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Abstract

Arabidopsis thaliana is increasingly employed to investigate questions in evolution and ecology. It is thus critical to understand population structure and dynamics of wild populations at a scale relevant to individuals. We collected seeds from >1000 individuals in 78 populations within 25 km of Tuebingen, Germany. We genotyped all plants at 436 single nucleotide polymorphism (SNP) markers distributed across all chromosomes. We found pronounced variation among sites in genetic diversity and heterozygosity. About 70% of sites contain at least two distinct genotypes. Sites were strongly isolated and genetic identities of individuals spaced more than a few dozen meters apart were very rare. Distinct genotypes within populations tended to be more closely related than those from different populations. Pairwise genetic distance comparisons among genotypes in neighboring populations were often lower than comparisons among more distant populations and nonparametric clustering often groups individuals from nearby populations together. Some populations had surprisingly high estimated outcrossing rates – up to 20% - while others were completely homozygous with no evidence of past or ongoing outcrossing. We observed striking differences between sites in rural and urban settings. Rural sites have more distinct genotypes, higher genetic diversity, higher heterozygosity, and evidence of past recombination. The picture emerging from our work, together with other studies, is that A. thaliana exists in the wild in isolated populations that differ greatly in structure, stability and natural history. Outcrossing is sufficiently high in some populations to maintain overall genetic variation and generate novel haplotypes with a regional stamp. These patterns have implications for sampling for natural variation and ecological adaptation studies.