Resolving Rapid Radiations within Angiosperm Families Using Anchored Phylogenomics

Area of Science:

• Plant molecular evolution
• Phylogenomics
• Angiosperm phylogeny

Background:

• Traditional plant phylogenetic studies rely on limited DNA regions like plastid and nuclear ribosomal DNA (nrDNA).
• These markers have limitations including linked loci and insufficient characters, leading to low confidence in phylogenetic estimates, particularly for rapidly radiating lineages.
• Previous work introduced flowering plant-specific anchored enrichment probes for conserved nuclear genes.

Purpose of the Study:

• To address challenges in phylogenetic reconstructions below the family level, specifically weak or unresolved backbones caused by rapid radiations.
• To test the effectiveness of a large nuclear gene dataset for resolving phylogenetic relationships in the Cariceae-Dulichieae-Scirpeae (CDS, Cyperaceae) clade.

Main Methods:

• Generated a nuclear phylogenetic matrix using 461 conserved nuclear genes via anchored hybrid enrichment.
• Compared this nuclear dataset with a traditional Sanger sequencing dataset (plastid genes matK, ndhF, and nrDNA marker ETS).
• Performed both concatenated and coalescence-based phylogenetic analyses.

Main Results:

• The nuclear dataset resolved short backbone internodes with high support, outperforming the traditional Sanger dataset.
• Nuclear gene tree incongruence was found to be inversely proportional to phylogenetic information content, suggesting gene tree estimation error.
• Phylogenetic estimates were robust and congruent with previous morphological and molecular analyses.

Conclusions:

• Large numbers of conserved nuclear loci provide more accurate phylogenetic trees than rapidly evolving regions prone to saturation and long-branch attraction.
• Anchored hybrid enrichment with numerous nuclear genes is effective for resolving phylogenetic relationships in flowering plants, even below the family level.
• The findings support a comprehensive tribal revision of the CDS clade (Cyperaceae).