Rosa Rubicondior: Creationism Refuted - Complex Life Evolved Almost a Billion Years Earlier That We Thought

December: Complex life developed earlier than previously thought, new study reveals | News and features | University of Bristol

Research led by the University of Bristol and published in the journal Nature a few days ago suggests that the transition from simple prokaryote cells to complex eukaryote cells began almost 2.9 billion years ago – nearly a billion years earlier than some previous estimates. Prokaryotes — bacteria and archaea — had been the dominant, indeed the only, life forms for the preceding 1.1 billion years, having arisen about 300 million years after Earth coalesced 4 billion years ago.

Creationists commonly forget that for the first billion or more years of life on Earth, it consisted solely of single-celled prokaryotes — bacteria and archaea. They routinely post nonsense on social media about the supposed impossibility of a complex cell spontaneously assembling from ‘non-living’ atoms — something no serious evolutionary biologist has ever proposed as an explanation for the origin of eukaryote cells.

There is now little doubt among biologists that complex eukaryote cells arose through endosymbiotic relationships between archaea and bacteria, which may have begun as parasitic or predator–prey interactions before evolving into symbioses as the endpoint of evolutionary arms races. The only questions concern when exactly eukaryote cells first began to emerge, and what triggered their evolution.

The team collected sequence data from hundreds of species and, combined with fossil evidence, reconstructed a time-resolved tree of life. They then used this framework to resolve the timing of historical events across hundreds of gene families, focusing on those that distinguish prokaryotes from eukaryotes.

One surprising finding was that mitochondria were late to the party, arising only as atmospheric oxygen levels increased for the first time — linking early evolutionary biology to Earth’s geochemical history.

Bacteria vs Archaea. Bacteria

Ubiquitous single-celled organisms found in virtually every habitat on Earth.
Cell membranes contain fatty acids linked to glycerol by ester bonds.
Cell walls usually contain peptidoglycan, a key distinguishing feature.
Many are pathogens, but most are harmless or beneficial.
Enormous metabolic diversity, from photosynthesis to nitrogen fixation.

Archaea

Also single-celled and superficially similar to bacteria in size and shape.
Membrane lipids use ether bonds and sometimes form monolayers, giving exceptional stability.
No peptidoglycan in their cell walls.
Known for thriving in extreme environments (e.g., hot springs, hypersaline lakes), but also abundant in oceans, soils, and even the human microbiome.
Genetically and biochemically closer to eukaryotes than to bacteria.

Prokaryotes vs Eukaryotes Prokaryotes (Bacteria + Archaea)

Lack a membrane-bound nucleus; DNA exists as a single circular chromosome in the cytoplasm.
No membrane-bound organelles such as mitochondria or chloroplasts.
Typically much smaller and structurally simpler.
Reproduce asexually by binary fission.
Metabolically versatile and capable of inhabiting extreme environments.

Eukaryotes

Possess a true nucleus enclosed by a membrane.
Contain membrane-bound organelles, notably mitochondria (and chloroplasts in plants and algae).
Larger, more complex cells capable of forming multicellular organisms.
DNA arranged in multiple linear chromosomes.
Include animals, plants, fungi, and protists.

Their work is summarised in a Bristol University press release.

Complex life developed earlier than previously thought, new study reveals
Complex life began to develop earlier, and over a longer span of time, than previously believed, a groundbreaking new study has revealed. The research sheds new light on the conditions needed for early organisms to evolve and challenges several long-standing scientific theories in this area.
Led by the University of Bristol and published in the journal Nature today [3 December], the research indicates that complex organisms evolved long before there were substantial levels of oxygen in the atmosphere, something which had previously been considered a prerequisite to the evolution of complex life.
The earth is approximately 4.5 billion years old, with the first microbial life forms appearing over 4 billion years ago. These organisms consisted of two groups – bacteria and the distinct but related archaea, collectively known as prokaryotes.

Anja Spang, co-author
Department of Marine Microbiology and Biogeochemistry
Royal Netherlands Institute for Sea Research (NIOZ)
Den Burg, The Netherlands.

Prokaryotes were the only form of life on earth for hundreds of millions of years, until more complex eukaryotic cells including organisms such as algae, fungi, plants and animals evolved.

Previous ideas on how and when early prokaryotes transformed into complex eukaryotes has largely been in the realm of speculation. Estimates have spanned a billion years, as no intermediate forms exist and definitive fossil evidence has been lacking.

Professor Davide Pisani, co-corresponding author
Bristol Palaeobiology Group
School of Biological Sciences
University of Bristol
Bristol, UK.

However, the collaborative research team has developed a new way of probing these questions, by extending on the ‘molecular clocks’ method which is used to estimate how long ago two species shared a common ancestor.

