Molecular investigation of genetic assimilation during the rapid adaptive radiations of East African cichlid fishes

Adaptive radiations are characterized by adaptive diversification intertwined with rapid speciation within a lineage resulting in many ecologically specialized, phenotypically diverse species. It has been proposed that adaptive radiations can originate from ancestral lineages with pronounced phenotypic plasticity in adaptive traits, facilitating ecologically driven phenotypic diversification that is ultimately fixed through genetic assimilation of gene regulatory regions. This study aimed to investigate how phenotypic plasticity is reflected in gene expression patterns in the trophic apparatus of several lineages of East African cichlid fishes, and whether the observed patterns support genetic assimilation. This investigation used a split brood experimental design to compare adaptive plasticity in species from within and outside of adaptive radiations. The plastic response was induced in the crushing pharyngeal jaws through feeding individuals either a hard or soft diet. We find that nonradiating, basal lineages show higher levels of adaptive morphological plasticity than the derived, radiated lineages, suggesting that these differences have become partially genetically fixed during the formation of the adaptive radiations. Two candidate genes that may have undergone genetic assimilation, gif and alas1, were identified, in addition to alterations in the wiring of LPJ patterning networks. Taken together, our results suggest that genetic assimilation may have dampened the inducibility of plasticity related genes during the adaptive radiations of East African cichlids, flattening the reaction norms and canalizing their feeding phenotypes, driving adaptation to progressively more narrow ecological niches.     

On the fate of seasonally plastic traits in a rainforest butterfly under relaxed selection

Many organisms display phenotypic plasticity as adaptation to seasonal environmental fluctuations. Often, such seasonal responses entails plasticity of a whole suite of morphological and life‐history traits that together contribute to the adaptive phenotypes in the alternative environments. While phenotypic plasticity in general is a well‐studied phenomenon, little is known about the evolutionary fate of plastic responses if natural selection on plasticity is relaxed. Here, we study whether the presumed ancestral seasonal plasticity of the rainforest butterfly Bicyclus sanaos (Fabricius, 1793) is still retained despite the fact that this species inhabits an environmentally stable habitat. Being exposed to an atypical range of temperatures in the laboratory revealed hidden reaction norms for several traits, including wing pattern. In contrast, reproductive body allocation has lost the plastic response. In the savannah butterfly, B. anynana (Butler, 1879), these traits show strong developmental plasticity as an adaptation to the contrasting environments of its seasonal habitat and they are coordinated via a common developmental hormonal system. Our results for B. sanaos indicate that such integration of plastic traits – as a result of past selection on expressing a coordinated environmental response – can be broken when the optimal reaction norms for those traits diverge in a new environment.     

Evidence for lower plasticity in CTMAX at warmer developmental temperatures

Understanding the capacity for different species to reduce their susceptibility to climate change via phenotypic plasticity is essential for accurately predicting species extinction risk. The climatic variability hypothesis suggests that spatial and temporal variation in climatic variables should select for more plastic phenotypes. However, empirical support for this hypothesis is limited. Here, we examine the capacity for ten Drosophila species to increase their critical thermal maxima (CT_MAX) through developmental acclimation and/or adult heat hardening. Using four fluctuating developmental temperature regimes, ranging from 13 to 33 °C, we find that most species can increase their CT_MAX via developmental acclimation and adult hardening, but found no relationship between climatic variables and absolute measures of plasticity. However, when plasticity was dissected across developmental temperatures, a positive association between plasticity and one measure of climatic variability (temperature seasonality) was found when development took place between 26 and 28 °C, whereas a negative relationship was found when development took place between 20 and 23 °C. In addition, a decline in CT_MAX and egg‐to‐adult viability, a proxy for fitness, was observed in tropical species at the warmer developmental temperatures (26–28 °C); this suggests that tropical species may be at even greater risk from climate change than currently predicted. The combined effects of developmental acclimation and adult hardening on CT_MAX were small, contributing to a <0.60 °C shift in CT_MAX. Although small shifts in CT_MAX may increase population persistence in the shorter term, the degree to which they can contribute to meaningful responses in the long term is unclear.     

