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Neutral genomic differentiation between Dactylorhiza allopolyploids is rarely clearly diagnosable [ 48- 50, 72].
Genomic differentiation between subpopulations is a fundamental challenge in population genetics.
This fixation caused the high genomic differentiation between TS and temperate germplasms (Table 1, Figs. 2 and 3).
Characterizing the extent of genomic differentiation between recently diverged lineages provides an important context for understanding the early stages of speciation.
The results indicate a strong physiological and genomic differentiation between the desert and Mediterranean wild barley ecotypes and a closer relationship of the Mediterranean to cultivated barley.
The geographic consistency of genomic differentiation between M and S across locations was further reflected in the Neighbor-joining genetic distance tree.
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In these lineages the latter markers proved to be good for understanding genomic differentiation and distinguishing between species and evolutionary lines [ 37].
To unravel any possible link between the genomic differentiation and geographic stratification in the sample we created a pruned subset of SNPs in approximate linkage equilibrium with each other in order to capture the structure that reflects geographic origin.
Some studies have documented the pair-wise FST between subpopulations while considering genomic differentiation [ 9, 43, 44].
Below genus level, we find that genomic differentiation accumulates rapidly and reveals contrasting demographic histories between sympatric species on Lifou, indicative of past interspecific interactions.
To assess large-scale patterns of genomic differentiation, we calculated the mean difference in Contrast values between pools of M and S mosquitoes at each paired site in nonoverlapping windows of 50 adjacent SNPs.
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