The approach was two-fold: by collecting sequence data from hundreds of species and combining this with known fossil evidence, we were able to create a time-resolved tree of life. We could then apply this framework to better resolve the timing of historical events within individual gene families.

Professor Tom A. Williams, co-lead author
Department of Life Sciences
University of Bath
Bath, UK.

Image credit: Dr Christopher Kay

By collecting evidence from multiple gene families (more than a hundred in total) in multiple biological systems and focusing on the features which distinguish eukaryotes from prokaryotes, the team were able to begin to piece together the developmental pathway for complex life.

Surprisingly the researchers found evidence that the transition began almost 2.9 billion years ago – almost a billion years earlier than by some other estimates – suggesting that the nucleus and other internal structures appear to have evolved significantly before mitochondria.

The process of cumulative complexification took place over a much longer time period than previously thought.

Gergely Szöllősi, co-author Model-Based Evolutionary Genomics Unit
Okinawa Institute of Science and Technology Graduate University
Okinawa, Japan.

The data meant the scientists have been able to reject some scenarios put forward for eukaryogenesis (the evolution of complex life), and their data did not neatly fit with any existing theory. Consequently, the team has proposed a new evidence-based scenario for the emergence of complex life they have called ‘CALM’ - Complex Archaeon, Late Mitochondrion.

What sets this study apart is looking into detail about what these gene families actually do - and which proteins interact with which - all in absolute time. It has required the combination of a number of disciplines to do this: palaeontology to inform the timeline, phylogenetics to create faithful and useful trees, and molecular biology to give these gene families a context. It was a big job.

Dr Christopher Kay, lead author
Bristol Palaeobiology Group
School of Earth Sciences
University of Bristol
Bristol, UK.

One of our most significant findings was that the mitochondria arose significantly later than expected. The timing coincides with the first substantial rise in atmospheric oxygen. This insight ties evolutionary biology directly to Earth’s geochemical history. The archaeal ancestor of eukaryotes began evolving complex features roughly a billion years before oxygen became abundant, in oceans that were entirely anoxic.

Professor Philip C. J. Donoghue, Bristol Palaeobiology Group
School of Earth Sciences
University of Bristol
Bristol, UK.

Publication:
Kay, C.J., Spang, A., Szöllősi, G.J. et al.
Dated gene duplications elucidate the evolutionary assembly of eukaryotes. Nature (2025). https://doi.org/10.1038/s41586-025-09808-z

Abstract
The origin of eukaryotes was a formative but poorly understood event in the history of life. Current hypotheses of eukaryogenesis differ principally in the timing of mitochondrial endosymbiosis relative to the acquisition of other eukaryote novelties¹. Discriminating among these hypotheses has been challenging, because there are no living lineages representative of intermediate steps within eukaryogenesis. However, many eukaryotic cell functions are contingent on genes that emerged from duplication events during eukaryogenesis^2,3. Consequently, the timescale of these duplications can provide insights into the sequence of steps in the evolutionary assembly of the eukaryotic cell. Here we show, using a relaxed molecular clock⁴, that the process of eukaryogenesis spanned the Mesoarchaean to late Palaeoproterozoic eras. Within these constraints, we dated the timing of these gene duplications, revealing that the eukaryotic host cell already had complex cellular features before mitochondrial endosymbiosis, including an elaborated cytoskeleton, membrane trafficking, endomembrane, phagocytotic machinery and a nucleus, all between 3.0 and 2.25 billion years ago, after which mitochondrial endosymbiosis occurred. Our results enable us to reject mitochondrion-early scenarios of eukaryogenesis⁵, instead supporting a complexified-archaean, late-mitochondrion sequence for the assembly of eukaryote characteristics. Our inference of a complex archaeal host cell is compatible with hypotheses on the adaptive benefits of syntrophy^6,7 in oceans that would have remained largely anoxic for more than a billion years^8,9.

Main
The origin of eukaryotes was a formative event in the history of life, in which a new kind of cell with distinct functional, morphological and ecological modalities evolved through an evolutionary merger between at least two prokaryotes: an Asgard archaeal host and an alphaproteobacterial endosymbiont^1,2,7,10,11. How and when eukaryotes originated, and the order in which the eukaryotic characteristics evolved, are the subject of intense debate2. Perhaps the most contentious distinction between competing hypotheses of eukaryogenesis concerns the relative timing of mitochondrion acquisition and whether or not it was a fundamental prerequisite to all other steps in the evolution of a eukaryote-grade cell. Other points of difference include the number of endosymbiotic partners involved in eukaryogenesis. Although most hypotheses agree on archaeal and alphaproteobacterial ancestry, the syntrophy hypothesis includes an additional, ∂-proteobacterial partner, which is suggested to have served as the host to an endosymbiotic Asgard archaeon (the future nucleus), to explain the bacterial character of the eukaryotic membrane⁷; in such a scenario the alphaproteobacterial ancestor of the mitochondrion entered the symbiosis at a later stage. The serial endosymbiosis hypothesis¹² invokes multiple, transient endosymbiotic partners preceding mitochondrial endosymbiosis to explain the presence of genes of bacterial origin in the eukaryotic nucleus that are not alphaproteobacterial in origin. Testing among these competing hypotheses is challenging because we lack extant taxa that represent intermediate steps of eukaryogenesis.

