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      On the origins and domestication of the olive: a review and perspectives

      1 , 2 , 3 , 4 , 5
      Annals of Botany
      Oxford University Press (OUP)

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          Abstract

          <div class="section"> <a class="named-anchor" id="s1"> <!-- named anchor --> </a> <h5 class="section-title" id="d7221819e158">Background</h5> <p id="d7221819e160">Unravelling domestication processes is crucial for understanding how species respond to anthropogenic pressures, forecasting crop responses to future global changes and improving breeding programmes. Domestication processes for clonally propagated perennials differ markedly from those for seed-propagated annual crops, mostly due to long generation times, clonal propagation and recurrent admixture with local forms, leading to a limited number of generations of selection from wild ancestors. However, additional case studies are required to document this process more fully. </p> </div><div class="section"> <a class="named-anchor" id="s2"> <!-- named anchor --> </a> <h5 class="section-title" id="d7221819e163">Scope</h5> <p id="d7221819e165">The olive is an iconic species in Mediterranean cultural history. Its multiple uses and omnipresence in traditional agrosystems have made this species an economic pillar and cornerstone of Mediterranean agriculture. However, major questions about the domestication history of the olive remain unanswered. New paleobotanical, archeological, historical and molecular data have recently accumulated for olive, making it timely to carry out a critical re-evaluation of the biogeography of wild olives and the history of their cultivation. We review here the chronological history of wild olives and discuss the questions that remain unanswered, or even unasked, about their domestication history in the Mediterranean Basin. We argue that more detailed ecological genomics studies of wild and cultivated olives are crucial to improve our understanding of olive domestication. Multidisciplinary research integrating genomics, metagenomics and community ecology will make it possible to decipher the evolutionary ecology of one of the most iconic domesticated fruit trees worldwide. </p> </div><div class="section"> <a class="named-anchor" id="s3"> <!-- named anchor --> </a> <h5 class="section-title" id="d7221819e168">Conclusion</h5> <p id="d7221819e170">The olive is a relevant model for improving our knowledge of domestication processes in clonally propagated perennial crops, particularly those of the Mediterranean Basin. Future studies on the ecological and genomic shifts linked to domestication in olive and its associated community will provide insight into the phenotypic and molecular bases of crop adaptation to human uses. </p> </div>

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          Climate change, adaptation, and phenotypic plasticity: the problem and the evidence

          Many studies have recorded phenotypic changes in natural populations and attributed them to climate change. However, controversy and uncertainty has arisen around three levels of inference in such studies. First, it has proven difficult to conclusively distinguish whether phenotypic changes are genetically based or the result of phenotypic plasticity. Second, whether or not the change is adaptive is usually assumed rather than tested. Third, inferences that climate change is the specific causal agent have rarely involved the testing – and exclusion – of other potential drivers. We here review the various ways in which the above inferences have been attempted, and evaluate the strength of support that each approach can provide. This methodological assessment sets the stage for 11 accompanying review articles that attempt comprehensive syntheses of what is currently known – and not known – about responses to climate change in a variety of taxa and in theory. Summarizing and relying on the results of these reviews, we arrive at the conclusion that evidence for genetic adaptation to climate change has been found in some systems, but is still relatively scarce. Most importantly, it is clear that more studies are needed – and these must employ better inferential methods – before general conclusions can be drawn. Overall, we hope that the present paper and special issue provide inspiration for future research and guidelines on best practices for its execution.
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            Inferring human population size and separation history from multiple genome sequences

            The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model their ancestral relationship under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20-30 thousand years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The Multiple Sequentially Markovian Coalescent (MSMC) analyses the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. Results from applying MSMC to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago, and give information about human population history as recently as 2,000 years ago, including the bottleneck in the peopling of the Americas, and separations within Africa, East Asia and Europe.
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              An efficient multi-locus mixed model approach for genome-wide association studies in structured populations

              Population structure causes genome-wide linkage disequilibrium between unlinked loci, leading to statistical confounding in genome-wide association studies. Mixed models have been shown to handle the confounding effects of a diffuse background of large numbers of loci of small effect well, but do not always account for loci of larger effect. Here we propose a multi-locus mixed model as a general method for mapping complex traits in structured populations. Simulations suggest that our method outperforms existing methods, in terms of power as well as false discovery rate. We apply our method to human and Arabidopsis thaliana data, identifying novel associations in known candidates as well as evidence for allelic heterogeneity. We also demonstrate how a priori knowledge from an A. thaliana linkage mapping study can be integrated into our method using a Bayesian approach. Our implementation is computationally efficient, making the analysis of large datasets (n > 10000) practicable.
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                Author and article information

                Journal
                Annals of Botany
                Oxford University Press (OUP)
                0305-7364
                1095-8290
                February 16 2018
                March 05 2018
                January 30 2017
                February 16 2018
                March 05 2018
                January 30 2017
                : 121
                : 3
                : 385-403
                Affiliations
                [1 ]CNRS-UPS-ENSFEA-IRD, EDB, UMR 5174, Université Paul Sabatier, Toulouse Cedex , France
                [2 ]ISEM, UMR 5554, CNRS-Université de Montpellier-IRD-EPHE, Equipe Dynamique de la Biodiversité, Anthropo-écologie, Montpellier Cedex, France
                [3 ]International Associated Laboratory (LIA, CNRS) EVOLea, Zürich, Switzerland
                [4 ]Center for Adaptation to a Changing Environment, ETH Zürich, Zürich, Switzerland
                [5 ]GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
                Article
                10.1093/aob/mcx145
                5838823
                29293871
                e22357f1-4f65-405f-8ecd-b001a8c00749
                © 2017
                History

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