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Two-domain system

The two-domain system is a phylogenetic classification of cellular life that posits two primary domains—Bacteria and Archaea—with eukaryotes emerging from within the Archaea as a derived lineage rather than a separate domain.^[1]^[2] This model contrasts with the traditional three-domain system proposed by Carl Woese in 1990, which treats Bacteria, Archaea, and Eukarya as distinct, monophyletic groups branching from a common ancestor. The two-domain hypothesis gained traction through phylogenomic analyses in the 2010s, emphasizing shared genomic and cellular features between eukaryotes and certain archaeal lineages, such as the Asgard superphylum.^[3] Key evidence for the two-domain system derives from advanced phylogenetic methods that analyze thousands of gene families across diverse taxa, revealing eukaryotes as nested within Archaea rather than as a sister group to both Bacteria and Archaea.^[2] For instance, studies using site-heterogeneous evolutionary models and coalescent-based approaches have consistently placed eukaryotes in a clade with Heimdallarchaeota within the Asgard superphylum. One analysis supports a root for Archaea within the Euryarchaeota and a bacterial stem for the tree of life, while the exact rooting within Archaea remains debated among recent studies.^[1]^[3]^[4] These findings address long-standing issues in universal tree reconstruction, such as long-branch attraction artifacts, by separating archaeal-eukaryotic markers from bacterial-archaeal ones for more accurate inference. Proponents argue that this topology better reflects the evolutionary history of informational genes (e.g., translation machinery) shared between Archaea and eukaryotes, while operational genes often show bacterial contributions via horizontal transfer.^[1] Despite robust phylogenomic support, the two-domain system remains debated, as the three-domain model continues to dominate textbooks and broader classifications due to its simplicity and historical precedence.^[5] Recent reconstructions, including those from 2023 and 2025, reinforce the two-domain view through expanded genomic sampling and refined rooting strategies, yet some analyses still recover three domains under certain modeling assumptions.^[3]^[5] Implications for classification include redefining Archaea to encompass eukaryotes, potentially simplifying the tree of life while highlighting the chimeric nature of eukaryotic cells, which blend archaeal informational systems with bacterial metabolic components.^[2]

Historical Development

Origins of domain classification

The classification of life into domains emerged from efforts to resolve the diversity of microorganisms using molecular phylogenetics, departing from earlier morphology-based systems that grouped all microbes as prokaryotes under a single kingdom. In 1977, Carl Woese and colleagues pioneered the use of 16S ribosomal RNA (rRNA) sequencing to analyze evolutionary relationships, revealing that life comprises three major lineages: one eukaryotic and two distinct prokaryotic groups, later termed Bacteria and Archaea.^[6] This approach demonstrated that traditional prokaryote-eukaryote dichotomies obscured deep phylogenetic divisions among microbes, as rRNA sequences from diverse isolates clustered into separate primary kingdoms rather than a monophyletic prokaryotic clade.^[6] A key milestone in this work was the identification of methanogenic bacteria as a novel group distinct from both typical bacteria and eukaryotes. Woese's team found that methanogens possessed unique rRNA signatures, indicating they formed a separate archaebacterial lineage with no close relation to known prokaryotes.^[6] This discovery, published in 1977, highlighted the limitations of phenotypic classifications and established rRNA as a reliable marker for microbial phylogeny, prompting reevaluation of microbial diversity.^[7] Throughout the 1980s, Woese expanded on these findings, proposing initial frameworks for higher-level groupings such as superkingdoms to accommodate the two prokaryotic lines alongside eukaryotes. In a comprehensive 1987 review, he argued that the prokaryotic domain encompassed two fundamentally divergent superkingdoms—eubacteria and archaebacteria—each as distinct from one another as from eukaryotes, based on accumulated rRNA and other molecular data. This laid the groundwork for formal taxonomic restructuring. By 1990, Woese, Otto Kandler, and Mark Wheelis formalized the three-domain system in a seminal proposal, classifying all cellular life into Bacteria, Archaea, and Eukarya based on 16S/18S rRNA phylogenies, with each domain containing multiple kingdoms. However, emerging observations of horizontal gene transfer (HGT) in the 1980s and 1990s began to challenge the strict vertical descent implied by universal rRNA trees, as evidence of gene exchange between distant prokaryotic lineages complicated reconstructions of a singular tree of life. For instance, studies in the late 1980s documented HGT events like plasmid-mediated antibiotic resistance transfers, while 1990s genome analyses revealed mosaic prokaryotic genomes shaped by interdomain exchanges. These insights underscored the reticulated nature of early microbial evolution, influencing later debates on domain boundaries.

