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To take into account the uncertainty of phenotypic model under which multiple rare variants jointly influence phenotype, we simulated the phenotype under three phenotypic models.
We cast the problem of determining phenotypic models as that of finding representative time series for each phenotype cluster in the data.
In table S1, we list the interaction of various phenotypic models and genotypic encoding schemes by various tests.
As shown in figure 3, all tests have decreased power with increased gene length in all phenotypic models.
Note that other intermediate phenotypic models could also be the case for the trait, which will not be investigated in this study.
The proposed alternative phenotypic models, such as the network model, the mutualism model, and the index variable view, do not necessarily appeal to causal latent traits.
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Our three simulation studies suggest that at least part of the missing heritability problem of complex phenotypes may originate in misspecification of the phenotypic model.
We used the phenotypic model to simulate the behavior of individual phenotypes in various environments and measured the performance of each phenotype based on metrics appropriate to each ecological challenge.
Because the assumption of shared genetic basis among African populations could be violated in the case of the Pygmy phenotype, we pursued a second analysis with no premises regarding the phenotypic model.
Irrespective of the phenotypic model of choice, optimized modelling of the phenotypic part of the genotype-phenotype data improves the power to detect genetic variants.
The phenotypic model used to link drift load to phenotypic complexity was first formalized by R. A. Fisher [11].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com