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Combining conservative and variable markers to infer the evolutionary history of Prunus subgen. Amygdalus s.l. under domestication

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Abstract

The genus Prunus L. is large and economically important. However, phylogenetic relationships within Prunus at low taxonomic level, particularly in the subgenus Amygdalus L. s.l., remain poorly investigated. This paper attempts to document the evolutionary history of Amygdalus s.l. and establishes a temporal framework, by assembling molecular data from conservative and variable molecular markers. The nuclear s6pdh gene in combination with the plastid trnSG spacer are analyzed with bayesian and maximum likelihood methods. Since previous phylogenetic analysis with these markers lacked resolution, we additionally analyzed 13 nuclear SSR loci with the δµ2 distance, followed by an unweighted pair group method using arithmetic averages algorithm. Our phylogenetic analysis with both sequence and SSR loci confirms the split between sections Amygdalus and Persica, comprising almonds and peaches, respectively. This result is in agreement with biogeographic data showing that each of the two sections is naturally distributed on each side of the Central Asian Massif chain. Using coalescent based estimations, divergence times between the two sections strongly varied when considering sequence data only or combined with SSR. The sequence-only based estimate (5 million years ago) was congruent with the Central Asian Massif orogeny and subsequent climate change. Given the low level of differentiation within the two sections using both marker types, the utility of combining microsatellites and data sequences to address phylogenetic relationships at low taxonomic level within Amygdalus is discussed. The recent evolutionary histories of almond and peach are discussed in view of the domestication processes that arose in these two phenotypically-diverging gene pools: almonds and peaches were domesticated from the Amygdalus s.s. and Persica sections, respectively. Such economically important crops may serve as good model to study divergent domestication process in close genetic pool.

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Acknowledgments

The present study was funded by the “FruitMed Project”, distributed by the French Foundation Agropolis. N. Arrigo, N. Alvarez, A. Espíndola were funded by the Swiss National Science Foundation (Grant No. 132747, and an Ambizione fellowship PZ00P3_126624). Sequencing was done in Cornell University Life Sciences Core Laboratories Center (CLC) and genotyping in the ‘Service Commun de Marqueurs Génétiques en Ecologie’ of the UMR CEFE.

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    Authors and Affiliations

    1. Université Montpellier 2, Centre d’Ecologie Fonctionnelle et Evolutive UMR 5175, 1919 Route de Mende, 34293, Montpellier Cedex 5, France

      Malou Delplancke

    2. Genetic Resources Section, Biodiversity and Integrated Gene Management Program, International Center for Agricultural Research in Dry Areas (ICARDA), Beirut, 1108-2010, Lebanon

      Mariana Yazbek

    3. Department of Ecology and Evolutionary Biology, University of Arizona, 85721, Tucson, AZ, USA

      Nils Arrigo & Anahí Espíndola

    4. Department of Ecology and Evolution, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland

      Nadir Alvarez

    5. CIRAD, UPR 67, Centre d’Ecologie Fonctionnelle et Evolutive UMR 5175, 1919 Route de Mende, 34293, Montpellier Cedex 5, France

      Helene Joly

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    1. Malou Delplancke
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    Correspondence to Mariana Yazbek.

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    Malou Delplancke and Mariana Yazbek have contributed equally to this work.

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    Delplancke, M., Yazbek, M., Arrigo, N. et al. Combining conservative and variable markers to infer the evolutionary history of Prunus subgen. Amygdalus s.l. under domestication. Genet Resour Crop Evol 63, 221–234 (2016). https://doi.org/10.1007/s10722-015-0242-6

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