The deep archaeal roots of eukaryotes

Area of Science:

• Genomics
• Evolutionary Biology
• Molecular Biology

Background:

• Eukaryotic genomes contain genes with apparent archaeal and bacterial origins.
• The precise evolutionary relationship between eukaryotes and archaea, particularly concerning informational genes, remains debated.
• Existing hypotheses suggest eukaryotic genes originated from Euryarchaeota, Crenarchaeota, or outside known archaeal diversity.

Purpose of the Study:

• To identify and characterize a comprehensive set of eukaryotic genes of apparent archaeal origin.
• To investigate the phylogenetic placement of these archaeal-derived genes within eukaryotes.
• To test hypotheses regarding the specific archaeal ancestors of eukaryotic genes.

Main Methods:

• Ortholog detection and phylogenetic analysis were used to identify 355 eukaryotic genes of apparent archaeal origin.
• Phylogenetic hypothesis testing with constrained trees was employed to evaluate evolutionary relationships.
• A systematic search for homologous inserts in conserved proteins was conducted to find shared derived characters.

Main Results:

• The majority of the analyzed archaeal genes in eukaryotes are best explained by a phylogenetic tree placing the eukaryotic lineage outside extant archaea.
• A small subset of these genes showed affinities to Crenarchaeota and Euryarchaeota.
• Evidence suggests these archaeal genes originate from an ancient, distinct archaeal lineage.

Conclusions:

• Eukaryotic archaeal genes likely derive from an ancient, previously uncharacterized archaeal lineage.
• This lineage acquired some genes from Euryarchaeota and Crenarchaeota via horizontal gene transfer.
• The findings refine our understanding of early eukaryotic evolution and archaeo-eukaryotic relationships.