Data for: A histone demethylase links the loss of plasticity to nongenetic inheritance and morphological change

Plasticity is a widespread feature of development, enabling phenotypic change based on the environment. Although the evolutionary loss of plasticity has been linked both theoretically and empirically to increased rates of phenotypic diversification, molecular insights into how this process might unfold are generally lacking. Here, we show that a regulator of nongenetic inheritance links evolutionary loss of plasticity in nature to changes in plasticity and morphology as selected in the laboratory. Across nematodes of Diplogastridae, which ancestrally had a polyphenism, or discrete plasticity, in their feeding morphology, we use molecular evolutionary analyses to screen for change associated with independent losses of plasticity. Having inferred a set of ancestrally polyphenism-biased genes from phylogenetically informed gene-knockouts and gene-expression comparisons, selection signatures associated with plasticity’s loss identify the histone H3K4 di/monodemethylase gene spr-5/LSD1/KDM1A. Manipulations of this gene affect both sensitivity and variation in plastic morphologies, and artificial selection of manipulated lines drives multigenerational shifts in these phenotypes. Our findings thus give mechanistic insight into how traits are modified as they traverse the continuum of greater to lesser environmental sensitivity.

Methods
These data and R code  correspond to
-identification of morph-biased genes in Pristionchus fissidentatus (Pfi) constitutive mutants (files labeled MB),
-results from aBSREL tests of episodic, diversifying selection on assimilated species (files labeled PS),
-results from RELAX tests of weakened selection on assimilated species (files labeled RS),
-phenotyping of mouth form in various experiments in Pfi and Pristionchus pacificus (Ppa) (files labeled PTYPE), and
-geometric morphometrics of mouth form in spr-5 and wild-type lines (files labeled GM)
-inferred potential effects of amino acid substitutions in Pristionchus bucculentus and Pristionchus elegans (IA)