ArticleGenetics2005
A multilocus sequence survey in Arabidopsis thaliana reveals a genome-wide departure from a neutral model of DNA sequence polymorphism.
Article in Genetics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 107 papers.
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Who cites it
107 citing papers in PubMed.
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- High allelic diversity in Arabidopsis NLRs is associated with distinct genomic features.EMBO reports · 2024Article
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- Smart breeding approaches in post-genomics era for developing climate-resilient food crops.Frontiers in plant science · 2022Review
- Pan-genome: A promising resource for noncoding RNA discovery in plants.The plant genome · 2020Review
- Evolutionary rate variation among genes involved in galactomannan biosynthesis inEcology and evolution · 2020Article
- Article
- Relationship Among Intron Length, Gene Expression, and Nucleotide Diversity in the Pacific Oyster Crassostrea gigas.Marine biotechnology (New York, N.Y.) · 2018Article
- Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.).BMC evolutionary biology · 2018Article
- Adaptive diversification of growth allometry in the plantProceedings of the National Academy of Sciences of the United States of America · 2018Article
- Population structure and local selection yield high genomic variation in Mimulus guttatus.Molecular ecology · 2017Article
- A Novel Imprinted Gene NUWA Controls Mitochondrial Function in Early Seed Development in Arabidopsis.PLoS genetics · 2017Article
- A SNP-Enabled Assessment of Genetic Diversity, Evolutionary Relationships and the Identification of Candidate Genes in Chrysanthemum.Genome biology and evolution · 2016Article
- A subunit of the oligosaccharyltransferase complex is required for interspecific gametophyte recognition in Arabidopsis.Nature communications · 2016Article
- Genomic variations and distinct evolutionary rate of rare alleles in Arabidopsis thaliana.BMC evolutionary biology · 2016Article
- Genetic diversity and population structure of Arabidopsis thaliana along an altitudinal gradient.AoB PLANTS · 2015Article
47 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
The simultaneous analysis of multiple genomic loci is a powerful approach to studying the effects of population history and natural selection on patterns of genetic variation of a species. By surveying nucleotide sequence polymorphism at 334 randomly distributed genomic regions in 12 accessions of Arabidopsis thaliana, we examined whether a standard neutral model of nucleotide sequence polymorphism is consistent with observed data. The average nucleotide diversity was 0.0071 for total sites and 0.0083 for silent sites. Although levels of diversity are variable among loci, no correlation with local recombination rate was observed, but polymorphism levels were correlated for physically linked loci (<250 kb). We found that observed distributions of Tajima's D- and D/D(min)- and of Fu and Li's D-, D*- and F-, F*-statistics differed significantly from the expected distributions under a standard neutral model due to an excess of rare polymorphisms and high variances. Observed and expected distributions of Fay and Wu's H were not different, suggesting that demographic processes and not selection at multiple loci are responsible for the deviation from a neutral model. Maximum-likelihood comparisons of alternative demographic models like logistic population growth, glacial refugia, or past bottlenecks did not produce parameter estimates that were more consistent with observed patterns. However, exclusion of highly polymorphic "outlier loci" resulted in a fit to the logistic growth model. Various tests of neutrality revealed a set of candidate loci that may evolve under selection.
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