DOI: 10.5061/dryad.kh18932hv
title: Inheritance of color morphs in the meadow grasshopper

description: The green-brown polymorphism in Orthoptera is a prominent example of the
 coexistence of multiple color variants, especially since this polymorphism
 is shared by many species. The processes that maintain phenotypic
 polymorphisms depend on the underlying genetic and developmental
 regulation of body coloration, but these are not well understood for
 Orthoptera. Here we report on the inheritance of the green-brown
 polymorphism in the meadow grasshopper Pseudochorthippus parallelus, a
 species with four discrete color morphs that differ in the distribution of
 green coloration across the body. We provide the most detailed analysis of
 the green-brown polymorphism to date using half-sib full-sib breeding and
 phenotyping of 4,300 offspring. The data strongly support a simple
 Mendelian control of the presence/absence of green color in different
 regions of the body, involving four autosomal loci, two of which are
 genetically linked. However, estimation of population allele and haplotype
 frequencies using probabilistic simulations shows weak linkage
 disequilibrium in the population. The contrast between pedigree and
 population linkage suggests the presence of long-standing allelic
 variation and thus corroborates that long-term balancing selection is
 acting. Our study confirms and extends our understanding of inheritance
 patterns within the Chorthippus clade, providing unprecedented insights
 into the number and linkage of loci involved. The results have
 implications for the maintenance of polymorphisms and suggest that
 fluctuations in the phenotypic composition of populations can be generated
 by the segregation of genetic variants even in the absence of fluctuating
 selection.
description: # Inheritance of color morphs in the meadow grasshopper *Pseudochorthippus
 parallelus*
 [https://doi.org/10.5061/dryad.kh18932hv](https://doi.org/10.5061/dryad.kh18932hv) ### **Environment** ``` All analyses are performed in R version 4.1.3. ``` ### **Data Files** **1. GenV_parallelus.txt** * This file contains a table with phenotypic and parental information for lab-reared offspring of the meadow grasshopper * Detailed information about this file can be found in GenV_parallelus_README. **2. InheritanceSummary_4DL.txt** * This file contains a family-wise summary of the best-fitting inheritance models. * The original data for this summary is in GenV_parallelus.txt, but this file is a processed summary used in scripts for plotting. * Detailed information about this file can be found in InheritanceSummary_4DL_README. **3. MatingAll_4DL.RData** * This file is an output of *Step1_Screening.Rmd* and is used for running the four-locus model with loci D and L linked. * The file is generated by the script, but since runtime is long, the relevant lines are commented out, and stored results from previous runs are used instead. **4. Photograph.zip** * This .zip file contains lateral and dorsal photographs of lab-reared offspring individuals. * Each photograph is tagged with metadata, including: * **Morph**: Green (uniform green), Lateral (lateral green), Dorsal (dorsal green), Brown (uniform brown). * **Sex**: Male or Female. * **Individual ID**: Corresponding to the *GenV_parallelus.txt* file. * **View**: Either "top view" or "side view" indicating the angle of the photograph. * **Forewing**: Long wing or Short wing. ### **Scripts** #### **Main Analysis Scripts** The following R Markdown files should be run in the order listed: 1. Step1_Screening.Rmd 2. Step2_FitEvaluation.Rmd 3. Step3_AlleleFrequencies.Rmd ***Note:** Step1_Screening.Rmd generates MatingAll_4DL.RData, but since runtime is long, stored results are used instead.* #### Supplementary Analysis Scripts Supplement1_ColorHeritability.Rmd and Supplement2_ColorHeritability.Rmd 1. These scripts are used to produce Supplement 1 and Supplement 2 of the manuscript. 2. Both scripts require the helper script: Helper_PlotFunctions.R. ## Description of the data and file structure GenV_parallelus: A table holding the phenotypes and parental information for lab-reared offspring of the meadow grasshoppers *Pseudochorthippus parallelus*. InheritanceSummary_4DL:A table holding a family-wise summary of the best-fitting inheritance models. The original data is in GenV_parallelus.txt, while this is a summary and interpretation that is used in scripts for plotting. ### Files and variables #### File: InheritanceSummary\_4DL.txt \**Description:**A table holding a family-wise summary of the best-fitting inheritance models. The original data is in GenV_parallelus.txt, while this is a summary and interpretation that is used in scripts for plotting. ##### Variables * FemaleID:Individual identity of the mother. * MaleID:Individual identity of the father. * MorphFemale:Color morph of the mother (B = uniform brown, D = dorsal green, L = lateral green, G = uniform green). * MorphMale:Color morph of the father (B = uniform brown, D = dorsal green, L = lateral green, G = uniform green). * MatingComb:Color morph mating combination (format: Mother morph x Father morph). * MatingComb2:Color morph mating combination (format: Mother morph / Father morph). Same information as in MatingComb in different format. * nAll:Total number of phenotyped offspring in a family. * allB:Total number of uniform brown offspring in a family. * allD:Total number of dorsal green offspring in a family. * allL:Total number of lateral green offspring in a family. * allG:Total number of uniform green offspring in a family. * nOffspr:Number of phenotyped offspring in a family after removal of exceptional individuals (OutlierInd = "x") and family cages (OutlierFam = "x"). * B:Number of uniform brown offspring in a family after removal of exceptional individuals (OutlierInd = "x") and family cages (OutlierFam = "x"). * D:Number of dorsal green offspring in a family after removal of exceptional individuals (OutlierInd = "x") and family cages (OutlierFam = "x"). * L:Number of lateral green offspring in a family after removal of exceptional individuals (OutlierInd = "x") and family cages (OutlierFam = "x"). * G:Number of uniform green offspring in a family after removal of exceptional individuals (OutlierInd = "x") and family cages (OutlierFam = "x"). * Mode:Inheritance mode. Here always '4DL' for a four-locus model with loci D and L in linkage. * Pattern:Best fitting inheritance pattern in terms of offspring morph distribution (format %B-%D-%L-%G). * PatternRecomb:Potential recombinant inheritance patterns in terms of offspring morph distribution (assuming recombination between D and L locus). * genPatUq:Potential paternal genotypes. #### File: GenV\_parallelus.txt \**Description:**A table holding the phenotypes and parental information for lab-reared offspring of the meadow grasshoppers *Pseudochorthippus parallelus.* ##### Variables * IndID:Individual identity of the offspring. * CageID:Cage identity of the cage in which the offspring was raised. * Sex:Offspring sex (F = female, M = male). * Morph:Color morph of the offspring (B = uniform brown, D = dorsal green, L = lateral green, G = uniform green). * Cohort:Indicator of the cohort in which the offspring was raised (1-5). * FemaleID:Individual identity of the mother. * MaleID:Individual identity of the father. * MorphFemale:Color morph of the mother (B = uniform brown, D = dorsal green, L = lateral green, G = uniform green). * MorphMale:Color morph of the father (B = uniform brown, D = dorsal green, L = lateral green, G = uniform green). * MatingComb:Color morph mating combination (format: Mother morph x Father morph). * MatingComb2:Color morph mating combination (format: Mother morph / Father morph). Same information as in MatingComb in different format. * OutlierInd:Indicator whether an individual was of an exceptional color morph within a family ('x' = yes, '.' = no). * OutlierFam:Indicator whether an individual was from a cage with exceptional color morph distribution ('x' = yes, '.' = no). ### Version changes: **25th March 2025:** The only modification to the dataset is the addition of a new .zip file called Photograph.zip.