Branching the risks: architectural plasticity and bet‐hedging in Mediterranean annuals

It has been suggested that architectural plasticity in shoot size and number allows plants to manage environmental risks. Simpler structures require shorter development times and fewer resources, which secure minimal fitness even under risky and unfavourable conditions. Here we tested the hypothesis that the magnitude of such architectural plasticity depends on the species' developmental strategy. Specifically, species with late reproduction were expected to express the highest levels of architectural plasticity in response to environmental cues predicting high probability of abrupt deterioration in growth conditions. This hypothesis was tested by comparing Mediterranean and semi‐arid populations of three species, which differed in growth strategy: Trifolium purpureum, a determinate and late flowerer, and Emex spinosa and Hippocrepis unisiliquosa that flower indeterminately throughout the season. All plants were exposed to varying levels of water availability and competition, but only T. purpureum displayed plastic architectural responsiveness to the experimental manipulations. In contrast, the early and extended step‐by‐step flowering of both E. spinosa and H. unisiliquosa reflected a relatively deterministic bet‐hedging reproductive schedule, whereby minimum fitness is secured even under adverse conditions. These two opposing strategies gave contrasting results, with E. spinosa and H. unisiliquosa displaying reduced efficiency under favourable conditions under which T. purpureum had the highest reproductive efficiency. The evolutionary interplay between deterministic risk‐averse and plastic risk‐prone growth strategies might reflect contrasts in the probability and severity of environmental risks, and the costs of missed opportunities.     

Risk‐induced hatching timing shows low heritability and evolves independently of spontaneous hatching in red‐eyed treefrogs

Plasticity in the timing of transitions between stages of complex life cycles allows organisms to adjust their growth and development to local environmental conditions. Genetic variation in such plasticity is common, but the evolution of context‐dependent transition timing may be constrained by information reliability, lag‐time and developmental constraints. We studied the genetic architecture of hatching plasticity in embryos of the red‐eyed treefrog (Agalychnis callidryas) in response to simulated predator attacks using a series of paternal and maternal half‐sibs from a captive breeding colony of wild‐collected animals. We compared the developmental timing of induced early hatching across sibships and estimated cross‐environment genetic correlations between induced and spontaneous hatching traits. Additive genetic variance for induced early hatching was very low, indicating a constraint on the short‐term evolution of earlier hatching timing. This constraint is likely related to the maturation of the hatching mechanism. The most plastic genotypes produced the most extreme spontaneous hatching phenotypes, indicating that developmental range, per se, is not constrained. Cross‐environment genetic correlation in hatching timing was negligible, so the evolution of spontaneous hatching in this species has not depended on the evolution of risk‐induced hatching and vice versa.     

Sex‐specific compensatory growth in the larvae of the greater wax moth Galleria mellonella

Deficiency of food resources in ontogeny is known to prolong an organism's developmental time and affect body size in adulthood. Yet life‐history traits are plastic: an organism can increase its growth rate to compensate for a period of slow growth, a phenomenon known as ‘compensatory growth’. We tested whether larvae of the greater wax moth Galleria mellonella can accelerate their growth after a fast of 12, 24 or 72 h. We found that a subgroup of female larvae showed compensatory growth when starved for 12 h. Food deficiency lasting more than 12 h resulted in longer development and lower mass gain. Strength of encapsulation reactions against a foreign body inserted in haemocoel was the weakest in females that showed compensatory growth, whereas the strongest encapsulation was recorded in the males and females that fasted for 24 and 72 h. More specifically, we found sex‐biased immune reactions so that females had stronger encapsulation rates than males in one group that fasted for 72 h. Overall, rapidly growing females had a short larval development period and the shortest adult lifespan. These results suggest that highly dynamic trade‐offs between the environment, life‐history traits and sex lead to plasticity in developmental strategies/growth rates in the greater wax moth.     

