DOI: 10.5061/dryad.1zcrjdg33
title: Data from: Genomic parallelism defines repeated evolution of an inducible offense

description: The study for which these data were generated is summarized as follows: A
 common developmental response to resource competition is an inducible
 offense, which involves the facultative predation of competitors. At its
 extreme, this response involves the development of alternative phenotypic
 morphs, or polyphenism. However, how polyphenism evolves to meet
 ecological challenges, such as competitor species, is unknown. Using
 replicated experimental evolution, during which starved nematodes could
 consume heterospecific competitors, we investigated whether induction of a
 predatory morph could evolve and how generalizable the genetic basis of
 this change is. Fifty generations of evolution across multiple populations
 resulted in parallel changes in higher morph induction and parallel
 genomic responses, including repeated selection for a specific
 transcription-factor binding-site variant. In tandem, we artificially
 selected directly for tooth morphology and drove the predatory morph near
 fixation. That trait-specific selection promoted greater changes in
 predatory morph induction than experimental evolution indicates that
 polyphenism evolution is balanced by selection for whole-organism
 performance. Our results thus describe the predictability by which a
 resource polyphenism evolves amid scarce resources. These data include
 phenotypic and intermediate genome-wide data for analyzing shifts in
 phenotype production over generations between environments, effects of
 mutation on phenotype production, and divergence in allele frequencies
 among populations.
description: These data correspond to phenotypic and genetic data from an
 experimental evolution and artificial selection study exploring the
 genetic bases of polyphenism evolution in a new environment. Primary data
 include counts of predatory and microbivore feeding morphs over
 generations, downstream analysis of pool-sequencing data from 54
 populations of nematodes, functional phenotype and genetic information of
 mutant lines, and code for processing and analyzing the data.
description: # Data from: **Genomic parallelism defines repeated evolution of an
 inducible offense**
 [https://doi.org/10.5061/dryad.1zcrjdg33](https://doi.org/10.5061/dryad.1zcrjdg33) ## Description of the data and file structure *Pristionchus exspectatus* nematode populations were allowed to evolve in a microbivore-favoring environment or a predator-favoring environment. Morph was determined for 50 males and females every generation for 50 generations. Periodically, the morph of populations evolving in the predatory environment was also determined in the microbivore environment. In addition, artificial selection was used to specifically target the mouth morphology of worms. Predatory worms were selected for 20 generations. At the same time, control populations, where morphology was not considered when founding the next generation, were also maintained for 20 generations. Twenty-two population pairs from experimental evolution and five population pairs from artificial selection were then sequenced at the end of their experiments. The pool-seq data was used to generate sync files that served as input for downstream analysis of allele frequency divergence and various other intermediate files. Finally, functional tests of candidate loci was performed using CRISPR/Cas9 and the resulting phenotypic data were collected for wild-type and mutant *P. pacificus* individuals reared in different environments. The .sync files contain the chromosome name, the specific base position on that chromosome, the nucleotide bases and the read-groups. ### Files and variables #### File: AS.5kb.windows.parallel.sig.txt **Description:**  Windows showing significant parallel divergence between artificial selection conditions. ##### Variables * Chromosome: Chromosome * Window_Start: Window starting position * Window_Stop: Window ending position * GeoPvalue: Geometric mean q-value based on SNPs within that window. * Pos: Window position #### File: AS.5kb.windows.parallel.all.txt **Description:**  All windows from parallel divergence test between artificial selection conditions. ##### Variables * Chromosome: Chromosome * Window_Start: Window starting position * Window_Stop: Window ending position * GeoPvalue: Geometric mean q-value based on SNPs within that window. * Pos: Window position #### File: AS.female.reversal.data.txt **Description:** Phenotype data for females from predator artificial selection lines when reared in the control environment. ##### Variables * Line: The line * Generation: The generation for which the data are collected * Eu: The percent of individuals with the Eu (predatory) phenotype #### File: AS.male.reversal.data.txt **Description:** Phenotype data for males from predator artificial selection lines when reared in the control environment. ##### Variables * Line: The line * Generation: The generation for which the data are collected * Eu: The percent of individuals with the Eu (predatory) phenotype #### File: AS_female.data.txt **Description:** Phenotype data for females from artificial selection lines over generations. ##### Variables * Line: The line * 0: Generation before the experiment * 1:  Percent Eu at G1 * 2: Percent Eu at G2 * 3: Percent Eu at G3 * 4: Percent Eu at G4 * 5: Percent Eu at G5 * 6: Percent Eu at G6 * 7: Percent Eu at G7 * 8: Percent Eu at G8 * 9: Percent Eu at G9 * 10: Percent Eu at G10 * 11: Percent Eu at G11 * 12: Percent Eu at G12 * 13: Percent Eu at G13 * 14: Percent Eu at G14 * 15: Percent Eu at** **G15 * 16: Percent Eu at G16 * 17: Percent Eu at G17 * 18: Percent Eu at G18 * 19: Percent Eu at G19  * 20: Percent Eu at G20 #### File: AS_male.data.txt **Description:** Phenotype data for males from artificial selection lines over generations. ##### Variables * Line: the line * 0: Generation before the experiment * 1:  Percent Eu at G1 * 2: Percent Eu at G2 * 3: Percent Eu at G3 * 4: Percent Eu at G4 * 5: Percent Eu at G5 * 6: Percent Eu at G6 * 7: Percent Eu at G7 * 8: Percent Eu at G8 * 9: Percent Eu at G9 * 10: Percent Eu at G10 * 11: Percent Eu at G11 * 12: Percent Eu at G12 * 13: Percent Eu at G13 * 14: Percent Eu at G14 * 15: Percent Eu at** **G15 * 16: Percent Eu at G16 * 17: Percent Eu at G17 * 18: Percent Eu at G18 * 19: Percent Eu at G19  * 20: Percent Eu at G20 #### File: EE.5kb.windows.cmh.all.txt **Description:** All windows from parallel divergence test between experimental evolution conditions. ##### Variables * Chromosome: Chromosome - Window_Start: Window starting position - Window_Stop: Window ending position - GeoPvalue: Geometric mean q-value based on SNPs within that window #### File: EE.5kb.windows.parallel.sig.txt **Description:** Significant windows from parallel divergence test between experimental evolution conditions. ##### Variables * Chromosome: Chromosome - Window_Start: Window starting position - Window_Stop: Window ending position - GeoPvalue: Geometric mean q-value based on SNPs within that window - Pos: Window position #### File: AS.cmh.sig.snps.txt **Description:** Significant SNPs from parallel divergence test between artificial selection conditions. ##### Variables * test_statistic: The CMH test statistic * p.value: The test p-value * fdr: The false discovery rate corrected p-value (q-value) * Chromosome: The chromosome * position: The position on the chromosome #### File: EE.all.window.Fst.txt **Description:** Fst values between experimental evolution population pairs for windows across the genome ##### Variables * Chromosome: Chromosome * Start: Window start * End: Window end * Fst: Fst value * nSNPs: Number of SNPs contributing to Fst calculation * SourceFile: The sync file for that population pair #### File: EE.5kwindows.labeled.Fst.txt **Description:** A summary of characteristics for windows across the genome for experimental evolution populations. ##### Variables * Chromosome: The chromosome * Window_Start: Window start * Window_Stop: Window end * GeoPvalue: That window's geometric mean of q-values from that line's chi-square test of divergence * window.type: That window's classification as parallel, idiosyncratic, or none. * Fst: The Fst value for that window * SourceFile: The population pair * Address: Merged chromosome and position #### File: EE.chisq.sig.5kwindows.txt **Description:**  ##### Variables * Chromosome: The chromosome * Window_Start: Window start * Window_Stop: Window end * GeoPvalue: That window's geometric mean of q-values from that line's chi-square test of divergence - Pos: Window position - file: Population pair #### File: EE.cmh.sig.snps.txt **Description:**  Information on SNPs showing significant parallel divergence during experimental evolution. ##### Variables * test_statistic: CMH test statistic * p.value: P-value of the CMH test * fdr: The false discovery rate corrected p-value (q-value) * Chromosome: The chromosome * position: The position on the chromosome #### File: EE.female.reversal.data.txt **Description:** Phenotype data for females from predatory environment lines when reared in the microbivore environment. ##### Variables * Line: The line * Generation: The generation for which the data are collected * Eu: The percent of individuals with the Eu (predatory) phenotype #### File: EE.male.reversal.data.txt **Description:** Phenotype data for males from predatory environment lines when reared in the microbivore environment. ##### Variables * Line: The line * Generation: The generation for which the data are collected * Eu: The percent of individuals with the Eu (predatory) phenotype #### File: EE.parallel.blocks.delimited.txt **Description:** The locations of blocks of parallel divergence among experimental evolution populations ##### Variables * Chromosome: The chromosome for the block * merged_group_final: The block's number * Window_Start: The start of the block * Window_Stop: The end of the block * Merged_Window_Count: The number of windows that ended up merged * win_size: The size of the block in base pairs #### File: EE_female.data.txt **Description:** Phenotype data for females from experimental evoution lines over generations. ##### Variables * Line: The line * 0: Generation before the experiment * 1:  Percent Eu at G1 * 2: Percent Eu at G2 * 3: Percent Eu at G3 * 4: Percent Eu at G4 * 5: Percent Eu at G5 * 6: Percent Eu at G6 * 7: Percent Eu at G7 * 8: Percent Eu at G8 * 9: Percent Eu at G9 * 10: Percent Eu at G10 * 11: Percent Eu at G11 * 12: Percent Eu at G12 * 13: Percent Eu at G13 * 14: Percent Eu at G14 * 15: Percent Eu at** **G15 * 16: Percent Eu at G16 * 17: Percent Eu at G17 * 18: Percent Eu at G18 * 19: Percent Eu at G19  * 20: Percent Eu at G20 * 21: Percent Eu at G21 * 22: Percent Eu at G22 * 23: Percent Eu at G23 * 24: Percent Eu at G24 * 25: Percent Eu at G25 * 26: Percent Eu at G26 * 27: Percent Eu at G27 * 28: Percent Eu at G28 * 29: Percent Eu at G29 * 30: Percent Eu at G30 * 31: Percent Eu at G31 * 32: Percent Eu at G32 * 33: Percent Eu at G33 * 34: Percent Eu at G34 * 35: Percent Eu at G35 * 36: Percent Eu at G36 * 37: Percent Eu at G37 * 38: Percent Eu at G38 * 39: Percent Eu at G39 * 40: Percent Eu at G40 * 41: Percent Eu at G41 * 42: Percent Eu at G42 * 43: Percent Eu at G43 * 44: Percent Eu at G44 * 45: Percent Eu at G45 * 46: Percent Eu at G46 * 47: Percent Eu at G47 * 48: Percent Eu at G48 * 49: Percent Eu at G49 * 50: Percent Eu at G50 #### File: EE_male.data.txt **Description:** Phenotype data for females from experimental evoution lines over generations. ##### Variables * Line: The line * 0: Generation before the experiment * 1:  Percent Eu at G1 * 2: Percent Eu at G2 * 3: Percent Eu at G3 * 4: Percent Eu at G4 * 5: Percent Eu at G5 * 6: Percent Eu at G6 * 7: Percent Eu at G7 * 8: Percent Eu at G8 * 9: Percent Eu at G9 * 10: Percent Eu at G10 * 11: Percent Eu at G11 * 12: Percent Eu at G12 * 13: Percent Eu at G13 * 14: Percent Eu at G14 * 15: Percent Eu at** **G15 * 16: Percent Eu at G16 * 17: Percent Eu at G17 * 18: Percent Eu at G18 * 19: Percent Eu at G19  * 20: Percent Eu at G20 * 21: Percent Eu at G21 * 22: Percent Eu at G22 * 23: Percent Eu at G23 * 24: Percent Eu at G24 * 25: Percent Eu at G25 * 26: Percent Eu at G26 * 27: Percent Eu at G27 * 28: Percent Eu at G28 * 29: Percent Eu at G29 * 30: Percent Eu at G30 * 31: Percent Eu at G31 * 32: Percent Eu at G32 * 33: Percent Eu at G33 * 34: Percent Eu at G34 * 35: Percent Eu at G35 * 36: Percent Eu at G36 * 37: Percent Eu at G37 * 38: Percent Eu at G38 * 39: Percent Eu at G39 * 40: Percent Eu at G40 * 41: Percent Eu at G41 * 42: Percent Eu at G42 * 43: Percent Eu at G43 * 44: Percent Eu at G44 * 45: Percent Eu at G45 * 46: Percent Eu at G46 * 47: Percent Eu at G47 * 48: Percent Eu at G48 * 49: Percent Eu at G49 * 50: Percent Eu at G50 #### File: SW_Exp_Gene_PexsCon_ver5_100w-100s.txt **Description:** Expressed gene content for 100-kb windows from Yoshida, K., Rödelsperger, C., Röseler, W., Riebesell, M., Sun, S., Kikuchi, T., & Sommer, R. J. (2023). Chromosome fusions repatterned recombination rate and facilitated reproductive isolation during Pristionchus nematode speciation. *Nature Ecology & Evolution*, *7*(3), 424-439. ##### Variables * Chromosome: Chromosome * Start: Window start * End: Window end * Count: Number of expressed genes #### File: SW_GCcontent_PexsCon_ver5_100w-100s.txt **Description:** GC (and AT) content for 100-kb windows from Yoshida, K., Rödelsperger, C., Röseler, W., Riebesell, M., Sun, S., Kikuchi, T., & Sommer, R. J. (2023). Chromosome fusions repatterned recombination rate and facilitated reproductive isolation during Pristionchus nematode speciation. *Nature Ecology & Evolution*, *7*(3), 424-439. ##### Variables * Chromosome: Chromosome * Start: Window start * End: Window end * AT_count: The number of A or T in the window * GC_count: The number of G or C in the window #### File: EEAS.overlap.test.results.txt **Description:** Results from random