In a way, this article [see attached] is a sequel to the Moody et al. publication [The nature of the last universal common ancestor and its impact on the early Earth system. Nat Ecol Evol. 2024; 8: 1654-1666] — which was featured in our GEITP email blog on 25 Aug 2024. THAT paper was the first time we had seen “dated-gene-duplication” as a novel way to elucidate evolutionary-time molecular-clock methodology, using the sequential Bayesian approach. [This comes as no surprise, because both papers come from the same laboratory (Philip C.J. Donogue’s lab, School of Earth Sciences, University of Bristol, Bristol, UK) and they use the same dated-gene-duplication technology.]
Except the 2024 study described the earliest likely appearance of the last universal common ancestor (LUCA) — which of course defined prokaryotes (single-celled organisms belonging to the domains Bacteria and Archaea, characterized by the absence of a distinct nucleus and membrane-bound organelles, but the presence of a cell wall, ribosomes, and free-floating DNA), whereas the present study [see attached] decribes eukaryotes (organisms whose cells contain a distinct membrane-bound nucleus and specialized organelles — such as mitochondria and the endoplasmic reticulum; they denote a complex domain of life — including plants, animals, fungi and protists, which can be either multicellular or unicellular).
The origin of eukaryotes has been a formative but poorly understood event in our current studies of the history
of Life. Present-day hypotheses of eukaryogenesis differ principally in the timing of mitochondrial endosymbiosis relative to the acquisition of other eukaryote novelties (listed above). Discriminating among these hypotheses has been challenging, because there are no living lineages representative of intermediate steps within eukaryogenesis.
Many eukaryotic cell functions are contingent, however, on genes that emerged from duplication events during eukaryogenesis. Therefore, the timescale of these duplications can provide insights into the sequence of steps in the evolutionary assembly of the eukaryotic cell. Authors show [see attached pdf file], using a relaxed molecular clock and the sequential Bayesian approach, that the process of eukaryogenesis spanned the Mesoarchaean Era (lasting from 3.2 billion years ago (BYA) to 2.8 BYA) to the late Paleoproterozoic Era [1 BYA to 538.8 million-years-and-one-month ago (😉sarcastic joke) — which was a pivotal time of transition — featuring extreme climate shifts (“Snowball Earth”), assembly and breakup of the supercontinent Rodinia, and emergence of the first complex multicellular animal life (Ediacaran biota) ].
Within these constraints, authors dated the timing of these gene duplications — which reveal that the eukaryotic host cell already had complex cellular features before mitochondrial endosymbiosis, including an elaborate cytoskeleton, membrane trafficking, endomembrane, phagocytotic machinery, and a nucleus — all between 3.0 and 2.25 billion years ago, after which mitochondrial endosymbiosis occurred. [Mitochondrial endosymbiosis, the process by which an ancestral archaeal cell engulfed an alpha-proteobacterium, is generally believed to have occurred approximately 1.5 to 2.0 BYA. Classically, this foundational event in eukaryogenesis is presumed to have taken place during the Proterozoic Eon, preceding the last eukaryotic common ancestor (LECA)]
The data in this attached article therefore enable scientists to reject “the mitochondrion-early” scenarios of eukaryogenesis, instead supporting “a complexified-archaean, late-mitochondrion sequence for the assembly of eukaryote characteristics.” The authors’ inferred complex archaeal host cell is also compatible with hypotheses on the adaptive benefits of syntropy in oceans — that otherwise would have remained largely anoxic for more than a billion years.
[Syntropy is the propensity of systems to move toward higher order, complexity, organization, and life — acting as the opposite of entropy (disorder and chaos); syntropy represents a “turning together” or convergent tendency — often linked to energy concentration and life-sustaining processes. It is sometimes called negentropy.]
Therefore, this relatively new concept of the “dated-gene-duplication approach” as a novel way to elucidate evolutionary-time molecular-clock methodology using the sequential Bayesian approach — has definitely modified our way of thinking about the history of Life on early Earth. The (Moody et al., 2024) paper has inferred the origin of prokaryote Life on early Earth occurred by ~4.2 BYA, rather than the much-later estimates of ~3.5 BYA. The current 2026 study [Kay et al., see attached] strongly suggests that the origin of eukaryotes, the process of eukaryogenesis, had already occurred as early as ~3.2 BYA — rather than the classical thinking that “eukaryotes had originated much later (approximately 1.8 BYA to 2.7 BYA) through endosymbiosis (in which an archaeal host cell engulfed an alpha-proteobacterium that ultimately became the mitochondrion).” 😊
DwN
Nature. 5 Feb 2026; 650: 129-140
COMMENTS:
Dear David,
I must admit that I had never heard of Johan Peter Gogarten (Univ of Connecticut) or his research career before. ☹
—DwN
From: Nelson, David
Sent: Monday, April 13, 2026 9:08 AM
Dear Dan,
This advance [see attached pdf file] in dated gene-duplication methodology to infer evolutionary age — reminds me of Gogarten’s similar efforts “to date origins by gene duplications,” starting back in the 1990s. For examples, see:
Linkkila TP, Gogarten JP. (1991) Tracing origins with molecular sequences: Rooting the universal tree of life. Trends Biochem Sci 16: 287-288.
Gogarten JP. (1995) The early evolution of cellular life. Trends Ecol Evol 10: 147-151.
Gogarten JP, Olendzenski L. (1999) Orthologs, paralogs and genome comparisons. Curr Opin Genet Dev 9: 630-636.
Gogarten JP, Doolittle WF, Lawrence JG. (2002) Prokaryotic evolution in light of gene transfer. Mol Biol Evol 19: 2226-2238.
Zhaxybayeva O, Lapierre P, Gogarten JP (2006) Ancient gene duplications and the root(s) of the tree of life. Protoplasma 227: 53-64.
Williams TA, & seven others, (2017) Integrative modeling of gene and genome evolution roots the archaeal tree of life. Proc Natl Acad Sci USA 114: E4602-E4611.
—Although the methods are much more sophisticated today (i.e., with hundreds of Archaea and Bacteria genomes sequenced and available on the internet).