A Continuum of Behavioral Plasticity in Urban and Desert Black Widows

Behavioral plasticity marks an individual's ability to modulate behavior across functional contexts. Behavioral syndromes, on the other hand, appear as consistent individual variation in behavior that is both repeatable for individuals within a functional context (e.g., consistent voracity toward prey) and correlated across contexts (e.g., high voracity toward prey and high levels of boldness toward enemies). Thus, adaptive plasticity and syndromes represent two extremes of a behavioral plasticity continuum upon which most behavioral phenotypes fall. We tested for both adaptive plasticity and behavioral syndromes in the western black widow spider, Latrodectus hesperus. We measured behavior in three contexts: startle, startle + prey, and startle + mate, and found (1) classic behaviorally plastic responses to predation risk, (2) high repeatability of behavior within contexts, and (3) evidence of a correlation between startle + prey and startle + mate contexts, indicative of a behavioral syndrome. As relative behavioral plasticity may vary across populations, we also compared urban and desert populations to test whether spiders from these habitats exhibit different behaviors and/or behavioral syndromes. While we found that urban males used in mating trials courted urban females significantly more than desert females, we found no other differences in the behavior of urban and desert black widows. Thus, black widows, regardless of habitat, are characterized by both context‐specific behavioral plasticity and across‐context correlations, presenting a phenotypic complexity that is likely exhibited, to varying degrees, by most organisms.     

Interclonal proteomic responses to predator exposure in Daphnia magna may depend on predator composition of habitats

Phenotypic plasticity, the ability of one genotype to express different phenotypes in response to changing environmental conditions, is one of the most common phenomena characterizing the living world and is not only relevant for the ecology but also for the evolution of species. Daphnia, the water flea, is a textbook example for predator‐induced phenotypic plastic defences; however, the analysis of molecular mechanisms underlying these inducible defences is still in its early stages. We exposed Daphnia magna to chemical cues of the predator Triops cancriformis to identify key processes underlying plastic defensive trait formation. To get a more comprehensive idea of this phenomenon, we studied four genotypes with five biological replicates each, originating from habitats characterized by different predator composition, ranging from predator‐free habitats to habitats containing T. cancriformis. We analysed the morphologies as well as proteomes of predator‐exposed and control animals. Three genotypes showed morphological changes when the predator was present. Using a high‐throughput proteomics approach, we found 294 proteins which were significantly altered in their abundance after predator exposure in a general or genotype‐dependent manner. Proteins connected to genotype‐dependent responses were related to the cuticle, protein synthesis and calcium binding, whereas the yolk protein vitellogenin increased in abundance in all genotypes, indicating their involvement in a more general response. Furthermore, genotype‐dependent responses at the proteome level were most distinct for the only genotype that shares its habitat with Triops. Altogether, our study provides new insights concerning genotype‐dependent and general molecular processes involved in predator‐induced phenotypic plasticity in D. magna.     

PHENOTYPIC PLASTICITY AND HETEROCHRONY IN CICHLASOMA MANAGUENSE (PISCES,CICHLIDAE) AND THEIR IMPLICATIONS FOR SPECIATION IN CICHLID FISHES

Cichlid fishes in African rift lakes have undergone rapid speciation, resulting in “species flocks” with more than 300 endemic species in some of the lakes. Most researchers assume that there is little phenotypic variation in cichlid fishes. I report here extensive phenotypic plasticity in a Neotropical cichlid species. I examined the influence of diet on trophic morphology during ontogeny in Cichlasoma managuense. Two groups of full siblings were fed two different diets for eight months after the onset of feeding; thereafter both groups were fed a common diet. Phenotypes that differed significantly at 8.5 months converged almost completely at 16.5 months. If feeding on two different diets is continued after 8.5 months, the phenotypes remain distinct. Differences in diet and possibly in feeding mode are believed to have caused these phenotypic changes. Phenotypic plasticity is described in terms of a qualitative model of heterochrony in which phenotypic change in morphology is explained as retardation of the normal developmental rate. If phenotypic expression of morphology is equally plastic in African cichlid species as it may be in the American cichlids, as exemplified by C. managuense, then taxonomic, ecological, and evolutionary analyses of “species flocks” may be in need of revision. However, Old World cichlids may be less phenotypically plastic than New World cichlids, and this may contribute to the observed differences in speciation rate and degree of endemism.     

Adult plasticity in African cichlids: Rapid changes in opsin expression in response to environmental light differences

