Phylogenomic Analysis Reconstructed the Order Matoniales from Paleopolyploidy Veil

Area of Science:

• Evolutionary biology
• Plant systematics
• Genomics

Background:

• Phylogenetic conflicts obscure the evolution of early terrestrial plants, particularly concerning whole genome duplication events (polyploidization).
• Understanding the evolutionary mechanisms driving phylogenetic conflicts, such as polyploidization, is crucial for resolving plant evolutionary history.

Purpose of the Study:

• To reconstruct a robust phylogeny and network for early leptosporangiate ferns, incorporating a broad species sample and numerous orthologs.
• To identify and characterize whole genome duplication events within leptosporangiate fern lineages.
• To investigate the association between polyploidization, speciation rates, and mass extinction events.

Main Methods:

• Phylogenetic reconstruction using 1125 1-to-1 orthologs via coalescent and concatenation methods.
• Increased species sampling to represent all four orders and eight families of early leptosporangiate ferns.
• Identification and localization of whole genome duplication events.

Main Results:

• A robust phylogenetic tree and network for early leptosporangiate ferns were reconstructed, supporting the redefinition of Matoniales as an ordinal rank.
• At least 11 whole genome duplication events were identified within four leptosporangiate lineages.
• Polyploidization was associated with increased speciation rates and mass extinction events.

Conclusions:

• Paleopolyploidization may have facilitated the survival of leptosporangiate ferns during mass extinctions, such as at the end of the Permian period.
• Ancient polyploidy can drive rapid species radiation, contributing to phylogenetic conflicts while enabling plant survival and diversification.
• The study provides insights into how polyploidization impacts plant evolution, speciation, and adaptation to environmental changes.