A theoretical perspective on Waddington's genetic assimilation experiments

Genetic assimilation is the process by which a phenotype that is initially induced by an environmental stimulus becomes stably inherited in the absence of the stimulus after a few generations of selection. While the concept has attracted much debate after being introduced by C. H. Waddington 70 y ago, there have been few experiments to quantitatively characterize the phenomenon. Here, we revisit and organize the results of Waddington's original experiments and follow-up studies that attempted to replicate his results. We then present a theoretical model to illustrate the process of genetic assimilation and highlight several aspects that we think require further quantitative studies, including the gradual increase of penetrance, the statistics of delay in assimilation, and the frequency of unviability during selection. Our model captures Waddington's picture of developmental paths in a canalized landscape using a stochastic dynamical system with alternative trajectories that can be controlled by either external signals or internal variables. It also reconciles two descriptions of the phenomenon-Waddington's, expressed in terms of an individual organism's developmental paths, and that of Bateman in terms of the population distribution crossing a hypothetical threshold. Our results provide theoretical insight into the concepts of canalization, phenotypic plasticity, and genetic assimilation.

Pathogenicity of the root lesion nematode Pratylenchus neglectus depends on pre-culture conditions

The ability of a plant parasitic nematode to infect and reproduce within a host plant depends on its genotype and the environmental conditions before and during infection. We studied the culturing conditions of the root lesion nematode Pratylenchus neglectus to produce inoculum for plant infection tests. Nematodes were either cultivated on carrot calli for different periods or directly isolated from the roots of the host plants. After infection of wheat and barley plants in the greenhouse, nematodes were quantified by RT-qPCR and by visual counting of the nematodes. We observed drastically reduced infection rates after long-term (> 96 weeks) cultivation on carrot callus. In contrast, fresh isolates from cereal roots displayed much higher pathogenicity. We recommend using root lesion nematodes cultivated on carrot calli no longer than 48 weeks to guarantee uniform infection rates.

Multidimensional competition of nematodes affects plastic traits in a beetle ecosystem

Resource competition has driven the evolution of novel polyphenisms in numerous organisms, enhancing fitness in constantly changing environmental conditions. In natural communities, the myriad interactions among diverse species are difficult to disentangle, but the multidimensional microscopic environment of a decaying insect teeming with bacteria and fighting nematodes provides pliable systems to investigate. Necromenic nematodes of the family Diplogastridae live on beetles worldwide, innocuously waiting for their hosts’ deaths to feast on the blooming bacteria. Often, more than one worm species either affiliates with the insect or joins the microbial meal; thus, competition over limited food ensues, and phenotypic plasticity provides perks for species capable of employing polyphenisms. The recently established system of cockchafer Gymnogaster bupthalma and its occasional co-infestation of Pristionchus mayeri and Acrostichus spp. has revealed that these worms will simultaneously utilize two polyphenisms to thrive in a competitive environment. While both genera maintain plastic capacities in mouth form (strictly bacterial-feeding and omnivorous predation) and developmental pathway (direct and arrested development, dauer), P. mayeri employs both when faced with competition from Acrostichus. Here, we took advantage of the malleable system and added a third competitor, model nematode Pristionchus pacificus. Intriguingly, with a third competitor, P. mayeri is quicker to exit dauer and devour available food, while Acrostichus hides in dauer, waiting for the two Pristionchus species to leave the immediate environment before resuming development. Thus, experimental manipulation of short-lived ecosystems can be used to study the roles of polyphenisms in organismal interactions and their potential significance for evolution.

Phylum Nematoda: feeding habits for all valid genera using a new, universal scheme encompassing the entire phylum, with descriptions of morphological characteristics of the stoma, a key, and discussion of the evidence for trophic relationships

This paper details a system for classifying the trophic relationships of the entire Phylum Nematoda, together with a table specifying the categories of every valid genus. This system encompasses both the diets of nematodes and how the food is obtained. The types of evidence used to evaluate trophic relationships and the inferences that can be drawn from each are evaluated. The general morphological and ecological characteristics of each trophic type are detailed, and a morphological key is presented. This information will enable the trophic relationships of any valid genus of nematodes to be assessed, along with currently undescribed genera, provided their affinities to existing genera can be ascertained. The system and list can add value to ecological, environmental and biodiversity studies where there is no morphological information, for example in environmental sequencing or metabarcoding studies.  

