DOI: 10.5061/dryad.98sf7m0nm
title: Data for: A histone demethylase links the loss of plasticity to nongenetic inheritance and morphological change

description: 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.
description: These data and R code  correspond to<br>-identification of
 morph-biased genes in <em>Pristionchus</em>
 <em>fissidentatus</em> (Pfi) constitutive mutants (files
 labeled MB),<br>-results from aBSREL tests of episodic, diversifying
 selection on assimilated species (files labeled PS),<br>-results
 from RELAX tests of weakened selection on assimilated species (files
 labeled RS),<br>-phenotyping of mouth form in various experiments in
 Pfi and <em>Pristionchus</em> <em>pacificus</em>
 (Ppa) (files labeled PTYPE), and<br>-geometric morphometrics of
 mouth form in spr-5 and wild-type lines (files labeled
 GM)<br>-inferred potential effects of amino acid substitutions in
 <em>Pristionchus</em> <em>bucculentus</em> and
 <em>Pristionchus</em> <em>elegans</em>
 (IA)
description: R, Excel or similar spreadsheet software, text editor
description: # A histone demethylase links the loss of plasticity to nongenetic
 inheritance and morphological change --- 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) ## Description
 of the Data and file structure ### MB files *
 MB_Polyphenism.gene.lists.xlsx: Excel file with three tabs. Tabs one and
 two include the list of polyphenism genes identified for P. fissidentatus
 (Pfi) and P. pacificus. Columns indicate the morph a gene is associated
 with based on weighted gene co-expression network analysis (WGCNA_Morph)
 or differential expression analysis (Deseq_morph), whether these two match
 (N/A if only analysis is applicable) , a summary of the gene's match
 type (the same between analysis, disagreement between them, or only a
 single analysis applies), and the final morph bias assigned to the gene.
 If there was disagreement, the Deseq morph was chosen In columns, B and C,
 N/A indicates that gene was not present in that analysis result. The third
 tab includes the 'core' list of genes. Column D shows the best
 match of column B to the Ppa El Paco genome with V3 annotations. Column E
 is the assigned annotation based on Column D's best match to C.
 elegans. Useful for sorting and identifying candidate polyphenism
 associated genes. * MB_pfi_wgcna.R: R code for weighted gene co-expression
 network analysis of Pfi mutant gene expression data * MB_pfi.deseq2.R: R
 code for differential expression analysis of Pfi mutant gene expression
 data * MB_pfi.wgnca.geneInfo.csv: Comma-separated file summarizing module
 membership of Pfi genes. This file has a row for each gene and its morph
 association and module membership statistics for each module described in
 wgcna.R analysis * MB_pfi.mutants.counts.table.txt: Tab-separated file
 containing expression counts used as input for R scripts ### PS files
 PS_absrel.test.results.xlsx: Excel file with five tabs labeled for species
 contained therein. Columns indicate orthogroup to which a gene belongs,
 the gene name, the p-value, and the false discovery rate (fdr) corrected
 p-value. For individual species tabs, there is additionally the best
 match, if any, to the Pristionchus pacificus V3 genome annotation (PPA
 anno) and corresponding gene ID (Ppa gene) and morph bias of the gene
 (Poly morph) if any. These data might be useful for identifying genes
 based on morph association, gene name, or significance level. ### RS files
 RS_relax.test.results.xlsx: Excel file with five tabs labeled for
 contents: all results, significant results, significant relaxed results,
 P. bucculentus + P. elegans significant relaxed results, and D. magnus +
 L.texanum significant relaxed results. These data might be useful for
 identifying genes based on morph association, gene name, or significance
 level. Under all results, orthogroups in Dmag and Ltex are the same and
 Pel and Pbuc are the same, but those of Dmag and Ltex do not correpsond to
 the same groups as Pbuc and Pel. Columns denote the test statistic from
 HyPhy's likelihood ratio test (LRT), the corresponding p-value (P),
 the relaxation intensity parameter from Hyphy (Relax parameter), the
 orthogroup, species, false discovery rate corrected p-value (fdr), a
 representative gene from a given orthogroup of genes, the representativ
 egene's best match to Pristionchus pacificus V3 genome (if any) and
 the gene's morph bias, if any. ### PTYPE files * PTYPE_pfi.R: R code
 for assembling Pfi wild-type mouth form data into a dataframe and
 analyzing them * PTYPE_spr5.R: R code for assembling dataframes of mouth
 form data from various spr-5 experiments and analyzing the data *
 PTYPE_spr5.plasticity.R: R code for assembling dataframes of mouth form
 data from environmental induction experiments using spr-5 mutants *
 PTYPE_spr5.rs5200b.plasticity.R: R code for assembling dataframes of mouth
 form data from environmental induction experiments using spr-5 mutants in
 RS5200B background ### GM files * GM_spr5_initial_geomorph.rmd: R markdown
 file for initial analysis of spr-5 mutant and wild-type geometric
 morphometric data * GM_spr5_geomorph_AS.rmd: R markdown file file for
 analysis of spr-5 mutant geometic morphometric data following artificial
 selection * GM_NGIAS.lands_final.txt: Landmark data as input for
 GM_spr5_geomorph_AS.rmd file * GM_lands.final.txt: Landmark data as input
 for GM_spr5_initial_geomorph.rmd file * GM_spr5.double.mutant.rmd: R
 markdown file file for analysis of spr-5 mutant and eud-1 overexpression
 lines * GM_lands.double.txt: Landmark data as input for
 GM_lands.double.mutant.rmd file ### IA files *
 IA_inferred_ancestor_plus_Pbu.Pel.aln: Alignment of SPR-5 amino acid for
 P. bucculentus, P. elegans, and the inferred amino acid sequence for their
 shared node * IA_RAxML_bestTree_allPristionchus-rooted.tre: Tree file of
 the rooted, manually curated Pristionchus spr-5 gene tree *
 IA_spr5_functional_changes.xlsx: Excel file summarizing potential effects
 on SPR-5 function of sites likely experiencing and not experiencing
 positive selection in P. bucculentus and P.elegans. Amino acid positions
 used for the Phyre2 input and from the inferred ancestor are noted and
 aligned against each other and SPR-5 protein domains in the 'Phyre to
 inferred position' tab. This tab also contains mutational sensitivity
 (Mut. sens), site conservation (Conservation), presnece of catalytic
 activity, presence of pockets, and interface sites (PI site). The second
 and third tabs indicated the position, the ancestral amino acid at that
 position, the amino acid of the focal species, and whether or not that
 site had evidence of positive selection. These tabs further show the
 number of sites with and without positive selection evidence in each of
 the SPR-5 protein domains.