Questions about the order in which eukaryotic features emerged could be answered by determining when the genes that underpin key eukaryotic traits were acquired by proto-eukaryotes^2,3,12. Estimating the age of eukaryote novelties is complicated because gene trees do not have a node corresponding to mitochondrial acquisition; instead, they provide an estimate of the genetic distance to the last common ancestor of the eukaryotic and prokaryotic versions of a gene¹. Furthermore, eukaryotes have at least two stem lineages: one emerging from within Archaea (nuclear first eukaryotic common ancestor (nFECA)) and the other from within Bacteria (mitochondrial first eukaryotic common ancestor (mFECA))¹. However, gene duplication is a hallmark of eukaryotes^2,13, and previous work has shown that many genes that underpin important features of eukaryotic biology in the nucleus, cytoskeleton and mitochondrion underwent gene duplications in the eukaryote stem lineages, prior to the last eukaryotic common ancestor (LECA)^2,12. In many cases, the paralogues arising from these pre-LECA duplications have distinct roles in the implementation of eukaryote-specific features, such as the Sm–LSm complexes in the spliceosome¹⁴, actin and the actin-related proteins in the cytoskeleton¹⁵. These duplications are represented in gene trees by a duplication node that unites two descendant LECA clades. Dating this node provides a maximum estimate for the timing of origin of their paralogue-specific functions, identifying evolutionary events along the two stems. Thus, it should be possible to dissect the sequence of innovations in eukaryogenesis on the basis of the timing of duplication of paralogues associated with eukaryote innovations¹.

Our aim here is to establish a relative and absolute timeline for the evolutionary assembly of the eukaryotic cell. We use relaxed molecular clock methodology to date pre-LECA duplications, in order to constrain when each evolutionary novelty emerged along the nuclear and mitochondrial eukaryote stem lineages (Fig. 1a). To overcome difficulties with a lack of temporal resolution from short single-gene alignments, we use a sequential Bayesian approach to calibrate gene trees using age estimates for speciation nodes obtained from a dated species tree of archaea, bacteria and eukaryotes (following refs. ^4,16). Finally, we compare the fit of our estimates for the sequence of emergence of eukaryotic features against the geologic record and existing models of eukaryogenesis.

Fig. 1: Time-resolved species tree and gene duplications by prokaryotic origin.

a, A time-resolved tree of life. A cross-braced tree was produced using MCMCTree calibrated with 18 fossil calibrations (Supplementary Note 4). Nuclear and mitochondrial eukaryotic clades were asserted to have the same topology and root, and the plastid clade has a distinct topology resulting from secondary plastid acquisition events. Equivalent nodes containing the same species were cross-braced (as in ref. ³⁸)—that is, fixed to the same age. LPCA, last plastid common ancestor; LUCA, last universal common ancestor. b, Important node dates and their confidence intervals. c, Time-resolved gene duplications of archaeal and bacterial origins were binned into 100-Myr intervals and overlaid. Among the sample of genes that were amenable to analysis, archaeal duplications are more numerous and began earlier, perhaps reflecting elaboration of the archaeal host genome prior to mitochondrial endosymbiosis. d, Comparison of the individual duplication ages of alphaproteobacterial origin and all other bacterial duplications. The onset of alphaproteobacterial duplications happens rapidly after the divergence of mFECA from other alphaproteobacteria, suggesting a short bacterial stem. We align mitochondrial endosymbiosis to the onset of these duplications at around 2.2 Ga. e, Gene families of non-alphaproteobacterial origin are shown by the time of their divergence from their bacterial lineage of origin (black vertical lines), and subsequent pre-LECA duplications (blue vertical lines), joined by a horizontal rule. Duplications of bacterial origin have divergence ages up to 2.9 Ga, but most undergo duplication after mitochondrial endosymbiosis.

Fig. 2: Key gene duplications defining the cytoskeleton and nuclear compartment.

a, Eukaryotes inherited two families of cytoskeletal filament-forming proteins from Asgard archaea, which underwent multiple rounds of duplication before LECA and provide information about the evolution of cytoskeletal complexity. The nuclear compartment is defined by apparently eukaryote-specific gene families, although constraints on nuclear formation can be inferred from duplications in genes whose maturation pathways and function involve transport between compartments. b,c, Pre-LECA duplications in the RNA polymerase (b) and Sm–LSm (c) complexes. Symbols next to each gene family indicate lineage of descent (a, Asgard). Green shapes connect duplication events expected to have a similar age.