Nematode Interactions on Beetle Hosts Indicate a Role of Mouth-Form Plasticity in Resource Competition

Competition is rampant across kingdoms, arising over potential mates, food resources, and space availability. When faced with opponents, phenotypic plasticity proffers organisms indispensable advantageous strategies to outcompete rivals. This tactic is especially crucial on decaying insect hosts as myriad microbes and numerous nematodes struggle to establish thriving populations and ensure resource availability for future generations. Scarab beetles and their associated nematode symbionts on La Réunion Island have provided exceptional systems to study complicated cross-phylum interactions in soil, and recently we have identified a previously unexplored beetle host, Gymnogaster bupthalma, to be reliably co-infested with diplogastrids Pristionchus mayeri and Acrostichus spp. These nematodes maintain the capacity to plastically respond to environmental conditions by developing disparate mouth forms, a strict bacterial-feeding morph or an omnivorous morph that enables predation on other nematodes. In addition, under stressful settings these worms can enter an arrested development stage called dauer, non-feeding dispersal larvae that resume development into reproducing adults when conditions improve. By investigating this beetle-nematode system in a natural context, we uncovered a novel Pristionchus strategy, wherein dauer dispersal from the carcass is gradual and a reproducing population is sustained. Remarkably, usually preferential-bacterial morph P. mayeri develop as predators in populations dense with competitors.

Nematode biphasic 'boom and bust' dynamics are dependent on host bacterial load while linking dauer and mouth-form polyphenisms

Cross-kingdom interactions involve dynamic processes that shape terrestrial ecosystems and represent striking examples of co-evolution. The multifaceted relationships of entomopathogenic nematodes with their insect hosts and symbiotic bacteria are well-studied cases of co-evolution and pathogenicity. In contrast, microbial interactions in soil after the natural death of insects and other invertebrates are minimally understood. In particular, the turnover and succession of nematodes and bacteria during insect decay have not been well documented - although it represents a rich ecological niche with multiple species interactions. Here, we utilize developmentally plastic nematode Pristionchus pacificus and its associated scarab beetles as models. On La Réunion Island, we collected rhinoceros beetle Oryctes borbonicus, induced death, and placed carcasses in cages both on the island and in a mock-natural environment in the laboratory controlling for high spatial and temporal resolution. Investigating nematode population density and dispersal dynamics, we were able to connect two imperative plasticities, dauer and mouth form. We observed a biphasic 'boom and bust' dispersal dynamic of dauer larvae that corresponds to bacterial load on carcasses but not bacterial type. Strikingly, all post-dauer adults have the predatory mouth form, demonstrating novel intricate interactions on decaying insect hosts. Thus, ecologically relevant survival strategies incorporate critical plastic traits.

Phenotypic Plasticity: From Theory and Genetics to Current and Future Challenges

Phenotypic plasticity is defined as the property of organisms to produce distinct phenotypes in response to environmental variation. While for more than a century, biologists have proposed this organismal feature to play an important role in evolution and the origin of novelty, the idea has remained contentious. Plasticity is found in all domains of life, but only recently has there been an increase in empirical studies. This contribution is intended as a fresh view and will discuss current and future challenges of plasticity research, and the need to identify associated molecular mechanisms. After a brief summary of conceptual, theoretical, and historical aspects, some of which were responsible for confusion and contention, I will formulate three major research directions and predictions for the role of plasticity as a facilitator of novelty. These predictions result in a four-step model that, when properly filled with molecular mechanisms, will reveal plasticity as a major factor of evolution. Such mechanistic insight must be complemented with comparative investigations to show that plasticity has indeed created novelty and innovation. Together, such studies will help develop a true developmental evolutionary biology.

Cilia drive developmental plasticity and are essential for efficient prey detection in predatory nematodes

Cilia are complex organelles involved in a broad array of functions in eukaryotic organisms. Nematodes employ cilia for environmental sensing, which shapes developmental decisions and influences morphologically plastic traits and adaptive behaviours. Here, we assess the role of cilia in the nematode Pristionchus pacificus, and determine their importance in regulating the developmentally plastic mouth-form decision in addition to predatory feeding and self-recognition behaviours, all of which are not present in Caenorhabditis elegans. An analysis of a multitude of cilia-related mutants including representatives of the six protein subcomplexes required in intraflagellar transport (IFT) plus the regulatory factor X transcription factor daf-19 revealed that cilia are essential for processing the external cues influencing the mouth-form decision and for the efficient detection of prey. Surprisingly, we observed that loss-of-function mutations in the different IFT components resulted in contrasting mouth-form phenotypes and different degrees of predation deficiencies. This observation supports the idea that perturbing different IFT subcomplexes has different effects on signalling downstream of the cilium. Finally, self-recognition was maintained in the cilia deficient mutants tested, indicating that the mechanisms triggering self-recognition in P. pacificus may not require the presence of fully functional cilia.

