Fig. 6: Indirect (social) genetic effects on microbiome phenotypes (Mic-IGE).

A Schematic illustrating how Mic-IGE arise from the coupling of host genetic effects (Mic-DGE) and horizontal transmission. B QQ plot comparing the observed Mic-IGE −log₁₀ p-values to the Mic-IGE −log₁₀ p-values values expected under the null hypothesis of no Mic-IGE (p-values from LRT, see “Methods” section on Mic-IGE). We show in Supplementary Fig. 12 that Mic-IGE p-values are calibrated, i.e., follow the expected uniform distribution in the absence of Mic-IGE. C Bar plots comparing the total genetic variance explained by Mic-DGE, Mic-IGE and their covariance to the genetic variance explained by Mic-DGE in a model not including Mic-IGE. The grey boxplots show the total genetic variance when cage mates’ assignments are permuted (hence Mic-IGE cannot be captured). Supplementary Fig. 13A shows the variance explained by Mic-IGE when cage mates' assignments are permuted. D DGE (e.g., Mic-DGE) estimates from 1000 phenotypes simulated with DGE, IGE and cage effects and analysed either with a model including IGE or not. See Supplementary Fig. 14 for the MI cohort.