Phenotypic plasticity allows organisms to adapt quickly to local environmental conditions and could facilitate adaptive radiations. Cichlids have recently undergone an adaptive radiation in Lake Malawi where they inhabit diverse light environments and tune their visual sensitivity through differences in cone opsin expression. While cichlid opsin expression is known to be plastic over development, whether adults remain plastic is unknown. Adult plasticity in visual tuning could play a role in cichlid radiations by enabling survival in changing environments and facilitating invasion into novel environments. Here we examine the existence of and temporal changes in adult visual plasticity of two closely related species. In complementary experiments, wild adult Metriaclima mbenji from Lake Malawi were moved to the lab under UV‐deficient fluorescent lighting; while lab raised M. benetos were placed under UV‐rich lighting designed to mimic light conditions in the wild. Surprisingly, adult cichlids in both experiments showed significant changes in the expression of the UV‐sensitive single cone opsin, SWS1, in only 3 days. Modeling quantum catches in the light environments revealed a possible link between the light available to the SWS1 visual pigment and SWS1 expression. We conclude that adult cichlids can undergo rapid and significant changes in opsin expression in response to environmental light shifts that are relevant to their habitat and evolutionary history in Lake Malawi. This could have contributed to the rapid divergence characteristic of these fantastic fishes.     

Additive genetic variance and developmental plasticity in growth trajectories in a wild cooperative mammal

Individual variation in growth is high in cooperative breeders and may reflect plastic divergence in developmental trajectories leading to breeding vs. helping phenotypes. However, the relative importance of additive genetic variance and developmental plasticity in shaping growth trajectories is largely unknown in cooperative vertebrates. This study exploits weekly sequences of body mass from birth to adulthood to investigate sources of variance in, and covariance between, early and later growth in wild meerkats (Suricata suricatta), a cooperative mongoose. Our results indicate that (i) the correlation between early growth (prior to nutritional independence) and adult mass is positive but weak, and there are frequent changes (compensatory growth) in post‐independence growth trajectories; (ii) among parameters describing growth trajectories, those describing growth rate (prior to and at nutritional independence) show undetectable heritability while associated size parameters (mass at nutritional independence and asymptotic mass) are moderately heritable (0.09 ≤ h² < 0.3); and (iii) additive genetic effects, rather than early environmental effects, mediate the covariance between early growth and adult mass. These results reveal that meerkat growth trajectories remain plastic throughout development, rather than showing early and irreversible divergence, and that the weak effects of early growth on adult mass, an important determinant of breeding success, are partly genetic. In contrast to most cooperative invertebrates, the acquisition of breeding status is often determined after sexual maturity and strongly impacted by chance in many cooperative vertebrates, who may therefore retain the ability to adjust their morphology to environmental changes and social opportunities arising throughout their development, rather than specializing early.     

Population genomics reveals multiple drivers of population differentiation in a sex‐role‐reversed pipefish

A major goal of molecular ecology is to identify the causes of genetic and phenotypic differentiation among populations. Population genomics is suitably poised to tackle these key questions by diagnosing the evolutionary mechanisms driving divergence in nature. Here, we set out to investigate the evolutionary processes underlying population differentiation in the Gulf pipefish, Syngnathus scovelli. We sampled approximately 50 fish from each of 12 populations distributed from the Gulf coast of Texas to the Atlantic coast of Florida and performed restriction‐site‐associated DNA sequencing to identify SNPs throughout the genome. After imposing quality and stringency filters, we selected a panel of 6348 SNPs present in all 12 populations, 1753 of which were not physically linked. We identified a genome‐wide pattern of isolation by distance, in addition to a more substantial genetic break separating populations in the Gulf of Mexico from those in the Atlantic. We also used several divergence outlier approaches and tests for genotype–environment correlations to identify 400 SNPs putatively involved in local adaptation. Patterns of phenotypic differentiation and variation diverged from the overall genomic pattern, suggesting that selection, phenotypic plasticity or demographic factors may be shaping phenotypes in distinct populations. Overall, our results suggest that population divergence is driven by a variety of factors in S. scovelli, including neutral processes and selection on multiple traits.     

Phylogenomics of pike cichlids (Cichlidae: Crenicichla): the rapid ecological speciation of an incipient species flock

The rapid rise of phenotypic and ecological diversity in independent lake‐dwelling groups of cichlids is emblematic of the East African Great Lakes. In this study, we show that similar ecologically based diversification has occurred in pike cichlids (Crenicichla) throughout the Uruguay River drainage of South America. We collected genomic data from nearly 500 ultraconserved element (UCEs) loci and >260 000 base pairs across 33 species, to obtain a phylogenetic hypothesis for the major species groups and to evaluate the relationships and genetic structure among five closely related, endemic, co‐occurring species (the Uruguay River species flock; URSF). Additionally, we evaluated ecological divergence of the URSF based on body and lower pharyngeal jaw (LPJ) shape and gut contents. Across the genus, we recovered novel relationships among the species groups. We found strong support for the monophyly of the URSF; however, relationships among these species remain problematic, likely because of the rapid and recent evolution of this clade. Clustered co‐ancestry analysis recovered most species as well delimited genetic groups. The URSF species exhibit species‐specific body and LPJ shapes associated with specialized trophic roles. Collectively, our results suggest that the URSF consists of incipient species that arose via ecological speciation associated with the exploration of novel trophic roles.     

