The genetic diversity (He) of the intermediate altitude class (He = 0.65) was significantly higher (Wilcoxon signed-paired rank test, after Bonferroni correction, P = 0.03) than that of the high altitude class (He = 0.57).
Moreover, the average frequency of private alleles that showed a frequency higher than 5% was 0.00 for seasons, 0.063 for districts, and 0.085 for altitude classes.
The T3 cluster was mostly present at intermediate and high altitudes, while T4 was present in all of the altitude classes.
In Ethiopia, a recent study found that differentiation among altitude classes was several times higher than differentiation among geographic districts, with the greatest amount of population differentiation found in the lowest altitude class (Hadado et al. 2010).
This divergence between different districts but within the same altitude class is consistent with the selection hypothesis, and it is suggestive of different selection intensities at low and high altitudes.
The differentiation among the low altitude classes of the three districts was higher (FST = 0.10, P < 0.01) than that among the three districts within the intermediate (FST = 0.04, P > 0.05) and high (FST = 0.01, P > 0.05) altitude classes.
Among the altitude classes, the levels of differentiation were higher compared to seasons and districts, both for FST (0.10, P < 0.001) and RST (0.09, P < 0.001).
The divergence between seasons, districts, and altitude classes for each of the SSR loci was analysed, and the averages were quantified with FST [ 63] and RST (R-statistics, [ 64]) estimators.
The divergence (FST and RST) estimates between seasons, districts and altitude classes for each of the SSR loci analysed are given in Additional file 2. The individual SSR loci divergence (FST,) between seasons was significant for four loci (Bmag0013, HVM67, Bmac0040, and Bmac0134), even if the values were low, and varied from 0.02 to 0.05 (Additional file 2).
Finally, compared to seasons and districts, the altitude classes had a higher number of private alleles (17; 26%), four of which (one for <2,300 m a.s.l., and three for >2,800 m a.s.l).l
