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      Adaptive Introgression: An Untapped Evolutionary Mechanism for Crop Adaptation


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          Global environmental changes strongly impact wild and domesticated species biology and their associated ecosystem services. For crops, global warming has led to significant changes in terms of phenology and/or yield. To respond to the agricultural challenges of this century, there is a strong need for harnessing the genetic variability of crops and adapting them to new conditions. Gene flow, from either the same species or a different species, may be an immediate primary source to widen genetic diversity and adaptions to various environments. When the incorporation of a foreign variant leads to an increase of the fitness of the recipient pool, it is referred to as “adaptive introgression”. Crop species are excellent case studies of this phenomenon since their genetic variability has been considerably reduced over space and time but most of them continue exchanging genetic material with their wild relatives. In this paper, we review studies of adaptive introgression, presenting methodological approaches and challenges to detecting it. We pay particular attention to the potential of this evolutionary mechanism for the adaptation of crops. Furthermore, we discuss the importance of farmers’ knowledge and practices in shaping wild-to-crop gene flow. Finally, we argue that screening the wild introgression already existing in the cultivated gene pool may be an effective strategy for uncovering wild diversity relevant for crop adaptation to current environmental changes and for informing new breeding directions.

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          Hybridization and speciation.

          Hybridization has many and varied impacts on the process of speciation. Hybridization may slow or reverse differentiation by allowing gene flow and recombination. It may accelerate speciation via adaptive introgression or cause near-instantaneous speciation by allopolyploidization. It may have multiple effects at different stages and in different spatial contexts within a single speciation event. We offer a perspective on the context and evolutionary significance of hybridization during speciation, highlighting issues of current interest and debate. In secondary contact zones, it is uncertain if barriers to gene flow will be strengthened or broken down due to recombination and gene flow. Theory and empirical evidence suggest the latter is more likely, except within and around strongly selected genomic regions. Hybridization may contribute to speciation through the formation of new hybrid taxa, whereas introgression of a few loci may promote adaptive divergence and so facilitate speciation. Gene regulatory networks, epigenetic effects and the evolution of selfish genetic material in the genome suggest that the Dobzhansky-Muller model of hybrid incompatibilities requires a broader interpretation. Finally, although the incidence of reinforcement remains uncertain, this and other interactions in areas of sympatry may have knock-on effects on speciation both within and outside regions of hybridization. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.
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            Testing for ancient admixture between closely related populations.

            One enduring question in evolutionary biology is the extent of archaic admixture in the genomes of present-day populations. In this paper, we present a test for ancient admixture that exploits the asymmetry in the frequencies of the two nonconcordant gene trees in a three-population tree. This test was first applied to detect interbreeding between Neandertals and modern humans. We derive the analytic expectation of a test statistic, called the D statistic, which is sensitive to asymmetry under alternative demographic scenarios. We show that the D statistic is insensitive to some demographic assumptions such as ancestral population sizes and requires only the assumption that the ancestral populations were randomly mating. An important aspect of D statistics is that they can be used to detect archaic admixture even when no archaic sample is available. We explore the effect of sequencing error on the false-positive rate of the test for admixture, and we show how to estimate the proportion of archaic ancestry in the genomes of present-day populations. We also investigate a model of subdivision in ancestral populations that can result in D statistics that indicate recent admixture.
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              The hitch-hiking effect of a favourable gene.


                Author and article information

                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                01 February 2019
                : 10
                : 4
                [1] 1Institut de Recherche pour le Développement, UMR DIADE , Montpellier, France
                [2] 2DIADE, Université de Montpellier , Montpellier, France
                [3] 3Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR AGAP , Montpellier, France
                [4] 4AGAP, Université de Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Institut National de la Recherche Agronomique, Montpellier SupAgro , Montpellier, France
                [5] 5Laboratoire National de Recherches sur les Productions Végétales, Institut Sénégalais de Recherches Agricoles , Dakar, Senegal
                [6] 6Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux , Dakar, Senegal
                [7] 7Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UPR GREEN , Montpellier, France
                [8] 8GREEN, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Université de Montpellier , Montpellier, France
                [9] 9Bureau d’Analyses Macro-Economiques, Institut Sénégalais de Recherches Agricoles , Dakar, Senegal
                Author notes

                Edited by: Genlou Sun, Saint Mary’s University, Canada

                Reviewed by: Giorgio Bertorelle, University of Ferrara, Italy; Hong An, University of Missouri, United States; Jose Maria Iriondo, Universidad Rey Juan Carlos, Spain

                *Correspondence: Concetta Burgarella, concetta.burgarella@ 123456gmail.com Cécile Berthouly-Salazar, cecile.berthouly@ 123456ird.fr

                This article was submitted to Evolutionary and Population Genetics, a section of the journal Frontiers in Plant Science

                Copyright © 2019 Burgarella, Barnaud, Kane, Jankowski, Scarcelli, Billot, Vigouroux and Berthouly-Salazar.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                : 20 June 2018
                : 04 January 2019
                Page count
                Figures: 3, Tables: 2, Equations: 0, References: 179, Pages: 17, Words: 0
                Funded by: Agence Nationale de la Recherche 10.13039/501100001665
                Plant Science

                Plant science & Botany
                crops,wild relatives,domestication,selection,gene flow,adaptive introgression,farmer’s practices


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