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The Effects of Artificial Selection on the Maize Genome
Analysis of single-nucleotide polymorphisms in 774 genes indicates that 2 to 4% of these genes experienced artificial selection, and candidate selected genes with putative function in plant growth are clustered near quantitative trait loci that contribute to phenotypic differences between maize and teosinte.
Rates and patterns of molecular evolution in inbred and outbred Arabidopsis.
No significant difference in the rates of protein evolution is observed between selfing and outcrossing Arabidopsis species and no consistent overall difference in codon bias is observed, although for low-biased genes A. lyrata shows significantly higher major codon usage.
Patterns of Polymorphism and Demographic History in Natural Populations of Arabidopsis lyrata
Nucleotide diversity in six natural populations of Arabidopsis lyrata was studied, finding evidence of population divergence over the past 19,000 to 47,000 years involving non-equilibrium demographic events that reduced the effective size of most populations.
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions
Sequencing of genomes from three Brassicaceae species and their joint analysis with six previously sequenced crucifer genomes confirm that most of the identified CNSs are evolving under medium to strong purifying selection, and highlight both similarities and several key differences between the regulatory DNA of plants and other species.
Transposon diversity in Arabidopsis thaliana.
- Quang Hien Le, S. Wright, Z. Yu, T. Bureau
- BiologyProceedings of the National Academy of Sciences…
- 20 June 2000
This report uses sequence similarity search and analysis protocols to perform a fine-scale analysis of a large sample of the Arabidopsis thaliana genome for transposons, and provides evidence that most minedtransposons have a clear distribution preference for A + T-rich sequences and shows that structural variation for many mined transposon is partly due to interelement recombination.
The HKA Test Revisited
Application of the maximum-likelihood-ratio test of the standard neutral model to polymorphism data from 18 loci from a population of Arabidopsis lyrata provides significant evidence for a balanced polymorphism at a candidate locus thought to be linked to the centromere.
Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata.
- S. Wright, C. Yau, M. Looseley, B. Meyers
- Biology, Environmental ScienceMolecular biology and evolution
- 1 September 2004
Analysis of the complete genome sequence of Arabidopsis thaliana and sequence data from 83 genes in the outcrossing A. lyrata reveals a significant correlation between gene expression level and amino acid substitution rate, which indicates that the degree of tissue specialization may be an important determinant of the rate of protein evolution inArabidopsis.
Recent speciation associated with the evolution of selfing in Capsella
- J. Foxe, T. Slotte, E. Stahl, B. Neuffer, H. Hurka, S. Wright
- BiologyProceedings of the National Academy of Sciences
- 31 March 2009
The hypothesis that selfing was favored during colonization as new habitats emerged after the last glaciation and the expansion of agriculture is supported and suggests that natural selection for reproductive assurance can lead to major morphological evolution and speciation on relatively short evolutionary timescales.
Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana.
It is shown that, despite TE accumulation near the centromeres, recombination does not generally correlate with TE abundance, suggesting that selection against ectopic recombinationdoes not influence TE distribution in A. thaliana.
Subdivision and haplotype structure in natural populations of Arabidopsis lyrata
Analysis of patterns of DNA polymorphism within and between four populations of the outcrossing plant Arabidopsis lyrata suggests lower recombination than predicted based on the variability together with physical recombination rates estimated from A. thaliana, suggesting either a population bottleneck in North American populations or recent admixture involving diverged European populations.