SNPs genotypes of southern beech Nothofagus dombeyi

Geogenomics seeks to understand geological processes linked to lineage
divergence. However, the mechanisms that conserve ancient signals despite
gene flow are still unclear. In the southern beech, the deep lineage
divergence produced by vicariant events is associated with ancient marine
transgressions. We hereby evaluate the hypothesis that this divergence is
maintained by diversifying selection. The lineage divergence
using AMOVA, principal coordinate analysis, assignment tests, and multiple
matrix regression analyses was assessed using chloroplast DNA and neutral
and outlier SNPs. Several environmental variables were used to
characterize potential within-species niche structuring and
genotype-environment associations. Two deep-rooted latitudinally
structured lineages resulted from cpDNA, the northern cluster being more
genetically diverse than the southern one. Of the total of 2,943 SNPs, 33
were identified as outliers and produced two genetic clusters. Neutral
SNPs yielded no structure by AMOVA, whereas higher
(>75%) Fst values were obtained for cpDNA and outlier
SNPs. Precipitation variables were mostly associated with population
clusters and suggested two climatic niches, consisting of cold and dry in
the south and more variable precipitation, temperature, and soil
conditions in the north. Associations of genetic distance with environment
and geography suggested IBD and IBE effects. Ancient lineage
divergence in N. dombeyi, originally driven by vicariance, has
been maintained by diversifying selection under distinct environmental
conditions that also define distinct within-species niches. Deeply rooted
phylogeographic breaks can be conserved in continuously distributed
species in the absence of current geographic barriers. Yet physical
gradients exert differential selective pressures, which are maintained in
the face of potential gene flow. As a result, selection can lead to
geographically localized and differentially adapted groups of populations
that can be detected by a combination of traditional phylogeographic and
novel genomic methods.