Unveiling the Patterns of Reticulated Evolutionary Processes with Phylogenomics: Hybridization and Polyploidy in the...

Area of Science:

• Evolutionary Biology
• Phylogenetics
• Genomics

Background:

• Reticulation (hybridization and polyploidization) significantly shapes plant evolution but is underrepresented in phylogenetic studies.
• Existing methods for analyzing reticulate evolution with broad taxon sampling are limited, hindering comprehensive evolutionary history reconstruction.
• The genus Rosa, with its numerous species and prevalence of hybridization/polyploidization, serves as a challenging model for phylogenetic analysis.

Purpose of the Study:

• To develop a general phylogenetic framework that incorporates reticulation patterns for the genus Rosa.
• To investigate the evolutionary relationships among Rosa species, considering hybridization and polyploidization.
• To provide a methodological approach applicable to other complex plant groups.

Main Methods:

• Utilized amplicon sequencing to analyze both nuclear and chloroplast genomes.
• Generated robust plastid and nuclear phylogenies.
• Employed a maximum pseudo-likelihood approach for hybridization scenario testing on taxon subsets.
• Implemented a diploid-first strategy followed by hybrid and polyploid grafting.

Main Results:

• Successfully recovered distinct plastid and nuclear phylogenies for Rosa.
• Resolved major evolutionary relationships among Rosa subgenera, sections, and species using the developed framework.
• Demonstrated the effectiveness of the stepwise strategy in handling complex reticulate evolution.

Conclusions:

• The proposed framework effectively accounts for reticulation in phylogenetic studies of species-rich genera like Rosa.
• The findings offer new insights for revising the infrageneric classification of Rosa.
• The methodology is adaptable for reconstructing phylogenies in other challenging taxonomic groups with extensive hybridization and polyploidy.