Data from: Pea aphid wing plasticity variation has a multigenic basis
Data files
Dec 23, 2025 version files 21.42 KB
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genotype_data.csv
1.22 KB
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phenotype_data.csv
14.42 KB
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phenotype_parents_lowdensity_data.csv
213 B
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README.md
5.57 KB
Abstract
Phenotypic plasticity, the ability of a single genotype to produce a range of phenotypes in response to environmental cues, can exhibit genetic variation like any trait. Discovering the genetic basis of plasticity and plasticity variation is critical to understand how populations will respond to the ongoing environmental challenges brought about by, for example, climate change. Here, we investigate the genetic basis of the pea aphid (Acyrthosiphon pisum) wing plasticity variation. In this species, genetically identical, highly fecund wingless and dispersive winged individuals are produced by pea aphid mothers in uncrowded versus crowded environments, respectively. We focus specifically on the genetic basis of the propensity to produce winged individuals in response to crowding. We crossed a low- to high-plasticity line and examined plasticity variation in backcross progeny (F1 x low parent), finding that differences between lines had a strong genetic component and that multiple loci likely contributed to this variation. We employed RFLP genotyping to assess a candidate locus that we hypothesize may contribute to variation in wing plasticity. This project also has an RNAseq component, which can be accessed via the NCBI Sequence Read Archive (PRJNA1172746).
Dataset DOI: https://doi.org/10.5061/dryad.rbnzs7hnz
Description of the data and file structure
This repository contains data and analysis scripts related to the paper "Pea aphid wing plasticity variation has a multigenic basis" (Driscoll et al. 2025). In this work, we investigated the genetic basis of the pea aphid (Acyrthosiphon pisum) wing plasticity variation. We crossed a low to a high plasticity line and examined plasticity variation in backcross progeny (F1 x low parent). We employed RFLP genotyping to assess a candidate locus that we hypothesize may contribute to variation in wing plasticity. This repository includes plasticity phenotype data as well as RFLP genotype data, along with the relevant analysis and visualization scripts.
Files and variables
File: phenotype_data.csv
Description: Plasticity phenotype data for a laboratory cross between low and high plasticity lines, including phenotypes for the low plasticity parent line, the high plasticity parent line, F1, and backcross progeny (F1 x low parent).
Variables
- cross: The role of this aphid line in the laboratory cross - parent, F1, or backcross. "low_parent" = low plasticity parent, "high_parent" = high plasticity parent, "F1" = F1 of low x high parents, "backcross" = backcross progeny from F1 x low parent.
- Line: The name of the aphid line that was phenotyped. "HP" = high plasticity parent, "LP" = low plasticity parent, "F1" = single F1 offspring; lines beginning with "I" are different backcross progeny from F1 x LP.
- color_morph: The body color of the aphid, pink or green.
- testing_round: The round/batch of phenotype testing in which the data was collected. Plasticity phenotype testing was performed in batches rather than all at once because the test is time and labor-intensive.
- crowding_replicate: Which crowding dish did the phenotype data was obtained from? Each crowding dish contained 12 aphids from the given line, and three or more replicate dishes were tested in parallel or in sequence for each line.
- total_mom: The number of mother aphids from the dish (out of 12) that were found alive at the end of 24 hours of crowding and 24 hours of reproduction on plants.
- total_winged: The total number of winged offspring produced by mothers in this crowding dish during 24 hours of post-crowding reproduction.
- total_wingless: The total number of wingless offspring produced by mothers in this crowding dish during 24 hours of post-crowding reproduction.
- total_chimeric: The total number of chimeric (wing-asymmetric, or with other unusual wing phenotypes that are not straightforwardly winged or wingless) offspring produced by mothers in this crowding dish during 24 hours of post-crowding reproduction.
- offspring: The total number of offspring produced by mothers in this crowding dish, including winged, wingless, and chimeric (i.e., total_winged + total_wingless + total_chimeric = offspring).
- num_plants: The number of plants (fava bean seedlings) that mothers were placed on and offspring were found on. Generally, the 12 mother aphids from a crowding dish were distributed across 3 plants, with 4 mother aphids placed on each plant.
- percent_winged: The percentage of all offspring produced by mothers in this crowding dish that were winged (i.e., total_winged/offspring * 100).
File: phenotype_parents_lowdensity_data.csv
Description: Plasticity phenotype data for low plasticity and high plasticity parent lines of the cross, taken under low conspecific density conditions to set a baseline for plastic changes in response to crowding.
Variables
- line: The name of the aphid line that was phenotyped. "HP" = high plasticity parent, "LP" = low plasticity parent.
- winged: The number of winged offspring produced.
- wingless: The number of wingless offspring produced.
- total_offspring: The total number of offspring produced, including both winged and wingless (i.e., winged + wingless = total_offspring).
- percent_winged: The percentage of all offspring produced that were winged (i.e., winged/total_offspring * 100).
File: genotype_data.csv
Description: RFLP genotyping data of all lines in the cross (parents, F1, backcrosses) at one locus of interest in the plasticity and two control loci.
Variables
- line: The name of the aphid line that was genotyped. "HP" = high plasticity parent, "LP" = low plasticity parent, "F1" = single F1 offspring; lines beginning with "I" are different backcross progeny from F1 x LP.
- auto_1_locus: The genotype at the locus on autosome 1. This is the locus of interest for the plasticity. "hom cut" = homozygous for the allele which is cut by the enzyme, "hom uncut" = homozygous for the allele which is not cut by the enzyme, "het" = heterozygote.
- auto_2_locus: The genotype at the locus on autosome 2. This is a control locus. "hom cut", "hom uncut", and "het" are as above.
- auto_3_locus: The genotype at the locus on autosome 3. This is a control locus. "hom cut", "hom uncut", and "het" are as above.
Code/software
Two analysis/visualization scripts are included, wpv_statistical_analysis_part1. Rmd and wpv_statistical_analysis_part2.Rmd. These are R Markdown files created by the authors that include descriptive headings, R code for analysis and visualization, and code comments. R software and package versions are all listed near the top of wpv_statistical_analysis_part1.Rmd.