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 structu..., , , # SNP genotypes of the southern beech *Nothofagus dombeyi*

This dataset contains genotypes for 2943 SNPs of 113 *N. dombeyi* individuals classified a priori as belonging to each of two intraspecific lineages (populations 1 and 2) using chloroplast sequences.

## Description of the Data and file structure

Each individual consists of a homozygous or heterozygous genotype through changes in one base as A, C, G, T. Missing data codes: none

## Sharing/Access Information

Newly generated DNA sequences are deposited in GenBank (accession numbers OP473928-OP473939 and OP491426-OP491431). Data matrices containing genomic information that supports the findings of this study are available from Universidad Nacional del Comahue Institutional Digital Repository RDI Unco URI (link in Related Works section).