Genomic inference of complex domestication histories in three Solanaceae species. (10th November 2020)

• Record Type: Journal Article
• Authors: Arnoux, Stéphanie; Fraïsse, Christelle; Sauvage, Christopher
• Is Part Of: Journal of evolutionary biology. Volume 34:Number 2(2021)
• Page Start: 270
• Page End: 283
• Publication Date: 2020-11-10
• Subjects: allele frequency spectrum -- demographic inference -- domestication -- population genomics -- Solanaceae; Evolution (Biology) -- Periodicals; Biology -- Periodicals; 576.8
• DOI: 10.1111/jeb.13723
• Languages: English
• ISSNs: 1010-061X

Abstract

Abstract: Domestication is a human‐induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species‐specific demographic processes between species. A convergent history of domestication with gene flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a "protracted period" of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species‐specific and supported by the few historical records available. Abstract : Transcriptomic data of crop and wild populations helped us to reconstruct demographic processes in three Solanaceae species (eggplant, pepper, tomato): historical gene flow, effective population size changes and their timing. Our findings were supported by historical records, and could confirm that divergent management strategies of modern cultivar could affect both gene flow and reduction in effective size