The complex evolutionary history of apricots: Species divergence, gene flow and multiple domestication events

Abstract

Domestication is an excellent model to study diversification and this evolutionary process can be different in perennial plants, such as fruit trees, compared to annual crops. Here, we inferred the history of wild apricot species divergence and of apricot domestication history across Eurasia, with a special focus on Central and Eastern Asia, based on microsatellite markers and approximate Bayesian computation. We significantly extended our previous sampling of apricots in Europe and Central Asia towards Eastern Asia, resulting in a total sample of 271 cultivated samples and 306 wild apricots across Eurasia, mainly Prunus armeniaca and Prunus sibirica, with some Prunus mume and Prunus mandshurica. We recovered wild Chinese species as genetically differentiated clusters, with P. sibirica being divided into two clusters, one possibly resulting from hybridization with P. armeniaca. Central Asia also appeared as a diversification centre of wild apricots. We further revealed at least three domestication events, without bottlenecks, that gave rise to European, Southern Central Asian and Chinese cultivated apricots, with ancient gene flow among them. The domestication event in China possibly resulted from ancient hybridization between wild populations from Central and Eastern Asia. We also detected extensive footprints of recent admixture in all groups of cultivated apricots. Our results thus show that apricot is an excellent model for studying speciation and domestication in long‐lived perennial fruit trees.

Genetic Structure of a Worldwide Germplasm Collection of Prunus armeniaca L. Reveals Three Major Diffusion Routes for Varieties Coming From the Species’ Center of Origin

“…Overall, our study provided strong support that the region of Central Asia including China constituted the center of origin of apricot species which included a high and particular genetic diversity that can be considered as a reservoir of potentially interesting genes to sustain modern breeding programs. For the Central Asian cluster, the ABC method revealed that the apparent increased effective population size may be the consequence of the massive introgression of highly diverse wild material in the cultivated gene pool which would have raised genetic diversity as also suggested by Liu et al (2019).…”

“…Thus, vegetative propagation enables more controlled selection of favored phenotypic characteristics than under sexual reproduction (Denham et al, 2020). Conversely, no bottlenecks were identified from the wild genetic pool in Central Asia to European, Southern Central Asia and Chinese cultivated apricots (Decroocq et al, 2016;Liu et al, 2019). This is probably explained by the limited number of generations since domestication due to long juvenile phases, ongoing gene flow between domesticated and wild accessions (Miller and Gross, 2011;Gaut et al, 2015) and, to a lesser extent, to clonal propagation (because it is difficult to carry out on apricot species in comparison with plum, peach, apple and grape).…”

Congruent population genetic structures and divergence histories in anther‐smut fungi and their host plants Silene italica and the Silene nutans species complex

“…We ran the ABC procedure modified from Liu et al (2019). Briefly, we simulated data sets with 22 fungal microsatellite markers using the abctoolbox program (Wegmann, Leuenberger, Neuenschwander, & Excoffier, 2010) and used fastsimcoal 2.5 for coalescent‐based simulations (Excoffier & Foll, 2011).…”

“…The divergence history of the host has already been inferred (Martin et al, 2016(Martin et al, , 2017Van Rossum et al, 2018). To increase our power to distinguish between different evolutionary scenarios, we performed model choice and parameter estimation by comparing scenarios or groups of scenarios in sequential rounds, each round testing a particular type of evolutionary event, either divergence time, order of divergence or presence of gene flow (Estoup, Raynal, Verdu, & Marin, 2018;Liu et al, 2019) (Table 1; Table S5). We built scenarios based on the genetic clusters obtained using microsatellite markers and on previous analyses of divergence of anther-smut fungi and their host species (Badouin et al, 2017;Gladieux et al, 2013;Martin et al, 2016Martin et al, , 2017Van Rossum et al, 2018).…”

Modern Strategies to Assess and Breed Forest Tree Adaptation to Changing Climate

“…ML has historically been utilized in functional genomics (Libbrecht and Noble, 2015) and ecological niche modeling (Phillips et al, 2017). Yet, it is now transitioning into GWAS-coupled MAS (Cortés et al, 2015a), GP (Crossa et al, 2019;Abdollahiarpanahi et al, 2020), GWSS (Schrider and Kern, 2018), and demographics-as when coupled with Approximate Bayesian Computation (Elleouet and Aitken, 2018;Liu et al, 2019).…”