bootstrapping to determine number of expected shared windows of parallel divergence between experimental evolution and artificial selection studies ##### Variables * total_samples: The total number of samples based on the sum of actual experimental evolution and artificial selection windows with parallel divergence * total_shared_samples: The number of samples that overlap when the pool of experimental evolution and the pool artificial selection parallel windows are each sampled from at random #### File: SW_gene_density_PexsCon_ver5_100w-100s.txt **Description:** The number of genes in 100-kb windows from Yoshida, K., Rödelsperger, C., Röseler, W., Riebesell, M., Sun, S., Kikuchi, T., & Sommer, R. J. (2023). Chromosome fusions repatterned recombination rate and facilitated reproductive isolation during Pristionchus nematode speciation. *Nature Ecology & Evolution*, *7*(3), 424-439. ##### Variables * Chromosome: Chromosome * Start: Window start * End: Window end * Count: Number of genes #### File: ee.tbx.qpcr.data.txt **Description:** Input data for *tbx-2* gene expression analysis of populations that evolved in ancestral or predatory environment ##### Variables * Founder: The initial strain that a pair was split from * Condition: The evolutionary environment, C = control/ancestral, T= treatment/predatory * Group: Merged founder and condition for unique line combination * log2fC: The measure of gene expression, log2(fold-change) compared to control line of the that founder #### File: tbx.AGT.hap.txt **Description:** Haplotype frequences of SNPs upstream *tbx-2* for experimental evolution populations ##### Variables * Populaition: The population pair * Environment: The rearing environment: T = predatory, C = microbivore * Arcsine full: Arcsine square-root transformation of the prop.full data * Prop full: Proportion of reads with the AGT haplotype #### File: tbx.mutant.phenotypes.txt **Description:** Morph data for *P. pacificus tbx-2* enhancer mutants reared in various conditions ##### Variables * Eu: The number of predatory (Eu) individuals in the sample * St: The number of microbivore (St) individuals in the sample * % Eu: The percent of predatory (Eu) individuals in the sample * Condition: The rearing conditions * Genotype: The genotype for the sample * EJR10: wild-type * tbx-2 (v2): *iub54* * tbx-2 (v34): *iub55* * tbx-2 (v44): *iub56* #### File: Genotype_data_Pexs_EMS_hybrids.txt **Description:** Genotype data serving as input for recombination rate calculations from Yoshida, K., Rödelsperger, C., Röseler, W., Riebesell, M., Sun, S., Kikuchi, T., & Sommer, R. J. (2023). Chromosome fusions repatterned recombination rate and facilitated reproductive isolation during Pristionchus nematode speciation. *Nature Ecology & Evolution*, *7*(3), 424-439 #### File: EE.cmh.all.snps.txt **Description:** Results from CMH test of parallel divergence for all SNPs from experimental evolution study ##### Variables * test_statistic: The CMH test statistic * p.value: The p-value of the CMH test * fdr: The false discovery rate corrected p-value (q-value) * Chromosome: The chromosome  * position: The position on the chromosome #### File: Genotype_Pexs_EMS_hybrid_RQTL.csv **Description:** QTL data serving as input for recombination rate calculations from Yoshida, K., Rödelsperger, C., Röseler, W., Riebesell, M., Sun, S., Kikuchi, T., & Sommer, R. J. (2023). Chromosome fusions repatterned recombination rate and facilitated reproductive isolation during Pristionchus nematode speciation. *Nature Ecology & Evolution*, *7*(3), 424-439 #### File: randomized_output.csv **Description:** Results from CMH tests when experimental evolution populations were paired at random 500 times ##### Variables * Iteration: The number of the iteration of pairing * NumSignificant: The number of significantly parallel SNPs from each iteration * TotalLines: The total number of SNPs evaluated in the iteration #### File: mapdata_Pexspectaus_EMS_hybrids.Robj **Description:** Genome map data serving as input for recombination rate calculations from Yoshida, K., Rödelsperger, C., Röseler, W., Riebesell, M., Sun, S., Kikuchi, T., & Sommer, R. J. (2023). Chromosome fusions repatterned recombination rate and facilitated reproductive isolation during Pristionchus nematode speciation. *Nature Ecology & Evolution*, *7*(3), 424-439 #### File: ee.cmh.sig.sync **Description:** Pool-seq sync file restricted to positions showing significant parallel divergence in experimental evolution #### File: as.cmh.sig.sync **Description:** Pool-seq sync file restricted to positions showing significant parallel divergence in artificial selection #### File: AS.cmh.all.snps.txt **Description:** Results