Target Capture Sequencing Unravels Rubus Evolution

Area of Science:

• Botany
• Evolutionary Biology
• Genetics

Background:

• The genus Rubus (Rosaceae), encompassing raspberries and blackberries, is taxonomically complex with over 500 species.
• Existing taxonomic treatments are outdated, and challenges in phylogenetic estimation arise from polyploidy and hybridization.
• Understanding Rubus phylogeny is crucial for its systematic classification and evolutionary history.

Purpose of the Study:

• To estimate the phylogeny of diverse Rubus species and cultivars.
• To determine divergence times among major Rubus clades.
• To investigate the historical biogeography and diversification patterns of the genus.

Main Methods:

• Phylogenetic analysis using chloroplast DNA sequences.
• Target capture sequencing of approximately 1,000 low-copy nuclear genes.
• Divergence time estimation and biogeographical analysis.

Main Results:

• Eight major groups within Rubus were identified, with some traditional subgenera found to be polyphyletic.
• Evidence of multiple hybridization events at subgeneric levels, including between raspberry and blackberry lineages.
• The most recent common ancestor of Rubus likely originated in North America, with subsequent migrations to Asia and Europe during the Miocene.

Conclusions:

• Current Rubus taxonomy does not accurately reflect phylogenetic relationships, necessitating a subgeneric revision.
• Hybridization and incomplete lineage sorting contribute to phylogenetic discordance, highlighting the need for multi-method approaches.
• The study provides a phylogenetic framework for future research on Rubus systematics and evolution.