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The estimation on the locus will be compared with previous geophysical estimations (Kato et al. 2015; Maeda et al. 2015).
Since these have not been empirically identified in most genomes we first use the model to generate a maximum likelihood estimation of the two loci and discuss the accuracy of this approach.
Allelic richness (A R - [ 50]) was calculated for each SL using the rarefaction procedure implemented in FSTAT 2.9.3 [ 45], which also allowed estimation of the multi-locus F IS.
For a reliable estimation of the recombination rates, loci with more than 10% missing data in at least one population were discarded from the analysis.
However, an estimation of the number of loci affecting this trait cannot be provided, given that the presence vs absence of sex-allocation plasticity is evaluated qualitatively at the group level.
For the estimation of inter-locus LD, the alignments of PAL, COMT, CCoAOMT1, and CCoAOMT2 ([ 18, 21], unpublished results) were included.
Additionally, estimation of the frequencies of multiple-locus haplotypes revealed potential risk haplotypes (GCCT) for SARS infection.
The IBD distribution was plotted with R. A conservative estimation of the number of SNP loci needed to differentiate related cacao accessions (i.e. determine off-types) was performed.
Thirdly, the high variance in coalescent times across loci makes estimation of the divergence time based on a single genetic locus inaccurate, and highlights the need to use multiple unlinked loci.
As an illustration, consider a rare allele of large effect which will be relatively imprecisely estimated in the estimation sample, but because the contribution of the locus to total variance is small there is only a small impact upon the accuracy of further predictions within the same population.
As the substantial correlations among multiple tests would potentially distort the estimation of the true proportion of DM loci (Leek and Storey, 2007), we further compared the DM loci lists detected from HNSCC_PB, OVC_PB and HNSCC_SR datasets using different thresholds of P-value with M-L DM loci list.
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