Interspecific hybridization events have played a major role in plant speciation, yet the evolutionary origin of hybrid species often remains enigmatic. Here, we inferred the evolutionary origin of the allotetraploid species Coffea arabica, which is widely cultivated for Arabica coffee production. We estimated genetic distances between C. arabica and all species that are known to be closely related to C. arabica using genotyping-by-sequencing (GBS) data. In addition, we reconstructed a time-calibrated multilabeled phylogenetic tree of 24 species to estimate the age of the C. arabica hybridization event. Ancestral states of self-compatibility were also inferred to shed new light on the evolution of self-compatibility in Coffea. Coffea canephora and C. eugenioides were confirmed as the putative progenitor species of C. arabica. These species most likely hybridized between 1.08 million and 543 000 years ago, coinciding with periods of environmental upheaval, which may have induced range shifts of the progenitor species that facilitated the emergence of C. arabica.

中文翻译：

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系统基因组学分析阐明了小粒咖啡的进化起源

种间杂交事件在植物物种形成中发挥了重要作用，但杂交物种的进化起源往往仍然是个谜。在这里，我们推断了异源四倍体物种Coffea arabica的进化起源，该物种被广泛种植用于生产阿拉比卡咖啡。我们使用基因分型测序 (GBS) 数据估计了C. arabica与已知与C. arabica密切相关的所有物种之间的遗传距离。此外，我们重建了 24 个物种的时间校准多标记系统发育树，以估计C. arabica杂交事件的年龄。还推断了自交的祖先状态，以揭示自交的进化咖啡。Coffea canephora和C. eugenioides被确认为C. arabica的推定祖先物种。这些物种最有可能在 108 万至 543 000 年前杂交，当时环境动荡时期可能导致祖先物种的范围变化，从而促进了C. arabica的出现。