Second, they do not inform the investigator as to which loci are polymorphic for the populations under study.
In small populations, the drift-induced linkage disequilibrium may be an important factor (Hill 1981) and reduce the degree to which loci provide independent information about coancestry.
However, for most traits, it remains unclear how genetically complex they are, how the trait variation is distributed across the loci, and the degree to which loci act additively or epistatically.
The two members corresponding to miR156a-j (paralogous loci yield similar mature sequences which makes it difficult to judge which locus is expressed) and miR156l loci are almost equally represented in our sequences (about 565 times), whereas the third member (156 k) is also expressed but at 50 times lower level compared to the other 2 variants.
The first step was performed to establish which locus had the strongest effect in initial models with single point effects of HLA-A and HLA-DRB1.
To understand which locus or loci play important roles within this gene family, we identified all available MIR156 transfer-DNA (T-DNA) knockout plants (Samson et al., 2002; Alonso et al., 2003; Woody et al., 2007; Figure 1A and supplementary file 1A).
When inconsistencies are found, HI will decide whether or not, and at which loci, to change the haplotype reconstructions according to its calculations.
Furthermore, to determine which loci are cofactors and accounts for large effect on the Xoo resistance, MLMM was performed.
The objectives of the current study are two-fold: 1) to quantify universal application (PCR and sequencing) and sequence divergence among a phylogenetically diverse set of species pairs for nine putative barcode loci and, 2) to determine which loci, if more than one locus is required, will maximize species identification when combined as a barcode.
