Phylogenomics Resolves Deep Phylogenetic Uncertainties and Hybridization in Rapidly Radiated Horseshoe Bats...

Area of Science:

• Evolutionary biology
• Genomics
• Bioinformatics

Background:

• Phylogenetic reconstruction is crucial for understanding evolutionary history and biogeography.
• Rapid radiation events, like in the bat genus Rhinolophus, pose challenges for resolving species-level phylogenies due to limited data and taxonomic sampling.
• Previous studies lacked comprehensive data to identify the ancestral clade within Rhinolophus.

Purpose of the Study:

• To resolve deep evolutionary relationships within the rapidly diversifying bat genus Rhinolophus.
• To investigate the role of introgression in the diversification and adaptation of Rhinolophus.
• To identify the ancestral clade and major clades within Rhinolophus using genome-wide data.

Main Methods:

• Utilized genome-wide nuclear datasets with comprehensive taxon sampling.
• Employed concatenation and coalescent-based phylogenetic reconstruction approaches.
• Conducted PhyloNet analyses to account for gene flow and genome-scale introgression analyses.

Main Results:

• Robustly recovered two sister clades: the Afro-Palaearctic and Asian clades within Rhinolophus.
• Resolved Rhinolophus hipposideros as the ancestral lineage of the Afro-Palaearctic clade.
• Observed significant mito-nuclear discordance, indicating widespread historical introgression, including adaptive introgression of antiviral genes (RANBP2, SERINC3).

Conclusions:

• Genome-scale data are powerful for resolving deep evolutionary relationships in rapidly radiating groups.
• Hybridization and introgression are significant mechanisms driving mammal diversification and adaptation, particularly in viral resistance.
• The study provides a robust phylogenetic framework for Rhinolophus and highlights the evolutionary impact of introgression.