In order to examine the variation selected by humans over our long relationship with rice, we must first look at the ancestors of our modern cultivars.
The remaining seven (12.5%) variations were selected by dominant amino acids in the presence of a specific HLA type.
There were no plateaus when no-variation genes were chosen randomly, only n−1/2 decays, and differences were small when no-variation genes were selected by decreasing p-values.
Among the 56 HLA-associated amino acid variations, 49 (87.5%) were selected by non-dominant amino acids in the presence of the specific HLA type.
Besides favorable mutations and stable epigenetic variations that have been selected by man and the environment, it is probable that without the filter of sexual reproduction, the sweet orange genome accumulated unfavorable mutations in a heterozygous status.
A general approach to increasing quantitative resistance (to any disease) stems from viewing plant breeding as a greatly accelerated form of natural selection, in which variation in traits is selected by breeders and inherited by the next generation of cultivars.
Maximum likelihood phylogenetic trees were estimated with PAUP* 4.0 [62] using the general time reversible nucleotide substitution model specifying the proportion of invariant sites and a gamma distributed rate variation, which had been selected by MODELTEST [63], and tree-bisection-recombination branch-swapping.
A final filtered gene list of 2777 probes selected by variation filter provided by dChip-software was used.
In the selection-centric logic, amino acid or protein sequence varies according to nucleotide variation but sometimes is selected by external forces when the number of individuals in a population, possessing either advantageous or disadvantageous mutations, changes toward either maxima or minima.
Among these methods, scoring by experts selected 36 items, coefficient of variation selected 46 items, discriminatory analysis selected 46 items, multiple regression selected 32 items, Cronbach'α coefficient selected 59 items, coefficient of correlation selected 53 items, factor analysis selected 54 items, and cluster analysis selected 46 items (see additional file 3).
