Regulators of an ancient polyphenism evolved through episodic protein divergence and parallel gene radiations

Abstract

Polyphenism is a form of developmental plasticity that transduces environmental cues into discontinuous, often disparate phenotypes. In some cases, polyphenism has been attributed to facilitating morphological diversification and even the evolution of novel traits. However, this process is predicated on the origins and evolutionary maintenance of genetic mechanisms that specify alternate developmental networks. When and how regulatory loci arise and change, specifically before and throughout the history of a polyphenism, is little understood. Here, we establish a phylogenetic and comparative molecular context for two dynamically evolving genes, eud-1 and seud-1, which regulate polyphenism in the nematode Pristionchus pacificus. This species is dimorphic in its adult feeding-structures, allowing individuals to become microbivores or facultative predators depending on the environment. Although polyphenism regulation is increasingly well understood in P. pacificus, the polyphenism is far older than this species and has diversified morphologically to enable an array of ecological functions across polyphenic lineages. To bring this taxonomic diversity into a comparative context, we reconstructed the histories of eud-1 and seud-1 relative to the origin and diversification of polyphenism, finding that homologues of both genes have undergone lineage-specific radiations across polyphenic taxa. Further, we detected signatures of episodic diversifying selection on eud-1, particularly in early diplogastrid lineages. Lastly, transgenic rescue experiments suggest that the gene's product has functionally diverged from its orthologue's in a non-polyphenic outgroup. In summary, we provide a comparative framework for the molecular components of a plasticity switch, enabling studies of how polyphenism, its regulation, and ultimately its targets evolve.

Keywords: developmental switch; gene duplication; nematodes; phenotypic plasticity; sulfotransferase; sulphatase.

Figure 1.

Diversifcation of mouthpart polyphenism among diplogastrid nematodes. Since its origin, which coincided with the evolution of movable teeth (false-coloured yellow), polyphenism has diversified in its morphology, environmental sensitivity and ecological function, shown here by representatives of Koerneria, Parapristionchus and Pristionchus. In other lineages, a single morph, together with some novel structures such as the dorsal tooth, has become fixed (e.g. Levipalatum). Tree is simplified from one previously inferred using wider taxon sampling [18]. Mouthparts shown in sagittal plane, with dorsal to right. Scale bar, 5 µm; all images to same scale. (Online version in colour.)

Figure 2.

Reconstructed history of eud-1/sul-2 switch-gene homologues in Diplogastridae and outgroups. Genes from monomorphic taxa shown in brown. Node support values are given as: bootstrap support (BS) from maximum likelihood (ML) inference of sulphatase-domain coding sequences (left, purple values); posterior probabilities following Bayesian inference (middle, red values); BS of ML inference of amino acid sequences (right, blue values). Triangles mark inferred gene duplication events; a five-pointed star indicates single inferred duplication of sul-2.2 into supergene loci eud-1 and sul-2.2.1. Asterisks indicate 100% support; dashes indicate less than 50% support or node absence. Reconstructed nodes (R) subtended by branches of arbitrary length. Letters suffixed to gene names are arbitrary by species. (Online version in colour.)

Figure 3.

Reconstructed history of seud-1/ssu-1 switch-gene homologues in Diplogastridae and outgroups. Genes from monomorphic taxa shown in brown. Node support values are given as: bootstrap support (BS) from maximum likelihood (ML) inference of sulphatase-domain coding sequences (left, purple values); posterior probabilities following Bayesian inference (middle, red values); BS of ML inference of amino acid sequences (right, blue values). Triangles mark inferred gene duplication events. Asterisks indicate 100% support; dashes indicate less than 50% support or node absence. Reconstructed nodes (R) subtended by branches of arbitrary length. Letters suffixed to gene names are arbitrary by species. (Online version in colour.)

Figure 4.

Transgenic, functional assay of sul-2 from a non-polyphenic outgroup to Diplogastridae. Mouth-polyphenism phenotypes of Pristionchus pacificus (Ppa) eud-1 mutants over-expressing eud-1/sul-2 sequences. In lines expressing the heterologous rescue construct (right two bars), a full sul-2 coding sequence from Caenorhabditis elegans (Cel) is flanked by endogenous Ppa-eud-1 regulatory sequences. Mouth-phenotypes are given as proportions per line, with confidence intervals (whiskers) calculated by a binomial test.