Comparative demographic study: reconstructing the evolutionary history of Solanaceae species to better understand the domestication process and outcome. - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Accéder directement au contenu
Communication Dans Un Congrès Année : 2019

Comparative demographic study: reconstructing the evolutionary history of Solanaceae species to better understand the domestication process and outcome.

Résumé

Background: The process of domestication is an ideal framework to study the interplay of evolutionary forces that induced molecular changes over short-time scales. These changes can now be tracked at the genome-wide scale, offering a unique opportunity to decipher the most probable demographic scenarios that occurred and characterize them. In this context and for the first time in plant, we performed a comparative genomic approach to infer the parallelism in the evolutionary history of three major crop species of the Solanaceae family, the eggplant, the pepper and the tomato. In each species, we analyzed and compared the summary statistics of two groups of crop and wild accessions, constituting prior knowledge for demographic inferences. Inferring the demographic scenarios of these three species is an unprecedented opportunity to further characterize each domestication event duration, and therefore improve the inference of the demographic history that were hypothesized through indirect means (human and cultivation history of the areas, ancient written records). Material/Methods : To infer the past demographic events, scenarios of domestication were inferred from the comparison of site frequency spectrum in crop and wild groups. We implemented over 10 demographic models to test whether the divergence between the crop and wild groups occurred (i) in the absence/presence of gene flow, (ii) with gradual/instantaneous change in their effective population size, (iii) in one or two steps. For each species, the most probable scenario was selected according to its Akaike Information Criterion, and associated parameters and their precision were estimated. These parameters were translated to human timing by the use of a range of mutation rate to avoid any bias. Abstract: Results (maximum 1300 characters spaces included) : The comparative study of the demographic inferences modeling the domestication of the three species revealed common features of the domestication processes in the Solanaceae family. In the three species the presence of a bottleneck corroborates the stage of domestication related to cultivation. That specific stage induced a reduction in effective size due to the extraction of few individuals from their wild environment to cultivate them in human managed fields. The demographic models inferred the duration of the domestication event such as the divergence time between the crop and their wild relatives, or when occurred the bottleneck. Consequently, using two mutation rates we could provide a range of estimation: the eggplant domestication occurred 5,938-3,087 years ago, the pepper sampled allowed to estimate the stage of cultivation related to a bottleneck at 6,760-3,514 years before common era (BCE), and for the tomato the domestication seems to have occurred between 7,901 and 4,107 years BCE. Another parameter was the asymmetric gene flow between the wild and crop compartment. Our results highlight that both pepper and tomato have experienced a stronger gene flow from the wild to the crop compartment than crop to wild when it is the opposite for eggplant. Discussion and conclusion Overall, our study provides insights into the convergence of the domestication processes in the Solanaceae family. Our results point out the influence of sympatry and allopatry between the crop and the wild compartments to explain the gene flows. These inferences bring as well new details about the timing of domestication and therefore insights into human history and how and when societies domesticated species. It confirms the importance of understanding how plant species respond to human manipulation. By knowing the past behavior of crops facing domestication events, we may potentially improve modern breeding efforts to sustain future crop breeding.
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hal-03562873 , version 1 (09-02-2022)

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  • HAL Id : hal-03562873 , version 1

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Stéphanie Arnoux, Christelle Fraïsse, Renaud Duboscq, Mathilde Causse, Christopher Sauvage. Comparative demographic study: reconstructing the evolutionary history of Solanaceae species to better understand the domestication process and outcome.. Capsicum and Eggplant EUCARPIA Meeting 2019, Sep 2019, Avignon, France. ⟨hal-03562873⟩
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