol and drug dependence. Combined with our results, this suggests that the 3′‐untranslated region of the POMC gene may play a role in its regulation in distant vertebrates. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 160–168.     

Identification of a Novel Uromodulin-Like Gene Related to Predator-Induced Bulgy Morph in Anuran Tadpoles by Functional Microarray Analysis

Tadpoles of the anuran species Rana pirica can undergo predator-specific morphological responses. Exposure to a predation threat by larvae of the salamander Hynobius retardatus results in formation of a bulgy body (bulgy morph) with a higher tail. The tadpoles revert to a normal phenotype upon removal of the larval salamander threat. Although predator-induced phenotypic plasticity is of major interest to evolutionary ecologists, the molecular and physiological mechanisms that control this response have yet to be elucidated. In a previous study, we identified various genes that are expressed in the skin of the bulgy morph. However, it proved difficult to determine which of these were key genes in the control of gene expression associated with the bulgy phenotype. Here, we show that a novel gene plays an important role in the phenotypic plasticity producing the bulgy morph. A functional microarray analysis using facial tissue samples of control and bulgy morph tadpoles identified candidate functional genes for predator-specific morphological responses. A larger functional microarray was prepared than in the previous study and used to analyze mRNAs extracted from facial and brain tissues of tadpoles from induction-reversion experiments. We found that a novel uromodulin-like gene, which we name here pirica, was up-regulated and that keratin genes were down-regulated as the period of exposure to larval salamanders increased. Pirica consists of a 1296 bp open reading frame, which is putatively translated into a protein of 432 amino acids. The protein contains a zona pellucida domain similar to that of proteins that function to control water permeability. We found that the gene was expressed in the superficial epidermis of the tadpole skin.     

The role of learning by a predator,Rivulus hartii,in the rare‐morph survival advantage in guppies

Negative frequency‐dependent selection (NFDS), where rare types are favoured by selection, can maintain diversity. However, the ecological processes that mediate NFDS are often not known. Male guppies (Poecilia reticulata) exhibit extreme diversity of colour patterning and, in a previous field experiment, rare morphs had a survival advantage. Here, we test the hypothesis that predators impose NFDS because they are efficient at capturing familiar prey morphs, but are less efficient at capturing unfamiliar morphs. Over a series of trials, we presented Rivulus hartii, a natural predator of guppies, with male guppies with the same colour patterning (A trials); then, for a second series of trials, we presented the rivulus with guppies with a new colour pattern (B trials). The success of rivulus at capturing guppies on the first attack increased over successive A trials. First attack success decreased significantly for the early B trials, and then increased during successive B trials, eventually reaching the same level as in the best A trials. This experiment demonstrates that learning, perhaps through long‐term search image formation, plays a role in predation success on familiar vs. unfamiliar prey morphs. These results support the hypothesis that predator learning contributes to the maintenance of the extreme male guppy polymorphism seen in nature.