Developmental Plasticity and Robustness of a Nematode Mouth-Form Polyphenism

In the last decade, case studies in plants and animals provided increasing insight into the molecular mechanisms of developmental plasticity. When complemented with evolutionary and ecological analyses, these studies suggest that plasticity represents a mechanism facilitating adaptive change, increasing diversity and fostering the evolution of novelty. Here, we summarize genetic, molecular and evolutionary studies on developmental plasticity of feeding structures in nematodes, focusing on the model organism Pristionchus pacificus and its relatives. Like its famous cousin Caenorhabditis elegans, P. pacificus reproduces as a self-fertilizing hermaphrodite and can be cultured in the laboratory on E. coli indefinitely with a four-day generation time. However, in contrast to C. elegans, Pristionchus worms show more complex feeding structures in adaptation to their life history. Pristionchus nematodes live in the soil and are reliably found in association with scarab beetles, but only reproduce after the insects’ death. Insect carcasses usually exist only for a short time period and their turnover is partially unpredictable. Strikingly, Pristionchus worms can have two alternative mouth-forms; animals are either stenostomatous (St) with a single tooth resulting in strict bacterial feeding, or alternatively, they are eurystomatous (Eu) with two teeth allowing facultative predation. Laboratory-based studies revealed a regulatory network that controls the irreversible decision of individual worms to adopt the St or Eu form. These studies revealed that a developmental switch controls the mouth-form decision, confirming long-standing theory about the role of switch genes in developmental plasticity. Here, we describe the current understanding of P. pacificus mouth-form regulation. In contrast to plasticity, robustness describes the property of organisms to produce unchanged phenotypes despite environmental perturbations. While largely opposite in principle, the relationship between developmental plasticity and robustness has only rarely been tested in particular study systems. Based on a study of the Hsp90 chaperones in nematodes, we suggest that robustness and plasticity are indeed complementary concepts. Genetic switch networks regulating plasticity require robustness to produce reproducible responses to the multitude of environmental inputs and the phenotypic output requires robustness because the range of possible phenotypic outcomes is constrained. Thus, plasticity and robustness are actually not mutually exclusive, but rather complementary concepts.

Two independent sulfation processes regulate mouth-form plasticity in the nematode Pristionchus pacificus

Sulfation of biomolecules, like phosphorylation, is one of the most fundamental and ubiquitous biochemical modifications with important functions during detoxification. This process is reversible, involving two enzyme classes: a sulfotransferase, which adds a sulfo group to a substrate; and a sulfatase that removes the sulfo group. However, unlike phosphorylation, the role of sulfation in organismal development is poorly understood. In this study, we find that two independent sulfation events regulate the development of mouth morphology in the nematode Pristionchus pacificus. This nematode has the ability to form two alternative mouth morphologies depending on environmental cues, an example of phenotypic plasticity. We found that, in addition to a previously described sulfatase, a sulfotransferase is involved in regulating the mouth-form dimorphism in P. pacificus However, it is unlikely that both of these sulfation-associated enzymes act upon the same substrates, as they are expressed in different cell types. Furthermore, animals mutant in genes encoding both enzymes show condition-dependent epistatic interactions. Thus, our study highlights the role of sulfation-associated enzymes in phenotypic plasticity of mouth structures in Pristionchus.

The genetics of phenotypic plasticity in nematode feeding structures

Phenotypic plasticity has been proposed as an ecological and evolutionary concept. Ecologically, it can help study how genes and the environment interact to produce robust phenotypes. Evolutionarily, as a facilitator it might contribute to phenotypic novelty and diversification. However, the discussion of phenotypic plasticity remains contentious in parts due to the absence of model systems and rigorous genetic studies. Here, we summarize recent work on the nematode Pristionchus pacificus, which exhibits a feeding plasticity allowing predatory or bacteriovorous feeding. We show feeding plasticity to be controlled by developmental switch genes that are themselves under epigenetic control. Phylogenetic and comparative studies support phenotypic plasticity and its role as a facilitator of morphological novelty and diversity.

Environmental influence on Pristionchus pacificus mouth form through different culture methods

Environmental cues can impact development to elicit distinct phenotypes in the adult. The consequences of phenotypic plasticity can have profound effects on morphology, life cycle, and behavior to increase the fitness of the organism. The molecular mechanisms governing these interactions are beginning to be elucidated in a few cases, such as social insects. Nevertheless, there is a paucity of systems that are amenable to rigorous experimentation, preventing both detailed mechanistic insight and the establishment of a generalizable conceptual framework. The mouth dimorphism of the model nematode Pristionchus pacificus offers the rare opportunity to examine the genetics, genomics, and epigenetics of environmental influence on developmental plasticity. Yet there are currently no easily tunable environmental factors that affect mouth-form ratios and are scalable to large cultures required for molecular biology. Here we present a suite of culture conditions to toggle the mouth-form phenotype of P. pacificus. The effects are reversible, do not require the costly or labor-intensive synthesis of chemicals, and proceed through the same pathways previously examined from forward genetic screens. Different species of Pristionchus exhibit different responses to culture conditions, demonstrating unique gene-environment interactions, and providing an opportunity to study environmental influence on a macroevolutionary scale.

