The study presents the first phase of the 1001 Genomes Project, which aims to sequence geographically diverse *Arabidopsis thaliana* strains to identify genetic variation contributing to adaptation. The project sequenced 80 strains from eight regions across the species' native range, revealing a majority of common small-scale polymorphisms and larger insertions and deletions. The analysis identified the effects of these variants on gene function and patterns of linkage among them. The spectrum of mutations accumulated since *A. thaliana* diverged from its closest relative, *Arabidopsis lyrata*, was compared to that observed in the laboratory, revealing that recent species-wide selective sweeps are rare and that potentially deleterious mutations are more common in marginal populations. The study also explored the impact of various evolutionary forces, including recombination, gene conversion, mutation, selection, demography, and polyploidization, on sequence variation. The results provide insights into the genetic diversity and adaptation of *A. thaliana* and highlight the utility of whole-genome sequencing for identifying alleles responsible for phenotypic variation.The study presents the first phase of the 1001 Genomes Project, which aims to sequence geographically diverse *Arabidopsis thaliana* strains to identify genetic variation contributing to adaptation. The project sequenced 80 strains from eight regions across the species' native range, revealing a majority of common small-scale polymorphisms and larger insertions and deletions. The analysis identified the effects of these variants on gene function and patterns of linkage among them. The spectrum of mutations accumulated since *A. thaliana* diverged from its closest relative, *Arabidopsis lyrata*, was compared to that observed in the laboratory, revealing that recent species-wide selective sweeps are rare and that potentially deleterious mutations are more common in marginal populations. The study also explored the impact of various evolutionary forces, including recombination, gene conversion, mutation, selection, demography, and polyploidization, on sequence variation. The results provide insights into the genetic diversity and adaptation of *A. thaliana* and highlight the utility of whole-genome sequencing for identifying alleles responsible for phenotypic variation.