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In the validation stage, ten SNPs were selected based on the following criteria: 1) SNP with P < 1.0 × 10-5 for all GWAS samples; 2) when multiple SNPs showed a strong LD (r ≥ 0.8), SNPs previously reported in the literature were prior selected; 3) Clear genotyping clusters; 4) MAF ≥ 0.05.
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The specifications for these priors were selected to be relatively uninformative since little data exists to specify informative priors on the spline coefficients in our model.
A relaxed uncorrelated lognormal clock model and Yule speciation tree prior were selected.
Priors were selected as marginal reference priors.
All priors are selected to be slightly informative, since synchronization protocols and experimental conditions greatly affect posterior parameter estimates.
Priors were selected that equally divided the phenotypic variance among the random effects in the model.
Therefore uncorrelated lognormal relaxed clock priors were selected for rate comparisons.
In the simulations, the priors were selected for a gamma distribution with shape and scale parameters of 20 and 0.8, respectively.
The beta priors are selected because they are very flexible on (0, 1) and can represent a wide range of prior beliefs.
All definitions were prospectively selected prior to initiation of the study.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com