Emergence of the two-domain hypothesis

The eocyte hypothesis, originally proposed by James A. Lake in 1984, experienced a revival in the early 2000s through phylogenetic analyses that highlighted structural and sequence similarities between eukaryotic ribosomes and those of certain archaeal lineages, particularly the crenarchaeota (now part of the TACK superphylum). This resurgence challenged the prevailing three-domain model by suggesting that eukaryotes emerged from within the archaea rather than as a distinct primary domain. A pivotal contribution came in 2008, when Cox, Foster, Hirt, Harris, and Embley used expanded datasets of universal protein sequences to demonstrate an archaebacterial origin for eukaryotes, positioning them as a derived lineage within archaea and supporting a two-domain tree comprising Archaea (including Eukarya) and Bacteria.^[8] Building on this, Lake further refined the idea in 2011 by proposing that the earliest eocytes—thermophilic archaea—derived from a gram-positive bacterial ancestor resembling actinomycetes, which then gave rise to the eukaryotic lineage through archaeal diversification. This model emphasized the fusion of bacterial and archaeal traits in eukaryogenesis, aligning with the two-domain framework by rooting eukaryotes deeply within archaea. Concurrently, Patrick Forterre advanced the hypothesis in 2011, arguing that the eukaryotic informational machinery, including replication and translation systems, originated from archaeal ancestors via endosymbiotic gene transfer, thereby reconciling archaeal affinity with bacterial contributions to organelles like mitochondria. The discovery of Lokiarchaeota in 2015 by Spang et al. served as a major catalyst, revealing a novel archaeal phylum with genomes encoding eukaryotic signature proteins involved in membrane remodeling and vesicle trafficking, which formed a monophyletic group with eukaryotes in phylogenomic trees. This finding, along with related refinements from 2013–2015 by Spang and colleagues on novel archaeal lineages (such as the Asgard group, initially represented by Lokiarchaeota) that bridge prokaryotes and eukaryotes, provided empirical support for merging Eukarya into Archaea. These developments shifted the consensus toward a two-domain topology, where archaeal diversity encompasses the eukaryotic lineage.^[9] In 2020, Williams, Szöllősi, and Martin et al. formalized the two-domain tree through comprehensive phylogenomic analyses of over 1,000 universal proteins, demonstrating that eukaryotes robustly branch within Archaea—specifically sister to the Asgard superphylum—when accounting for compositional heterogeneity and incomplete lineage sorting. This work emphasized cellular domains over purely informational ones, as bacterial genes in eukaryotes (e.g., for energy metabolism) reflect endosymbiotic acquisition rather than a separate primary domain, solidifying the hypothesis as the leading model for life's tree. Subsequent studies from 2021 onward, including expanded genomic sampling of Asgard archaea, further reinforced this model.^[10]