Succession and dynamics of Pristionchus nematodes and their microbiome during decomposition of Oryctes borbonicus on La Réunion Island

Insects and nematodes represent the most species-rich animal taxa and they occur together in a variety of associations. Necromenic nematodes of the genus Pristionchus are found on scarab beetles with more than 30 species known from worldwide samplings. However, little is known about the dynamics and succession of nematodes and bacteria during the decomposition of beetle carcasses. Here, we study nematode and bacterial succession of the decomposing rhinoceros beetle Oryctes borbonicus on La Réunion Island. We show that Pristionchus pacificus exits the arrested dauer stage seven days after the beetles´ deaths. Surprisingly, new dauers are seen after 11 days, suggesting that some worms return to the dauer stage after one reproductive cycle. We used high-throughput sequencing of the 16S rRNA genes of decaying beetles, beetle guts and nematodes to study bacterial communities in comparison to soil. We find that soil environments have the most diverse bacterial communities. The bacterial community of living and decaying beetles are more stable but one single bacterial family dominates the microbiome of decaying beetles. In contrast, the microbiome of nematodes is relatively similar even across different families. This study represents the first characterization of the dynamics of nematode-bacterial interactions during the decomposition of insects.

Life History Responses and Gene Expression Profiles of the Nematode Pristionchus pacificus Cultured on Cryptococcus Yeasts

Nematodes, the earth's most abundant metazoa are found in all ecosystems. In order to survive in diverse environments, they have evolved distinct feeding strategies and they can use different food sources. While some nematodes are specialists, including parasites of plants and animals, others such as Pristionchus pacificus are omnivorous feeders, which can live on a diet of bacteria, protozoans, fungi or yeast. In the wild, P. pacificus is often found in a necromenic association with beetles and is known to be able to feed on a variety of microbes as well as on nematode prey. However, in laboratory studies Escherichia coli OP50 has been used as standard food source, similar to investigations in Caenorhabditis elegans and it is unclear to what extent this biases the obtained results and how relevant findings are in real nature. To gain first insight into the variation in traits induced by a non-bacterial food source, we study Pristionchus-fungi interactions under laboratory conditions. After screening different yeast strains, we were able to maintain P. pacificus for at least 50-60 generations on Cryptococcus albidus and Cryptococcus curvatus. We describe life history traits of P. pacificus on both yeast strains, including developmental timing, survival and brood size. Despite a slight developmental delay and problems to digest yeast cells, which are both reflected at a transcriptomic level, all analyses support the potential of Cryptococcus strains as food source for P. pacificus. In summary, our work establishes two Cryptococcus strains as alternative food source for P. pacificus and shows change in various developmental, physiological and morphological traits, including the transcriptomic profiles.

The Nuclear Hormone Receptor NHR-40 Acts Downstream of the Sulfatase EUD-1 as Part of a Developmental Plasticity Switch in Pristionchus

Developmental plasticity, the ability of one genotype to produce distinct phenotypes in different environments, has been suggested to facilitate phenotypic diversification, and several examples in plants and animals support its macroevolutionary potential [1-8]. However, little is known about associated molecular mechanisms, because environmental effects on development are difficult to study by laboratory approaches. One promising system is the mouth dimorphism of the nematode Pristionchus pacificus [9-12]. Following an irreversible decision in larval development, these nematodes form moveable teeth that occur in either of two discrete morphs. The "eurystomatous" (Eu) form has a wide mouth and two teeth, allowing predatory feeding on other nematodes. In contrast, the alternative ("stenostomatous"; St) form has diminutive mouthparts that largely constrain its diet to microbes. The sulfatase EUD-1 was previously discovered to execute a polyphenism switch based on dosage of functional alleles [13] and confirmed a prediction of evolutionary theory about how developmental switches control plasticity [1, 3]. However, the genetic context of this single gene, and hence the molecular complexity of switch mechanisms, was previously unknown. Here we use a suppressor screen to identify factors downstream of eud-1 in mouth-form regulation. We isolated three dominant, X-linked mutants in the nuclear hormone receptor gene nhr-40 that are haploinsufficient. Both eud-1 nhr-40 double and nhr-40 single mutants are all Eu, whereas transgenic overexpression of nhr-40 does not restore the wild-type phenotype but instead results in nearly all-St lines. Thus, NHR-40 is part of a developmental switch, suggesting that switch mechanisms controlling plasticity consist of multi-component hormonal signaling systems.