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In addition to the 135 samples from the Sonoran subjects, the 22 EA samples used in the initial resequencing project that initially identified all polymorphic sites were used in all genotyping assays to allow a check of concordance.
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Genotyping quality control was performed in 10% of samples via duplicate checking (rate of concordance in duplicates > 99%).
We note that this approach may affect the comparison of Model A and B in BayesTraits as an incorrect root node may hamper the detection of trait evolution, hence we repeated our analyses assigning another arbitrary individual bearing the most common haplotype to the root node and checked for concordance of results.
The same two investigators repeated data extraction after some weeks in order to check for concordance.
For our experiments we used a publicly available Dataset I to check the concordance of the HPC and Hadoop approaches and a synthetic Dataset (S) that was generated from the Arabidopsis thaliana TAIR10 [ 26] reference genome with the wgsim tool from the Samtools package, which mimicked Illumina HiSeq sequencing data.
In order to control the restriction digestion of the PCR products, genotyping assays were randomly repeated and results were checked for concordance.
Three quality control samples were duplicated within and between plates, and genotypes were checked for concordance.
The calls were checked for concordance with the validated genotypes from HapMap.
The assays included DHMRI control DNA (CEPH) on each plate in duplicate that were checked for concordance for each SNP.
To minimize human error, DM and MVH conducted data entry separately and checked for concordance between retrieved data.
MIP (14) was solved to check the possibility of further strengthening of concordance between ordering.
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