Core Principles

Eukaryotes as an archaeal lineage

The two-domain system posits that eukaryotes represent a specialized lineage derived from within the Archaea domain, rather than constituting a separate primary domain of life. This perspective arises from the evolutionary process known as eukaryogenesis, which involved an archaeal host cell engulfing an alphaproteobacterium approximately 2 billion years ago, leading to the establishment of the mitochondrial endosymbiosis that provided enhanced energy production capabilities.^[11] In this symbiotic event, the archaeal host contributed the foundational cellular machinery, while the bacterial endosymbiont's genes were primarily integrated for bioenergetic functions, such as oxidative phosphorylation, fundamentally shaping the eukaryotic cell's complexity. A key line of evidence supporting the archaeal ancestry of eukaryotes lies in the homology of information-processing genes, including those involved in transcription, translation, and DNA replication, which show stronger similarity to archaeal counterparts than to bacterial ones. For instance, eukaryotic RNA polymerases and ribosomal proteins exhibit structural and sequence affinities with archaeal versions, indicating that the eukaryotic core inherited these systems directly from an archaeal progenitor.^[12] This genetic dichotomy underscores that the eukaryotic informational apparatus is archaeal in origin, with bacterial contributions largely confined to metabolic and energetic pathways rather than core cellular processes.^[13] The identity of the archaeal host is closely linked to the Asgard superphylum, a diverse group of archaea that possess eukaryotic-like features such as genes for actin and other cytoskeletal elements, suggesting they represent the closest living relatives to the pre-eukaryotic ancestor. Recent analyses (2025) further refine this by positioning eukaryotes as a sister clade to Heimdallarchaeia within the Asgard superphylum.^[14] A pivotal model organism in this context is Promethearchaeum syntrophicum, isolated in 2020 from deep-sea sediments after a decade-long cultivation effort, which exemplifies pre-eukaryotic archaea through its possession of actin homologs capable of facilitating filopodia-like protrusions and potential phagocytic behaviors essential for endosymbiosis. This syntrophic archaeon, dependent on hydrogen-scavenging partners for growth, highlights the metabolic adaptations that may have preceded the engulfment of the alphaproteobacterial symbiont.^[15] Under the two-domain framework, eukaryotes are thus classified not as a distinct domain but as a subphylum or kingdom within Archaea, reflecting their derivation from an archaeal lineage modified by bacterial symbiosis. This reclassification emphasizes the chimeric nature of eukaryotic cells, where the archaeal-derived informational systems form the nucleus and operational core, while mitochondrial energetics drive their ecological success.^[16]

Redefinition of prokaryotic domains

In the two-domain system, the classification of life is restructured into two primary monophyletic domains—Bacteria and Archaea—defined by shared cellular structures, genetic ancestry, and evolutionary divergences, rather than the traditional dichotomy of prokaryotes versus eukaryotes.^[17] These domains are positioned as sister groups, with the root of the tree of life separating Bacteria from the Archaea-eukaryote lineage, emphasizing that the deep split occurs between these prokaryotic groups rather than between nucleated and non-nucleated cells.^[17] This redefinition challenges the three-domain model by recognizing Archaea as the encompassing group for eukaryotic origins, rendering "prokaryotes" a paraphyletic assemblage without formal taxonomic status as a domain.^[18] Archaea are characterized by informational processing systems—such as DNA replication, transcription, and translation machineries—that closely resemble those in eukaryotes, alongside cytoskeletal and membrane components that provided the foundational architecture for eukaryotic cellular complexity.^[17] For instance, archaeal RNA polymerase and histone-like proteins share structural homologies with eukaryotic counterparts, supporting the view that these features evolved within the archaeal domain before the emergence of the eukaryotic lineage.^[17] This integration highlights Archaea not merely as prokaryotes but as a domain with evolutionary innovations that bridge to eukaryotic biology, while Bacteria retain distinct operational genes for metabolism and cell wall synthesis.^[18] The term "prokaryote" persists in descriptive contexts to denote organisms lacking a membrane-bound nucleus and organelles, but it is explicitly demoted from taxonomic use in the two-domain framework, as all such organisms are distributed across the two domains without forming a cohesive clade.^[17] This shift underscores that prokaryotes represent a grade of organization rather than a unified evolutionary branch, with the domains Bacteria and Archaea capturing the fundamental divergences in ribosomal RNA sequences, membrane lipids, and core metabolic pathways.^[18] Updates from 2022 to 2025 have further solidified this redefinition through the genomic characterization of DPANN archaea—a diverse superphylum including lineages like Diapherotrites and Nanoarchaeota—as integral, early-diverging members of the Archaea domain.^[19] The phylogenetic position of DPANN archaea is debated, with some analyses placing them as early-diverging branches within Archaea, potentially basal to major lineages including Asgard, thereby reinforcing the monophyly of Archaea and the absence of a singular "prokaryotic" clade.^[20]^[19] These findings, based on expanded metagenomic datasets, illustrate how the two domains reflect ancient evolutionary bifurcations, with no overarching prokaryotic group encompassing both Bacteria and the archaeal radiation that includes eukaryotic precursors.^[19]

