We study how development and environment interact—that is, by developmental plasticity—to translate genotypes to phenotypes, how this interaction evolves, and how it influences the diversification of form.

The models for our research are nematodes, which lead virtually every lifestyle known to animals and include microbivores, omnivores, predators, and parasites of insects, vertebrates, and plants. The functional diversity of nematodes, which may be the most abundant and species-rich animals on earth, is reflected in their mouthparts. Our lab aims to understand the evolution of this diversity through approaches integrating developmental genetics, phylogenetics, genomics, and natural history.

The main reference point for our research is the "shark-tooth" nematode Pristionchus pacificus. This species has a structural innovation, moveable teeth that allow omnivorous feeding on bacteria, fungi, and even other nematodes.


Predatory feeding by P. pacificus


In response to starvation and, as sensed by pheromones, crowding (Bose et al., 2012), P. pacificus larvae develop into adults of one of two distinct feeding morphs ("eurystomatous" and "stenostomatous"). In this polyphenism (i.e., discrete developmental plasticity), the stenostomatous morph grows rapidly on a diet of bacteria, whereas the eurystomatous morph, which is more complex in form, has higher fitness than the stenostomatous morph when fed nematode prey (Serobyan et al., 2014).


Pristionchus pacificus dimorphism

Mouthpart polyphenism in P. pacificus


The ability to make major phenotypic differences from a single genotype, as shown by P. pacificus, may act as a facilitator of novelty and diversity (Susoy et al., 2015). Research in the lab tests this principle at a genetic level by investigating directly the genes that regulate developmental plasticity and their significance for downstream molecular evolution. Making this research practical is the analytical toolkit available for P. pacificus, a self-fertilizing species with a short (four-day) generation time. Because teeth are what allow nematodes to be predators, the interplay of ecology with genetic mechanisms for plasticity can be studied directly in this system.

A few goals of our research are:
1) A genetic understanding of how developmental plasticity is regulated;
2) To know how plasticity regulators diverge to produce new phenotypes;
3) To determine plasticity's impact on how genes and gene-networks change to produce morphological novelties.


Reconstruction of Pristionchus feeding structures

Reconstructed feeding structures of P. pacificus


The genetic basis for developmental polyphenism has been accessed through the use of P. pacificus as a model (Projecto-Garcia et al., 2017; Levis & Ragsdale, 2022). As a first proof of principle, a switch gene—which encodes the sulfatase EUD-1 (eurystomatous-form-defective)—was found to execute a switch for the mouth dimorphism (Ragsdale et al., 2013). This factor is a gene that has functionally specialized following a series of gene duplications (Ragsdale & Ivers, 2016).


Neuronal expression of a switch gene eud-1 for a morphological dimorphism

Expression of eud-1 in neurons channeling a polyphenism switch


We have since described other molecular factors making up the mechanism of the polyphenism switch. Specifially, we have taken an unbiased approach—forward screens—to identify the genes involved. One of these factors is NHR-40, a nuclear receptor acting downstream of EUD-1 to control the switch (Kieninger et al., 2016). The switch also hinges on another lineage-specific gene, which encodes the sulfotransferase SEUD-1 (suppressor-of-eud-1), whose expression is both environmentally influenced and localized to polyphenic tissue (Bui et al., 2018). 


Neuronal expression of a switch gene eud-1 for a morphological dimorphism

seud-1 expression in cells that produce dimorphic mouthparts


The discovery of SEUD-1 has given insight into how the genetic basis for plasticity evolves: in Pristionchus, the balance of transcriptional and genomic dosage between seud-1 and eud-1 has changed to create divergent polyphenism thresholds. Consequently, how morph-specific target genes ("environmentally sensitive loci") are expressed, and thereby how often they are exposed to selection, is mediated through the switch. Complemented by a cell-by-cell anatomical reference of the plastic trait (Harry et al., 2022), we are now working to understand other parts of this switch's molecular logic.


Regulatory model for morphological polyphenism

Regulatory model for morphological polyphenism in P. pacificus


Using genetic manipulations in this system, we are also identiyfing the targets of the switch, whose expression indeed underlies phenotypic variation in the polyphenism (Bui & Ragsdale, 2019). This suite of targets has evolved through the network integration of ancient plastic responses (i.e., diapause, metabolism) with highly connected genes undergoing rapid evolutionary turnover (Casasa et al., 2021).

Following these insights, we are now studying (i) the evolutionary origins of a polyphenism switch, (ii) how its genetic targets diverge to instruct diverse alternative morphologies, and (iii) the molecular effects of genetic assimilation on originally polyphenic traits. To this end, we are studying plasticity mechanisms at the scales of both macroevolution (functional genetics in other species) and microevolution (natural variation and experimental evolution). The reconstructed histories of polyphenism regulators already suggest that gene duplications, transcriptional changes, and rapid coding divergence may have each played a role in the polyphenism's evolution (Biddle & Ragsdale, 2020). As we test these ideas and others, we are supported by a deep source of morphological and life-history variation across the family Diplogastridae, which includes Pristionchus and other polyphenic lineages, many species of which are easily kept in laboratory culture.


Feeding-structure diversity of Diplogastridae


Moreover, the novel feeding morphologies that characterize Diplogastridae are being empirically placed into an increasingly rich ecological context (Ledón-Rettig et al., 2018). In a particularly striking example, polyphenism in one clade of Pristionchus species, associated with fig wasps in Afrotropical and Australasian figs, has diverged to include five morphs, each with its own putative ecological function (Susoy et al., 2016). Given the diversity of plastic responses, associated morphologies, and ecological function in Diplogastridae, comparisons in this system can reveal the genetic parameters for the relationship between environment and form.


Figs, fig wasps, and the multiple ecomorphs of their Pristionchus associates


Correlation of polyphenism with mouthpart complexity and diversity in macroevolution


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