The impact of Pleistocene glaciations and environmental gradients on the genetic structure of Embothrium coccineum

The South American temperate forests were subjected to drastic topographic and climatic changes during the Pliocene‐Pleistocene as a consequence of the Andean orogeny and glacial cycles. Such changes are common drivers of genetic structure and adaptation. Embothrium coccineum (Proteaceae) is an emblematic tree of the South American temperate forest (around 20°S of latitude) that has strongly been affected by topographic and climatic events. Previous studies have shown a marked genetic structure in this species, and distinct ecotypes have been described. Yet, little is known about their adaptive genetic responses. The main goal of this study was to investigate the effects of historical and contemporary landscape features affecting the genetic diversity and connectivity of E. coccineum throughout its current natural distribution. Using over 2000 single nucleotide polymorphisms (SNPs), we identified two genetic groups (a Northern and a Central‐Southern group) that diverged around 2.8 million years ago. The level of genetic structure was higher among populations within the Northern genetic group than within the Central‐Southern group. We propose that these differences in genetic structure may be due to differences in the assemblages of pollinators and in the evolutionary histories of the two genetic groups. Moreover, the data displayed a strong pattern of isolation by the environment in E. coccineum, suggesting that selection could have led to adaptive divergence among localities. We propose that in the Chilean temperate forest, the patterns of genetic variation in E. coccineum reflect both a Quaternary phylogenetic imprint and signatures of selection as a consequence of a strong environmental gradient.