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Evolutionary history of almond tree domestication in the Mediterranean basin

Authors

  • M. Delplancke,

    Corresponding author
    • Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175, Montpellier Cedex 5, France
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    • M. Delplancke and N. Alvarez contributed equally to this work and are considered as joint first authors.
  • N. Alvarez,

    1. Department of Ecology and Evolution, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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    • M. Delplancke and N. Alvarez contributed equally to this work and are considered as joint first authors.
  • L. Benoit,

    1. Centre International Recherche Agronomique Développement, UPR 67 UMR 5175, Montpellier Cedex 5, France
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  • A. Espíndola,

    1. Department of Ecology and Evolution, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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  • H. I Joly,

    1. Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175, Montpellier Cedex 5, France
    2. Centre International Recherche Agronomique Développement, UPR 67 UMR 5175, Montpellier Cedex 5, France
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  • S. Neuenschwander,

    1. Department of Ecology and Evolution, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
    2. Vital-IT, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
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  • N. Arrigo

    1. Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, USA
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Correspondence: Malou Delplancke, Fax: +33/0 4 67 41 21 38; E-mail: malou.delplancke@gmail.com

Abstract

Genetic diversity of contemporary domesticated species is shaped by both natural and human-driven processes. However, until now, little is known about how domestication has imprinted the variation of fruit tree species. In this study, we reconstruct the recent evolutionary history of the domesticated almond tree, Prunus dulcis, around the Mediterranean basin, using a combination of nuclear and chloroplast microsatellites [i.e. simple sequence repeat (SSRs)] to investigate patterns of genetic diversity. Whereas conservative chloroplast SSRs show a widespread haplotype and rare locally distributed variants, nuclear SSRs show a pattern of isolation by distance with clines of diversity from the East to the West of the Mediterranean basin, while Bayesian genetic clustering reveals a substantial longitudinal genetic structure. Both kinds of markers thus support a single domestication event, in the eastern side of the Mediterranean basin. In addition, model-based estimation of the timing of genetic divergence among those clusters is estimated sometime during the Holocene, a result that is compatible with human-mediated dispersal of almond tree out of its centre of origin. Still, the detection of region-specific alleles suggests that gene flow from relictual wild preglacial populations (in North Africa) or from wild counterparts (in the Near East) could account for a fraction of the diversity observed.

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