Fig. 3
From: Relative abundance data can misrepresent heritability of the microbiome
The use of relative abundances leads to biased heritability estimates when there exists host genetic and/or environmental correlations between microbes. A Illustrates the effects of genetic correlations. As an example, we show three host genotypes and two microbes that are both partly heritable (h.2 = 0.5), and with a strong genetic correlation (rG = 0.99). This implies that host breeding values for the two microbes are strongly correlated. As a consequence, the average absolute abundance of both microbes varies in the same way across host genotypes. Heritabilities can accurately be estimated when using these absolute abundances (estimates for both microbes:\({\widehat{\mathrm{h}}}^{2}=0.5\)). When calculating the relative abundances, however, any variation across host genotypes disappears. This leads to an incorrect heritability estimate \({\widehat{\mathrm{\varphi }}}^{2}=0\) for both microbes, completely masking the host genetic signal. B Illustrates the effects of environmental correlations. We here show three host genotypes and two microbes that show a strong environmental correlation (rE = 0.99). As a result, this decreases the amount of variation within genotypes. Heritabilities can be accurately estimated when using the absolute abundances. However, because variation in relative abundance within each genotype is greatly reduced, one obtains a wrong heritability estimate \({\widehat{\mathrm{\varphi }}}^{2}=1\) for both species. C–E Comparison of heritability estimates when based on absolute and relative abundances, varying the environmental correlation (C), the genetic correlation (D) or both (E). \(\mathrm{\alpha }=1;\) \(\mathrm{A}=100\); \({V}_{\mathrm{P}}={\left(\frac{1}{6}\right)}^{2}\); \(\mathrm{z}=100\cdot {\mathrm{V}}_{\mathrm{P}}\); \(\frac{\upomega }{\mathrm{z}}=0.25\). Crosses show results when we estimate heritabilities by fitting a mixed effects model on simulated relative abundance data. To this end, we simulated a population of hosts (500 genotypes × 500 replicates within each genotype) (more details in Additional file 1: Appendix S2.5)