Genotype by genotype indirect genetic effects (G × G IGEs) occur when the phenotype of an individual is influenced by an interaction between its own genotype and those of neighbour individuals. Little is known regarding the relative importance of G × G IGEs compared with other forms of direct and indirect genetic effects. We quantified the relative importance of IGEs in the filamentous fungus Aspergillus nidulans, a species in which IGEs are likely to be important as air-borne social interactions are known to affect growth. We used a collection of distantly related wild isolates, lab strains and a set of closely related mutation accumulation lines to estimate the contribution of direct and indirect genetic effects on mycelium growth rate, a key fitness component. We found that indirect genetic effects were dominated by G × G IGEs that occurred primarily between a focal genotype and its immediate neighbour within a vertical stack, and these accounted for 11% of phenotypic variation. These results indicate that G × G IGEs may be substantial, at least in some systems, and that the evolutionary importance of these interactions may be underappreciated, especially in microbes. We advocate for a wider use of the IGE framework in both applied (for example, choice of varietal mixtures in plant breeding) and evolutionary genetics (kin selection/kin competition studies).
Usage Notes:
Dataset used for the analyses
Mycelium growth rate data used of the linear mixed model analyses
DataRode_et_al2017.csv
Script for mixed model analyses
Script for the analyses with ASReml-R (see http://www.vsni.co.uk/downloads/asreml/version-3-upgrade/)
Mixed_Model_Analyses.Rmd
Script and figures from mixed model analyses
Output when knitting the file "Mixed_Model_Analyses.Rmd" using Rstudio (https://www.rstudio.com/)
PowerAnalyses.Rmd: Code for the power analyses
Mixed_Model_Analyses.html
Script for power analyses
Code for power analyses
PowerAnalyses.Rmd
Script and figures from power analyses
Output when knitting the file "PowerAnalyses.Rmd" using Rstudio (https://www.rstudio.com/)
PowerAnalyses.html
R environment for Fig. S4
R environment including the 1000 simulations for Fig. S4 (can be loaded using the command: "load(SimulFigS4new.R)")
SimulFigS4new.R
R environment for Fig. S5
R environment including the 1000 simulations for Fig. S5 (can be loaded using the command: "load(SimulFigS5new.R)")
SimulFigS5new.R
Estimates of the direct genetic effects
Estimates of the direct genetic effects of the 41 strains
DGEGenotypicValues20170113.csv
Estimates of the G x G indirect genetics effects
Estimates of the 417 GxG indirect genetic effects in the best model for dataset3 analyses (used for Fig. S6)
GbyGGenotypicValues20170113.csv