HybPhaser identifies hybrid evolution in Australian Thelypteridaceae

Area of Science:

• Evolutionary biology
• Genomics
• Bioinformatics

Background:

• Hybridization is recognized as a significant driver of evolution in ferns.
• Investigating evolutionary reticulation in ferns has been historically challenging due to complex genetic processes.

Purpose of the Study:

• To evaluate the effectiveness of target sequence capture and read-to-reference phasing for studying fern hybridization.
• To utilize Australian Thelypteridaceae as a model system to explore evolutionary reticulation.

Main Methods:

• Employed the HybPhaser bioinformatics workflow to analyze sequence data.
• Assessed allelic divergence and phased sequence reads to reference genomes.
• Constructed haplotypes resembling parental lineages for phylogenetic and network analyses.

Main Results:

• Identified two previously unknown hybrid lineages within Thelypteridaceae.
• One hybrid involved intergeneric hybridization between Abacopteris and Christella.
• The other hybrid was part of a complex within the Christella genus.
• Hybrid phasing enhanced phylogenetic resolution and reduced conflicting data in the fern phylogeny.

Conclusions:

• The developed bioinformatics approach is powerful for detecting and analyzing hybrids in reticulate evolutionary histories.
• This method significantly improves the reconstruction of evolutionary pathways in ferns.
• The study provides new insights into the role of hybridization in Thelypteridaceae evolution.