Scientists study the distant connection between Archaea and Bacteria

Researchers have discovered more evidence to support the idea that the two primary domains of life, Archaea and Bacteria, are detached by a long phylogenetic tree branch and thus indirectly linked. The findings were published on February 22^nd, 2022, in the journal eLife.

The study adds to the ongoing debate over how far the archaeal domain diverges from the bacterial domain and sheds light on the limitations of traditional techniques for calculating the evolutionary process of ancient organisms.

The Archaea, along with Bacteria and Eukarya, comprise the three domains of the tree of life. Originally, Archaea were assumed to be a type of Bacteria, distinguished by their ability to withstand harsh environments. However, the use of molecular data to rebuild phylogenetic trees, as well as advances in genetic sequencing, has converted the understanding of the diversity of these organisms, as well as their connection with Bacteria and Eukarya.

A long branch length between organisms in the tree of life coincides with a greater degree of genetic transformation. Studies investigating the evolutionary history of Archaea and Bacteria predicted branch length by comparing differences in a core set of important genes encoding cellular machinery responsible for protein production and genetic data processing.

However, researchers have recently used a larger set of genetic markers from Bacteria and Archaea to evaluate the genetic distance between the two domains and presented a much shorter branch length—implying that the two domains were more strongly related.

This recent work raised two important issues regarding estimates about the universal tree of life. First, that estimates of the genetic distance between Archaea and Bacteria from the classic ‘core genes’ may not be representative of ancient genomes as a whole and, second, that there may be many more suitable genes to investigate early evolutionary history than previously realized, which could improve the precision and accuracy of these estimates.”

Edmund Moody, Study First Author and PhD Candidate, School of Biological Sciences, University of Bristol

Moody and colleagues analyzed the evolutionary development of the expanded 381 gene marker set and re-evaluated marker gene sets used during past studies to investigate the problems. They discovered multiple features of the expanded marker set, including inter-domain gene transmissions and paralogous genes—genes that have evolved through duplication and code for proteins with equivalent but not similar functions.

Our data suggests that the inclusion of marker genes with such features could artificially shorten the branch that separates the archaeal and bacterial domains.”

Tara Mahendrarajah, Study Co-Author and PhD Candidate, Royal Netherlands Institute for Sea Research

Gene marker sets that have conventionally been used include genes for many proteins that make up the ribosome—the cell’s machinery for translating DNA. It was proposed that if ribosome proteins went through an accelerated period of evolution at any moment, it could result in an artificially long phylogenetic tree branch.

As a result, the researchers compared a set of ribosomal and non-ribosomal gene markers to estimate values of branch length and discovered that they were similar.

These results did not support the hypothesis that ribosomal proteins evolved any faster than non-ribosomal genes, and affirm that ribosomal proteins are useful markers for phylogeny. However, the analyses suggested that both the true Archaea-Bacteria branch length and diversity of Archaea may be underestimated even by the best current models.”

Anja Spang, Study Co-Senior Author and Senior Scientist, Royal Netherlands Institute for Sea Research

Co-senior author Tom Williams, Associate Professor in Molecular Evolution at the School of Biological Sciences, University of Bristol also adds, “The debate around these issues really speaks to more general limitations of the current models: for example, it is clearly unsatisfactory to base our view of early evolution or genetic diversity on a small set of genes.”

“Exploring the evolutionary signal in more of the genome than we have been able to previously is an important goal that previous studies have approached in different ways. Our work suggests that new methods, including more realistic models of gene duplication, transfer, and loss, could help resolve some of the differing views by enabling genome-wide estimates of evolution while accounting for the varying evolutionary histories of individual gene families,” he concludes.