Before the mid-1970s, evolution (or “The Tree of Life”) was simple: everything was divided up into “animals, plants, and bacteria.” Or, “eukaryotes” (having paired chromosomes inside a nucleus with a membrane to separate it from cytoplasm) and “prokaryotes” (having single unpaired chromosomes and no nuclear membrane). Then, biologist Carl Woese’s discovery of Archaebacteria (distinct from Eubacteria — although both have single unpaired chromosomes and no nuclear membrane) in 1977 led scientists to propose that the Tree of Life diverged long ago into three main trunks, or “domains” — one trunk gave rise to modern bacteria (eubacteria), 2nd archaebacteria, and 3rd eukaryotes. Debates soon erupted, however, over the structure of these trunks. A popular ‘three-domain’ model postulated that archaea and eukaryotes diverged from a common ancestor. But a two-domain model suggested that eukaryotes diverged directly from a subgroup of archaea [see attached editorial].
One more recent proposal (for the two-domain tree), using deep-sequencing of DNA, suggests that modern eukaryotes belong to the same archaeal group. If that is the case, then essentially all complex life — everything from green algae to humans — originally arose from archaea. But many evolutionary scientists remain unconvinced. What’s at stake is a deeper understanding of the Biological Leap that produced eukaryotes. Many on both sides agree that the origin of eukaryotes probably involved a step known as endosymbiosis (i.e. one symbiotic organism living inside, and being dependent on, the other). This theory holds that a simple host cell (living perhaps 2.8 to 2.2 billion years ago), somehow swallowed a bacterium, and the two struck up a mutually beneficial relationship. These “captive bacteria” eventually evolved into
mitochondria — the cellular substructures that produce energy — and the hybrid cells became what are now known as eukaryotes.
But what was the nature of the “engulfing cell?” One camp says the engulfer was an ancestral microbe, now extinct, a “proto-eukaryote” — “neither a modern archaeon nor a modern eukaryote.” In this model, there were several major splits in early evolution: first, billions of years
ago, when primeval organisms gave rise to both bacteria and an extinct group of microbes; then this latter group diverged into archaea and the group that became eukaryotes. In the other camp, the two-domain world, a primeval organism gave rise to bacteria and archaea; and the organism that eventually swallowed the bacterium was an archaeon. This model would make all eukaryotes an “advanced ancestor” of the archaebacteria [the second, lower, model illustrated in the diagram].
Today, researchers are turning to other lines of evidence that might support a two-domain tree. Eubacteria and eukaryotes have cell membranes consisting of one set of lipids, whereas archaeal membranes contain a different set of lipids (this would imply more relatedness between eubacteria and eukaryotes, with archaea being a separate entity), and it was believed that “the two sets of lipids could not mix together.” However, researchers have now succeeded in engineering bacteria having cell membranes that contain both archaeal and bacterial lipids. Scientists have also found bacteria in the Black Sea that have genes for making both types of lipids — implying that microbes could have had such mixed membranes during the transition from archaea to eukaryotes. The two possible Trees of Life with differing domains are illustrated in a diagram on page 324 of the attached editorial.
Nature 16 May 2019; 569: 322-324