Fig. 3: Pre-LECA duplications in eukaryotic vesicle trafficking proteins.

Several gene families of archaeal ancestry participate in the processes of material transport between components of the endomembrane system of extant eukaryotes. a, Gene families of archaeal ancestry involved in budding, fusion and targeting of endomembrane vesicles. By considering the function of the LECA nodes descending from a duplication (colour coded), we infer that complexification of the endoplasmic reticulum, Golgi and plasma membrane preceded the evolution of functions specific to the endolysosomal system. b, Furthermore, we observe that distinct gene families that participate in the same endolysosomal compartment appear to have duplicated at around the same time (95% confidence intervals overlap). Format of the age distributions are as in Fig. 2. Green shapes connect duplication events expected to have a similar age. Symbols next to each gene family indicate lineage of descent (a, Asgard; A, other archaea).

Fig. 4: Pre-LECA duplications in the mitochondrion and in endomembrane biology.

In contrast to the systems shown in Figs. 2 and 3, these systems have many bacterial origin pre-LECA duplications. a, Multiple gene families of alphaproteobacterial origin are seen to duplicate within 200 Myr of mFECA; we hypothesize that the onset of these duplications corresponds to the time of mitochondrial endosymbiosis. b, Membrane biogenesis involves families of both bacterial and archaeal descent, including paralogues of archaeal proteins that now function in bacterial membrane lipid biosynthesis. From this and other evidence, we infer an archaeal origin for the endomembrane system that was later elaborated with gene products of bacterial descent. c, The endolysosomal system forms the digestive and recycling compartments of the eukaryotic cell. Specification of these compartments can be inferred from trafficking proteins (Fig. 3), and from the ages of their membrane transporter families we infer that this functional specialization emerged at the same time. Green shapes connect duplication events expected to have a similar age. Symbols next to each gene family indicate lineage of descent (a, Asgard; A, other archaea; α alphaproteobacteria; B, other bacteria). AA, amino acid.

Fig. 5: Timeline of development for eukaryotic key apomorphies.

a, Our time-resolved species tree enables us to set a timeline for eukaryogenesis. Compared with other studies, our dates for nFECA and mFECA are among the oldest, whereas our date for LECA is intermediate^{19,37,38,39,40,42,43,69,70,71}. b, Based on duplications in specific eukaryotic systems, we suggest a timeline for the emergence of these features. Vertical lines are suggested minimum limits for the emergence of features, and dashed horizontal lines denote the period of time for possible development and emergence. c, A tentative model that considers the interdependency of these features (arrowheads imply dependency; lines without arrowheads imply co-emergence but with as yet undetermined order). Data in a,b are aligned to the time axis, whereas in c, the nodes are grouped in relation to the nFECA and mitochondrial endosymbiosis boundaries. EGT, endosymbiotic gene transfer; ER, endoplasmic reticulum; MTOC, microtubule-organizing centre.

Kay, C.J., Spang, A., Szöllősi, G.J. et al.
Dated gene duplications elucidate the evolutionary assembly of eukaryotes. Nature (2025). https://doi.org/10.1038/s41586-025-09808-z

Copyright: © 2025 The authors.
Published by Springer Nature Ltd. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Findings such as these strike at the heart of a favourite creationist trope — the claim that scientists believe a complex, fully formed eukaryote cell somehow “assembled itself” spontaneously from raw chemicals. No biologist has ever proposed such a thing. The emergence of complex cells was not a single magical event but a protracted evolutionary process involving countless intermediary stages, gene family expansions, symbiotic relationships, and environmental pressures playing out over hundreds of millions of years. This new research simply reinforces what evolutionary biology has long demonstrated: complexity arises gradually, by descent with modification, not by fiat.

The creationist caricature depends entirely on misrepresenting the science. By pretending that biologists argue for instantaneous complexity, apologists manufacture a straw man they can knock down for the benefit of an audience unlikely to check the accuracy of their claims. Studies like this expose the tactic for what it is — a deliberate distortion designed to trade on scientific illiteracy. The genuine picture revealed by genomics, fossil evidence, and geochemistry is far richer, far slower, and far more fascinating than the simplistic mythology offered by creationist polemicists.

That creationist advocates continue to repeat slogans flatly contradicted by modern research speaks volumes about their priorities. Their arguments are crafted not to explain the natural world but to reassure a target market whose understanding of biology can be relied upon to remain superficial. In contrast, science progresses by confronting new evidence, refining timelines, and embracing complexity. The story of early life on Earth is still unfolding — and every new discovery widens the gulf between evidence-based biology and the contrived narratives of creationist apologetics.

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