After removing closely related individuals, we detected neither high inbreeding in the different Mongolian breeds nor evidence for a bottleneck.
We tested the effect of taxon sampling on node support by removing closely related species from the dataset(Additional file 7: Table S4).
Quality control of samples included removing closely related individuals, individuals with an extreme inbreeding coefficient, individuals with a low call rate, individuals with a mislabelled sex and individuals with a high discordance rate to previously genotyped SNPs.
However, removing closely related animals did not decrease, but rather increased r2 between unlinked markers, indicating that the small sample size may have been the main reason for high LD between unlinked markers.
To remove closely related homologs outside KCNA, all retrieved sequences were subjected to Blastp searches against human Ensembl peptide database (version 53), and only those with best hit to a KCNA were retained.
In each measurement, we removed organisms closely related to B. subtilis and E. coli in the same taxonomic group, which are defined in KEGG.
Prior to orthology prediction, all peptides containing nonsense characters (e.g., #) and intercalary stop codons were removed, and closely related peptides (e.g., isoforms) whose headers grouped them into a cluster were filtered using the retain-one-per-cluster Python script described above.
After removing some closely linked markers lacking anchor markers (i.e., genetic distances <2 cM), a linkage map consisting of 75 SSR markers was used for QTL mapping (Fig. 3).
While removing the closely related individuals makes the sample set conform more to the models used by Mach and Beagle, their increased error rate is likely due to decreased statistical power provided by the smaller input.
