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Ancient hybridization and phylogenetic discordance: Exploring evolutionary complexity in Asteraceae
Paige A Ellestad1, Erika R Moore-Pollard1, Carolina M Siniscalchi1,2
1Department of Biological Sciences University of Memphis Memphis 38152 Tennessee USA.
Applications in Plant Sciences
|June 25, 2026
Summary
Phylogenetic discordance in Asteraceae reveals complex evolutionary histories driven by reticulation and whole-genome duplication (WGD). Our study provides insights into these processes and a tutorial for bioinformatic analyses in plant evolution.
Area of Science:
- Plant evolutionary biology
- Phylogenomics
- Bioinformatics
Background:
- Conflicting phylogenetic signals are common in plant phylogenomics.
- These signals often reflect complex evolutionary histories like hybridization, incomplete lineage sorting, and whole-genome duplication (WGD).
Purpose of the Study:
- To identify and assess complex evolutionary processes in the hyper-diverse Asteraceae family.
- To offer insights into the underlying causes of phylogenetic discordance within this family.
Main Methods:
- Utilized Hyb-Seq and transcriptome data to explore phylogenetic discordance.
- Tested for nuclear/plastid incongruences, whole-genome duplication (WGD), and reticulation events.
- Developed a tutorial for complex bioinformatic analyses to enhance transparency and reproducibility.
Main Results:
- Uncovered extensive discordance among nuclear gene trees and deep reticulation events, particularly in South American lineages.
- Detected signals of whole-genome duplication (WGD) across the family, though interpretation was challenging due to data complexity and ancient origins.
Conclusions:
- Reticulation and WGD play significant roles in the evolution of large, diverse plant clades like Asteraceae.
- The study highlights challenges in phylogenomic research and anticipates advancements in theoretical approaches for studying reticulate evolution.
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