Persistent conflict in palaeognath phylogeny revealed by quartet-based and ML analyses

Area of Science:

• Evolutionary Biology
• Genomics
• Bioinformatics

Background:

• Palaeognath bird evolutionary history is debated despite extensive phylogenomic studies.
• Ostrich is consistently the earliest diverging lineage, but relationships among other palaeognaths are unresolved.
• Conflicting topologies and low support across datasets hinder definitive conclusions.

Purpose of the Study:

• To reanalyze genomic datasets using advanced phylogenetic methods.
• To resolve the contentious evolutionary relationships among non-ostrich palaeognaths.
• To investigate the underlying causes of phylogenetic uncertainty.

Main Methods:

• Reanalysis of three genomic marker sets: CNEEs, UCEs, and INTRONs.
• Application of alternative maximum-likelihood (ML) approaches.
• Utilized the quartet-based SeaLion method to assess phylogenetic signal.

Main Results:

• Confirmed ostrich as the earliest diverging lineage and supported ratite paraphyly.
• Non-ostrich palaeognath relationships remained ambiguous across datasets.
• UCEs dataset suggested a 'tinamou-first' scenario, with tinamou + moa sister to others; rhea and kiwi formed a distinct pair.

Conclusions:

• Unresolved palaeognath relationships stem from intrinsic data limitations, not analytical flaws.
• Short internal branches and incomplete lineage sorting suggest a potential true polytomy.
• Future research requires more high-quality genomes for robust phylogenetic inference.