Diversification of chiles (Capsicum, Solanaceae) through time and space: New insights from genome-wide RAD-seq data

Area of Science:

• Botany
• Evolutionary Biology
• Genomics

Background:

• The genus *Capsicum* includes 43 American species, encompassing globally significant sweet and hot chiles.
• Understanding the evolutionary history and diversification of *Capsicum* is crucial for crop improvement and biodiversity conservation.

Purpose of the Study:

• To construct an updated, age-calibrated phylogenetic hypothesis for the *Capsicum* genus.
• To propose a novel model for the spatial diversification of *Capsicum* species.
• To provide the first dated evolutionary history for the genus, including most chile species.

Main Methods:

• Phylogenetic reconstruction using maximum likelihood approaches on genome-wide RAD-seq derived single nucleotide polymorphisms (SNPs).
• Estimation of divergence dates for major splits using an age-calibrated model.
• Inference of ancestral ranges and modeling of diversification events using Bayesian approaches.

Main Results:

• Nine well-supported clades representing genetically and geographically distinct lineages were identified, diversifying from the mid-upper Miocene.
• The Northern and Central Andes were inferred as the ancestral range for *Capsicum*.
• Diversification began in the Pliocene and continued through the Pleistocene, with the Central Andes playing a key role in domesticated pepper lineages.

Conclusions:

• The study provides high-resolution phylogenetic insights into *Capsicum* evolution and geographic expansion.
• A dated evolutionary history for the genus has been established, incorporating extensive species diversity.
• The findings highlight the significant role of the Central Andes in the diversification of chili peppers.