Phylogenomic Analysis of Deep-Branching Telonemid

Area of Science:

• Eukaryotic evolution
• Phylogenomics
• Protist diversity

Background:

• Eukaryotic supergroup evolutionary history is often hindered by sparse sampling in major groups.
• The phylum Telonemia, with two subgroups (TEL1 and TEL2), has limited multigene phylogenomic data, primarily from TEL1 species.
• Previous studies show instability in the placement of Telonemia and related supergroups like SAR, Hemimastigophora, Provora, and Haptista.

Purpose of the Study:

• To investigate the impact of a newly sequenced TEL2 subgroup telonemid on the phylogenetic placement of Telonemia.
• To resolve the evolutionary relationships between Telonemia, Stramenopila-Alveolata-Rhizaria (SAR), Hemimastigophora, Provora, and Haptista.

Main Methods:

• Isolation and single-cell transcriptome sequencing of a novel TEL2 telonemid from the Pacific Ocean.
• Phylogenomic analysis using maximum-likelihood (ML) and Bayesian inference methods.
• Systematic variation of Telonemia sampling, gene sampling, and alignment parameters to assess phylogenetic robustness.

Main Results:

• ML analysis consistently supported Telonemia as sister to Hemimastigophora, which together are sister to SAR, with Haptista and Provora forming a separate clade.
• Bayesian analysis failed to converge, indicating topological instability.
• The inclusion of the TEL2 telonemid did not significantly alter the observed phylogenetic relationships, but highlighted the inherent instability of these groups' placements across different analytical schemes.

Conclusions:

• The phylogenetic position of Telonemia remains complex and potentially unstable, despite the inclusion of new data.
• The sisterhood of Telonemia and Hemimastigophora is robustly supported by ML analyses, even when their relationship to SAR is resolved differently.
• This study underscores the challenges in resolving deep eukaryotic phylogeny due to data limitations and the dynamic nature of evolutionary relationships among sparsely sampled groups.