Inferring phylogeny and introgression using RADseq data: an example from flowering plants (Pedicularis:...

Area of Science:

• Evolutionary Biology
• Genomics
• Phylogenetics

Background:

• Resolving phylogenetic relationships among recently diverged species is challenging due to limited phylogenetic signal and gene tree conflicts.
• Reduced-representation genome sequencing, such as restriction-site associated DNA (RAD) sequencing, offers a powerful approach for phylogenetic inference in non-model organisms.
• Detecting ancestral hybridization is crucial for understanding speciation processes.

Purpose of the Study:

• To evaluate the utility of RAD sequencing for phylogenetic inference and ancestral hybridization detection in the systematically challenging Pedicularis section Cyathophora.
• To resolve the phylogenetic relationships and investigate hybridization events within this Orobanchaceae clade.

Main Methods:

• Employed restriction-site associated DNA (RAD) sequencing to generate a large dataset of phylogenetic markers (up to 40,000 loci).
• Applied maximum likelihood and Bayesian concordance methods for phylogenetic inference.
• Utilized Patterson's D-statistic test, including a novel extension, to detect and resolve introgression events among taxa.

Main Results:

• Both phylogenetic methods recovered two distinct clades: 'rex-thamnophila' (low floral diversity, widespread, lower elevations) and 'superba' (high floral diversity, isolated, higher elevations).
• Molecular divergence levels were comparable between subspecies within the 'rex-thamnophila' clade and species within the 'superba' clade.
• Significant introgression was detected among most taxa in the 'rex-thamnophila' clade, but not between clades or within the 'superba' clade.

Conclusions:

• RAD sequencing is effective for resolving phylogenetic relationships and detecting hybridization in recently diverged species.
• Geographic isolation plays a significant role in species barrier formation by facilitating local adaptation and differentiation.
• The findings underscore the importance of geographic isolation in driving speciation in the absence of homogenizing gene flow.