from CMH test of parallel divergence for all SNPs from artificial selection study ##### Variables * test_statistic: The CMH test statistic * p.value: The p-value of the CMH test * fdr: The false discovery rate corrected p-value (q-value) * Chromosome: The chromosome  * position: The position on the chromosome #### File: A.sync **Description:** Sync file for experimental evolution pair A #### File: B.sync **Description:** Sync file for experimental evolution pair B #### File: C.sync **Description:** Sync file for experimental evolution pair C #### File: ChrI.sync.txt **Description:** Sync file (as text file) for experimental evolution chromosome 1 for all populations #### File: ChrII.sync.txt **Description:** Sync file (as text file) for experimental evolution chromosome 2 for all populations #### File: EE.chisq.sig.5kwindows.labeled.txt **Description:**  Results and summary from pairwise tests of divergence for each population in experimental evolution ##### Variables * Chromosome: Chromosome * Window_Start: Window start * Window_Stop: Window end * GeoPvalue: Geometric mean of q-values from chi-square tests of divergence in the window * Pos: position of the window * file: Population pair * Address: Merged chromosome and position * Address.full: Merged file, chromosome, and position * snp.type: Window classification as parallel, idiosyncratic, or none #### File: ChrIII.sync.txt **Description:** Sync file (as text file) for experimental evolution chromosome 3 for all populations #### File: ChrIV.sync.txt **Description:** Sync file (as text file) for experimental evolution chromosome 4 for all populations #### File: ChrV.sync.txt **Description:** Sync file (as text file) for experimental evolution chromosome 5 for all populations #### File: D.sync **Description:** Sync file for experimental evolution pair D #### File: E.sync **Description:** Sync file for experimental evolution pair E #### File: F.sync **Description:** Sync file for experimental evolution pair F #### File: G.sync **Description:** Sync file for experimental evolution pair G #### File: ChrX.sync.txt **Description:** Sync file (as text file) for experimental evolution chromosome X for all populations #### File: H.sync **Description:** Sync file for experimental evolution pair H #### File: I.sync **Description:** Sync file for experimental evolution pair I #### File: J.sync **Description:** Sync file for experimental evolution pair J #### File: K.sync **Description:** Sync file for experimental evolution pair K #### File: L.sync **Description:** Sync file for experimental evolution pair L #### File: M.sync **Description:** Sync file for experimental evolution pair M #### File: N.sync **Description:** Sync file for experimental evolution pair N #### File: O.sync **Description:** Sync file for experimental evolution pair O #### File: P.sync **Description:** Sync file for experimental evolution pair P #### File: Q.sync **Description:** Sync file for experimental evolution pair Q #### File: R.sync **Description:** Sync file for experimental evolution pair R #### File: S.sync **Description:** Sync file for experimental evolution pair S #### File: T.sync **Description:** Sync file for experimental evolution pair T #### File: U.sync **Description:** Sync file for experimental evolution pair U #### File: V.sync **Description:** Sync file for experimental evolution pair V #### File: as.filt.sync.ordered **Description:** Sync file combined for all artificial selection populations Raw morph data for evolving populations and mutants are provided. Sequencing data is provided in the form of 'sync' files following upstream processing from raw sequencing reads. These files are commonly used for pool-seq data and serve as input for downstream tests of allele frequency divergence. Various intermediate files based on the sequencing data are also included as input for downstream analyses. ## Code/software The code files uploaded to Zenodo are used to generate the sync files for downstream analysis and for performing the downstream analyses. Downstream analyses are performed in R and each script indicates the packages and input files it uses. It is most useful to have the scripts and data in the same directory, and some scripts might need minor adjustments to the input data file paths. Programs for processing sequencing reads and generating sync files are generated using: * bwa (index,bwa-mem) * gatk (MarkDuplicates, RealignerTargetCreator, IndelRealigner) * samtools (view, sort, index, mpileup) * PoPoolation2 (mpileup2sync.jar) ## Access information Other publicly accessible locations of the data: * Raw sequencing reads are deposited on NCBI SRA (PRJNA1196962)