2005/05/20 by Magnus Nordborg, Tina T. Hu, Yoko Ishino +21 · 6 citations
Biochemistry, Genetics and Molecular Biology · #Genetic Mapping and Diversity in Plants and Animals #Genetic diversity and population structure #Evolution and Genetic Dynamics #Biology #Linkage disequilibrium #Genetics #Selfing #Genome #Evolutionary biology #Genomics #Natural selection #Population #Allele #Gene #Haplotype
paper · pdf · doi:10.1371/journal.pbio.0030196
openalex publication_date 2005/05/20 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/23
We resequenced 876 short fragments in a sample of 96 individuals of Arabidopsis thaliana that included stock center accessions as well as a hierarchical sample from natural populations. Although A. thaliana is a selfing weed, the pattern of polymorphism in general agrees with what is expected for a widely distributed, sexually reproducing species. Linkage disequilibrium decays rapidly, within 50 kb. Variation is shared worldwide, although population structure and isolation by distance are evident. The data fail to fit standard neutral models in several ways. There is a genome-wide excess of rare alleles, at least partially due to selection. There is too much variation between genomic regions in the level of polymorphism. The local level of polymorphism is negatively correlated with gene density and positively correlated with segmental duplications. Because the data do not fit theoretical null distributions, attempts to infer natural selection from polymorphism data will require genome-wide surveys of polymorphism in order to identify anomalous regions. Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics.