Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere

Abstract

The tree of life (TOL) is a powerful framework to depict the evolutionary history of cellular organisms through time, from our microbial origins to the diversification of multicellular eukaryotes that shape the visible biosphere today. During the past decades, our perception of the TOL has fundamentally changed in part due to profound methodological advances which allowed a more objective approach to studying organismal and viral diversity and led to the discovery of major new branches in the TOL as well as viral lineages. Phylogenetic and comparative genomics analyses of this data have, among others, revolutionized our understanding of the deep roots and diversity of microbial life, the origin of the eukaryotic cell, eukaryotic diversity as well as the origin and diversification of viruses. In this review, we provide an overview of some of the recent discoveries on the evolutionary history of cellular organisms and their viruses and discuss a variety of complementary techniques that we consider crucial for making further progress in our understanding of the TOL and its interconnection with the virosphere.

Highlight: Unraveling the Origins of LUCA and LECA on the Tree of Life

“…LUCA, last universal common ancestor; LECA, last eukaryotic common ancestor. Adapted from Spang et al (2022) .…”

“…Headlining this Virtual Issue is a review from Anja Spang, Tara A. Mahendrarajah, Pierre Offre, and Courtney W. Stairs titled “Evolving perspective on the origin and diversification of cellular life and the virosphere” ( Spang et al 2022 ). Their article summarizes recent findings regarding LUCA and LECA, as well as the potential role of viruses in the evolution of both prokaryotes and eukaryotes.…”

“…While it is generally assumed that the root of the tree of life lies in between archaea and bacteria, it is difficult to formally rule out alternatives due to the potential for phylogenetic artifacts. Furthermore, the root of the archaea and in particular the placement of the diverse DPANN archaea (an acronym based on the first five groups discovered: Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota), which represent many lineages with symbiotic and small genome members, remains uncertain ( Spang et al 2022 ). It is particularly challenging to accurately place symbionts in phylogenetic trees among others because they can exchange genes with their hosts and often experience faster evolutionary rates, which in turn can confound tree-building methods.…”

“…Despite this, they found that most large concatenated data sets were consistent with the monophyly of the DPANN superphylum in unrooted phylogenies, highlighting the difficulty in correctly inferring deep relationships among these lineages. While various concatenated gene tree inferences suggest that the DPANN form a monophyletic clade, it remains to be assessed whether they are monophyletic and deep-branching in rooted trees ( Spang et al 2022 ).…”

“…As detailed in the Spang et al (2022) review, phylogenetic analyses have recently suggested that the closest archaeal sister lineage to eukaryotes may be the Asgard archaea, a proposed superphylum consisting of the Lokiarchaeota, Thorarchaeota, Odinarchaeota, and Heimdallarchaeota. As further evidence for this, Penev et al (2020) discovered that the large ribosomal subunit (LSU) rRNA of the Lokiarchaeota and Heimdallarchaeota bridge the gap in size between prokaryotic and eukaryotic LSU rRNAs.…”