Supporting Evidence

Phylogenetic and genomic analyses

Phylogenetic analyses based on ribosomal RNA (rRNA) sequences have provided early molecular evidence supporting the two-domain topology. Since the 2010s, analyses of 16S/23S rRNA genes from diverse taxa have consistently placed eukaryotic 18S/28S rRNA sequences within the archaeal radiation, often as a sister group to specific archaeal lineages, rather than as a separate domain basal to both Bacteria and Archaea.^[21] These trees exhibit strong statistical support, with posterior probabilities exceeding 0.95 for the archaeal affiliation of eukaryotes in Bayesian reconstructions.^[17] Multi-gene phylogenomic datasets have further solidified this placement. A seminal 2013 study by Williams et al. analyzed 29 universal genes encoding informational proteins, such as those involved in translation and replication, and found that eukaryotes emerge from within the Archaea, forming a monophyletic group excluding Bacteria.^[17] Expanding on this, subsequent analyses incorporating hundreds of markers in concatenated alignments have confirmed the archaeal host scenario for eukaryotes, with eukaryotes nesting deeply within archaeal diversity.^[22] These datasets yield robust topologies, where the eukaryote-Archaea clade receives bootstrap support greater than 90% under maximum-likelihood inference.^[2] Rooting the tree of life has been pivotal in establishing the two-domain structure. Traditional rooting methods relied on outgroup comparisons, but recent approaches leverage ancient gene duplications, such as those in elongation factors EF-Tu and EF-G, which predate the last universal common ancestor (LUCA). These duplications place the root between Bacteria and the Archaea+Eukarya clade, supporting a binary division of cellular life without a separate eukaryotic domain.^[23] For instance, paralog-based rooting analyses of elongation factor sequences consistently recover this bipartition, with the archaeal+eukaryotic branch showing minimal long-branch attraction artifacts.^[1] Horizontal gene transfer (HGT) poses challenges to phylogenetic inference due to its prevalence in prokaryotic evolution, but advanced models have accounted for it to affirm the two-domain hypothesis. Bayesian phylogenomic frameworks, such as those using mixture models to detect and partition HGT-affected sites, demonstrate that even after filtering extensive bacterial-to-archaeal transfers, eukaryotes retain a strong affinity to Archaea.^[3] A 2023 study employing such methods on over 10,000 genes across archaeal and eukaryotic genomes confirmed the archaeal rooting of eukaryotes, with HGT contributions primarily affecting operational genes rather than core informational ones, yielding clade supports above 95% in posterior probabilities.^[3]

Key discoveries in archaeal diversity

A pivotal discovery in archaeal diversity occurred in 2015 with the metagenomic recovery of Lokiarchaeota from deep-sea hydrothermal vent sediments off the coast of Loki's Castle in the Mid-Atlantic Ridge. This lineage revealed a genome enriched with eukaryotic signature proteins, including components of the endosomal sorting complex required for transport (ESCRT) machinery, which is crucial for membrane remodeling and vesicle trafficking in eukaryotes.^[24] These findings positioned Lokiarchaeota as a bridge between prokaryotic archaea and eukaryotic cells, highlighting previously unrecognized genetic complexity in archaeal lineages. Building on this, metagenomic surveys in 2016-2017 identified additional members of the Asgard superphylum, including Heimdallarchaeota and Odinarchaeota, expanding the known diversity of archaea with eukaryotic-like features.^[25]^[26] Heimdallarchaeota genomes contain homologs of ubiquitin, a protein involved in protein degradation and signaling in eukaryotes,^[27] while both phyla encode actin-related proteins that could facilitate cytoskeletal functions akin to those in eukaryotic cells.^[28] These discoveries, derived from environmental DNA sequencing in marine and terrestrial subsurface environments, underscored the prevalence of eukaryotic-like information-processing and structural systems within the Asgard group. In 2020, the first cultured representative of the Asgard superphylum, Promethearchaeum syntrophicum, was isolated from marine sediment after over a decade of enrichment efforts.^[15] This anaerobic archaeon exhibits phagocytic-like capabilities, with electron microscopy revealing dynamic membrane protrusions that engulf bacterial cells, suggesting primitive endocytosis mechanisms. It maintains an obligate syntrophic relationship with partner bacteria, exchanging hydrogen and formate, which provides a model for how archaeal-bacterial interactions could have driven the acquisition of mitochondria during eukaryogenesis. Recent expansions in Asgard archaeal diversity from 2024-2025 have linked these microbes to early Earth geochemistries, such as hydrogen-rich hydrothermal settings reminiscent of Hadean conditions.^[14] Studies of diverse Asgard metagenomes indicate that syntrophic lifestyles, involving metabolite exchange in low-energy environments, likely played a key role in fostering the metabolic innovations leading to eukaryotic cells.^[14] Microscopy evidence further supports this, showing filamentous and protrusive structures in uncultured Asgard cells that resemble eukaryotic cytoskeletal precursors, observed in samples from subsurface and sediment habitats.^[29]