Effects of inbreeding on behavioural plasticity of parent–offspring interactions in a burying beetle

Inbreeding depression is defined as a fitness decline in progeny resulting from mating between related individuals, the severity of which may vary across environmental conditions. Such inbreeding‐by‐environment interactions might reflect that inbred individuals have a lower capacity for adjusting their phenotype to match different environmental conditions better, as shown in prior studies on developmental plasticity. Behavioural plasticity is more flexible than developmental plasticity because it is reversible and relatively quick, but little is known about its sensitivity to inbreeding. Here, we investigate effects of inbreeding on behavioural plasticity in the context of parent–offspring interactions in the burying beetle Nicrophorus vespilloides. Larvae increase begging with the level of hunger, and parents increase their level of care when brood sizes increase. Here, we find that inbreeding increased behavioural plasticity in larvae: inbred larvae reduced their time spent associating with a parent in response to the length of food deprivation more than outbred larvae. However, inbreeding had no effect on the behavioural plasticity of offspring begging or any parental behaviour. Overall, our results show that inbreeding can increase behavioural plasticity. We suggest that inbreeding‐by‐environment interactions might arise when inbreeding is associated with too little or too much plasticity in response to changing environmental conditions.     

Specialized morphology for a generalist diet: evidence for Liem's Paradox in a cichlid fish

The stable isotope ratio and seasonal changes in diet of Alluaud's haplo Astatoreochromis alluaudi, a cichlid fish with massive pharyngeal jaws well known for its ability to process hard‐bodied prey, are described. The diet of A. alluaudi was quantified in Lake Saka, Uganda, over a period of 30 months. Variation in physico‐chemical variables (mean monthly rainfall, water temperature, turbidity and dissolved oxygen), as well as potential competitor density and food abundance, was measured throughout the second half of the study (14 months). Stomach contents and isotope analysis revealed a diet comprised mainly of fishes and insects, with a low contribution of molluscs (0–33%) in any given month. No correlation was detected between diet and either macroinvertebrate abundance or competitor abundance. The running average rainfall was positively related to the percentage of fish consumed per month. Although A. alluaudi exhibits an apparent molluscivorous trophic morphology in Lake Saka, molluscs did not appear to compose a major portion of its diet. Gradients of rainfall seemed to be the most important environmental predictor of diet choice in Lake Saka. These results are discussed with reference to Liem's Paradox that apparently morphologically specialized fishes often function as generalist feeders in the wild.     

Density dependence and temporal plasticity of competitive interactions during utilisation of resources by a community of lepidopteran stemborer species

Interactions within and between species sharing the same resources are characterised by competition or facilitation, and can be influenced by factors such as larval numbers and phenotypic plasticity of the interactions. The effect of larval density on the survival and relative growth rate of the stemborers Busseola fusca (Fuller) and Sesamia calamistis Hampson (both Lepidoptera: Noctuidae), and Chilo partellus (Swinhoe) (Lepidoptera: Crambidae) were studied, as well as the temporal plasticity of their competitive interactions. These stemborers attack maize crops (Zea mays L.) (Poaceae) in sub‐Saharan Africa. Experiments were conducted in the laboratory under controlled conditions at the optimum development temperature (25 °C) for the three species. Surrogate stems filled with artificial diet were intra‐ and interspecifically infested with larvae of each species. The effect of larval density on competition was studied at low (six larvae) and high (12 larvae) levels of infestation, whereas the temporal plasticity of competition was evaluated at 7, 14, 21, or 28 days after infestation. The two experiments involved single‐ and multi‐species infestation treatments. Larval numbers and wet mass in each artificial stem were recorded in each experiment. Survival and relative growth rate of the three species were significantly higher at low‐infestation levels when facing either intra‐ or interspecific competition. The intensity of competition was also temporally plastic among the species and increased as the duration of competition increased. These results are discussed in terms of general infestations of cereal crops by borers.