Polyphenism of a Novel Trait Integrated Rapidly Evolving Genes into Ancestrally Plastic Networks

Abstract

Developmental polyphenism, the ability to switch between phenotypes in response to environmental variation, involves the alternating activation of environmentally sensitive genes. Consequently, to understand how a polyphenic response evolves requires a comparative analysis of the components that make up environmentally sensitive networks. Here, we inferred coexpression networks for a morphological polyphenism, the feeding-structure dimorphism of the nematode Pristionchus pacificus. In this species, individuals produce alternative forms of a novel trait-moveable teeth, which in one morph enable predatory feeding-in response to environmental cues. To identify the origins of polyphenism network components, we independently inferred coexpression modules for more conserved transcriptional responses, including in an ancestrally nonpolyphenic nematode species. Further, through genome-wide analyses of these components across the nematode family (Diplogastridae) in which the polyphenism arose, we reconstructed how network components have changed. To achieve this, we assembled and resolved the phylogenetic context for five genomes of species representing the breadth of Diplogastridae and a hypothesized outgroup. We found that gene networks instructing alternative forms arose from ancestral plastic responses to environment, specifically starvation-induced metabolism and the formation of a conserved diapause (dauer) stage. Moreover, loci from rapidly evolving gene families were integrated into these networks with higher connectivity than throughout the rest of the P. pacificus transcriptome. In summary, we show that the modular regulatory outputs of a polyphenic response evolved through the integration of conserved plastic responses into networks with genes of high evolutionary turnover.

Keywords: coexpression network; developmental plasticity; modularity; nematodes; phylogenomics; taxon-restricted genes.

Fig. 1.

Putative model for switch-mediated regulation of environmentally sensitive genes in Pristionchus pacificus. Two feeding-structure morphs (Eu, St) produce mouthparts that differ in their gape (arrows) and in the shape and number of their teeth (dorsal tooth of both morphs, false-colored pink; subventral tooth restricted to Eu morph, yellow), enabling different feeding strategies in response to local environmental signals (brown box). Similar, although not identical, signals likewise influence the decision to enter dauer diapause (green box) through processes with limited overlap with the mouth polyphenism. Specifically, the mouth-polyphenism switch (blue box) comprises a series of enzymes (the α-N-acetylglucosaminidases NAG-1 and NAG-2, sulfatase EUD-1, and sulfotransferase SEUD-1/SULT-1) that alternatively influence the activity of two nuclear receptors, NHR-40 and NHR-1. These receptors together control the development of the alternative forms, presumably through the regulation of polyphenism-specific GRNs (orange box).

Fig. 2.

Gene coexpression networks of the mouth polyphenism of Pristionchus pacificus. (A) Heat map of module–trait correlation, displaying the correlation values for each module (rows). Positive module correlation per trait (columns) is displayed in red, whereas negative is displayed in blue. Color swatches to left indicate polyphenism modules. Eu-correlated modules: 18, 19, 21, 22. St-correlated modules: 10, 31. (B) Visual representation of the six polyphenism modules (P < 0.01). Colors refer to modules in (A).

Fig. 3.

Anatomical expression of homologs of Pristionchus pacificus mouth-polyphenism genes in the nonpolyphenic species Caenorhabditis elegans. Idealized nematode diagram is colored by tissue that produces dimorphic mouthparts in P. pacificus (purple hues, pharynx; green, arcade syncytia; blue, hypodermis/epidermis) and also includes other anterior tissues possibly involved in the polyphenism (gray). Pie charts show relative representation among six polyphenism coexpression modules (colors correspond to fig. 1B and C), with size of chart indicating relative contribution by all polyphenism modules.

Fig. 4.

Overlap of genes coexpressed in the mouth-polyphenism with environmentally sensitive loci from more ancient processes. (A) Coexpressed genes in the Pristionchus pacificus mouth polyphenism with putative homologs whose expression is induced by starvation in Caenorhabditis elegans. Only genes with putative homologs in both species are counted. (B) Coexpressed genes both in the P. pacificus mouth polyphenism and during P. pacificus dauer diapause.

Fig. 5.

Phylogenetic context for Diplogastridae and genome-wide comparisons of taxon-restricted genes. Boldface font indicates species with original genome sequences. (A) Species tree for Diplogastridae inferred from 778 genome-wide orthologs. Diagrams to right show mouthpart diversity of Pristionchus and genera with species sequenced here, including nematodes with polyphenism (Eu morph shown) and those with a single assimilated morph. In contrast, Bunonema has relatively simple internal mouthparts, which are also the ancestral state for the sister group of Diplogastridae (Rhabditidae). Asterisks indicate 100% node support (both BS and, for tree inferred under a coalescent model, LPP). Representations of diplogastrid genera after Susoy et al. (2015). (B) Numbers of strict orthologs (as defined by reciprocal best BLAST), both genome-wide and of genes in P. pacificus polyphenism coexpression networks, conserved between P. pacificus and other species.

Fig. 6.

Gene-family evolution of loci contributing to coexpression networks of the Pristionchus pacificus mouth polyphenism. (A) Gene-family evolution across Diplogastridae. Values show numbers of gene-family expansions (left of each vertical bar) and contractions (right of bar) next to each internal branch and, for terminal branches, to right of taxon name. Yellow values, genome-wide events; blue values, events including homologs of polyphenism genes. (B) Network connectivity, measured as module membership (MM), of genes in all coexpression networks and networks specific to the mouth polyphenism.