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Subdivision and haplotype structure in natural populations of Arabidopsis lyrata

Authors

  • Stephen I. Wright,

    Corresponding author
    1. Institute of Cell, Animal and Population Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3JT, UK
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  • Beatrice Lauga,

    1. Institute of Cell, Animal and Population Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3JT, UK
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    • Present address: Laboratoire d’Ecologie Moléculaire, Université de Pau et des Pays de l’Ardour, UFR Sciences et Techniques, BP 1155–64013 Pau cedex, France.

  • Deborah Charlesworth

    1. Institute of Cell, Animal and Population Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3JT, UK
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S. I. Wright. *Present address: ICAPB, University of Edinburgh, Ashworth Laboratories, King's Buildings, West Mains Road, Edinburgh, EH9 3JT, UK. Fax: 0131 6506564; E-mail: stephen.wright@ed.ac.uk

Abstract

High levels of inbreeding are expected to cause a strong reduction in levels of genetic variability, effective recombination rates and in adaptation compared with related outcrossing populations. We examined patterns of DNA polymorphism at five nuclear loci and one chloroplast locus within and between four populations of the outcrossing plant Arabidopsis lyrata, a close relative of the highly self-fertilizing model species A. thaliana. The observed patterns are compared with species-wide polymorphism at orthologous loci, as well as within- and between-population patterns at other studied loci in A. thaliana. In addition to evidence for much higher average within-population diversity, species-wide levels of silent polymorphism are generally higher in A. lyrata than in A. thaliana, unlike the results from a previous study of the ADH locus. However, polymorphism is also low in the North American A. lyrata subspecies lyrata compared with the European subspecies petraea, suggesting either a population bottleneck in North American populations or recent admixture involving diverged European populations. Differentiation between the two subspecies is strong, although there are few fixed differences, suggesting that their isolation is recent. Estimates of intralocus recombination rates and analysis of haplotype structure in European A. lyrata populations indicate lower recombination than predicted based on the variability together with physical recombination rates estimated from A. thaliana. This may be due to strong population subdivision, or to recent departures from demographic equilibrium such as a bottleneck or population admixture. Alternatively, there may be consistently lower recombination rates in the outcrossing species. In contrast, estimates of recombination rates from species-wide samples of A. thaliana are close to the values expected assuming a high rate of self-fertilization. Complex population histories in both A. thaliana and A. lyrata complicate theoretical predictions and empirical tests of the effects of inbreeding on polymorphism and molecular evolution.

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