Extreme Deviations from Expected Evolutionary Rates in Archaeal Protein Families.

Area of Science:

• Genomics and Evolutionary Biology
• Computational Biology
• Molecular Evolution

Background:

• New biological functions arise through various mechanisms, including gene duplication and horizontal gene transfer.
• Neofunctionalization and subfunctionalization of proteins are often linked to paralogs evolving under relaxed or positive selection.
• Phylogenetic anomalies can indicate accelerated evolution and functional divergence in gene families.

Purpose of the Study:

• To develop and apply a computational pipeline for identifying lineage-specific subfamilies with anomalous evolutionary rates in archaeal genes.
• To detect potential instances of neofunctionalization and subfunctionalization within orthologous gene clusters.
• To investigate the evolutionary dynamics of gene families, including acceleration and deceleration of evolutionary rates.

Main Methods:

• Analyzed 1,834 orthologous clusters of archaeal genes using a custom computational pipeline.
• Focused on identifying gene subfamilies exhibiting significant deviations from expected evolutionary rates.
• Constructed phylogenetic trees to detect anomalies such as long branches and lineage-specific expansions.

Main Results:

• Identified multiple potential cases of neofunctionalization and subfunctionalization in ancient, housekeeping gene families (e.g., ribosomal protein S10, TFIIB, Hsp20).
• Observed that accelerated evolution is frequently associated with lineage-specific gene duplication and horizontal gene transfer.
• Noted that evolutionary rate deceleration is less common and its causes remain unclear, possibly involving increased functional constraints.

Conclusions:

• The developed pipeline effectively detects evolutionary anomalies indicative of functional innovation in archaeal gene families.
• The findings highlight the roles of gene duplication and horizontal gene transfer in shaping protein evolution and function.
• This approach provides a valuable tool for selecting experimental targets to uncover novel biological functions.