Fast-Evolving Alignment Sites Are Highly Informative for Reconstructions of Deep Tree of Life Phylogenies

Area of Science:

• Evolutionary Biology
• Phylogenetics
• Genomics

Background:

• The "slow-fast" analysis method assumes fast-evolving sites in sequence alignments lack phylogenetic signal due to substitution saturation.
• This method involves trimming fast-evolving sites, believing slower sites preserve a more accurate evolutionary record for phylogenetic reconstruction.
• This assumption is widely applied in Tree of Life studies using conserved proteins.

Purpose of the Study:

• To challenge the assumption that fast-evolving sites do not contain reliable phylogenetic information.
• To investigate the impact of trimming fast-evolving sites on the accuracy of phylogenetic reconstruction.
• To evaluate the phylogenetic signal in both slow- and fast-evolving sites using simulated and real datasets.

Main Methods:

• Simulated sequence alignments modeled after ribosomal protein datasets used in Tree of Life studies.
• Analysis of site-specific substitution rates and their correlation with the recovery of bipartitions.
• Examination of published Tree of Life sequence alignment datasets to assess phylogenetic signal consistency.
• Comparison of phylogenetic reconstruction outcomes using different site-trimming strategies (fast, slow, or both).

Main Results:

• Contrary to the "slow-fast" assumption, fast-evolving sites contain valuable phylogenetic information.
• Trimming fast-evolving sites negatively impacts phylogenetic reconstruction accuracy, with slow sites being less likely to recover true bipartitions.
• Site-specific substitution rates correlate positively with the accurate recovery of short-branched bipartitions.
• Both slow and fast sites exhibit similar levels of phylogenetic signal inconsistency, with fast sites' inconsistency often due to alignment quality issues.
• Trimming strategies significantly alter phylogenetic reconstruction, notably affecting the placement of Eukarya and Asgardarchaeota.

Conclusions:

• The "slow-fast" approach of trimming fast-evolving sites is not universally beneficial and can reduce phylogenetic accuracy.
• Fast-evolving sites, even in conserved proteins, retain significant phylogenetic information crucial for accurate evolutionary reconstructions.
• Alignment quality is a critical factor influencing the reliability of phylogenetic signals from fast-evolving sites.