Classification Scheme

Domain Bacteria

In the two-domain system of life, the Domain Bacteria encompasses the vast majority of non-archaeal prokaryotic organisms, characterized by their unicellular structure, lack of a nucleus, and diverse adaptations to nearly every environmental niche on Earth.^[30] Defining traits of Bacteria include a cell wall composed primarily of peptidoglycan, which varies between Gram-positive species with thick layers (20-80 nm) providing structural rigidity and Gram-negative species featuring a thinner peptidoglycan layer (1.5-10 nm) enveloped by an outer membrane containing lipopolysaccharides for protection against environmental stresses.^[31]^[32] Bacterial ribosomes are of the 70S type, distinct from the 80S ribosomes in eukaryotes and differing in composition from archaeal ribosomes, enabling efficient protein synthesis tailored to prokaryotic lifestyles.^[33] Metabolic diversity is a hallmark, ranging from chemolithoautotrophy and heterotrophy to oxygenic photosynthesis in phyla like Cyanobacteria, which use chlorophyll to generate oxygen and fixed carbon, fundamentally shaping global atmospheric composition.^[34] Bacterial taxonomy recognizes approximately 170 phyla, as classified by the Genome Taxonomy Database (GTDB) as of 2025, with Proteobacteria, Firmicutes, and Actinobacteria representing some of the most ecologically and phylogenetically prominent groups; Proteobacteria alone includes diverse subgroups like alpha-proteobacteria involved in nitrogen fixation and pathogenesis, while Firmicutes encompass spore-forming anaerobes vital for fermentation, and Actinobacteria contribute to soil decomposition and antibiotic production.^[35]^[36] These phyla, along with others such as Bacteroidetes and Chloroflexi, dominate Earth's prokaryotic biomass, accounting for the majority of microbial cellular material due to their ubiquity in soils, oceans, and host-associated environments.^[37] Evolutionarily, Bacteria descend from the last universal common ancestor (LUCA), with an ancient origin as one of the two primary domains of life and key contributions to eukaryogenesis through the endosymbiosis of an alpha-proteobacterium that evolved into the mitochondrion, providing eukaryotic cells with aerobic respiration capabilities around 1.9 billion years ago.^[38] Recent advances in metagenomics as of 2025 have expanded the known bacterial diversity through the identification of numerous candidate phyla, particularly within the Candidate Phyla Radiation (CPR) groups like Patescibacteria, revealing streamlined genomes adapted to symbiotic or parasitic lifestyles in energy-limited habitats without any detected affinities to eukaryotic lineages.^[39] Ecologically, Bacteria exhibit profound dominance, with an estimated global population of approximately 10^{30} cells, primarily in oceanic and terrestrial biofilms, where they drive essential biogeochemical cycles including carbon, nitrogen, and sulfur transformations that sustain planetary habitability.^[40]^[41] In contrast to Archaea, bacterial metabolisms emphasize oxidative and fermentative processes over the extremophilic adaptations common in the sister domain.^[30]

Domain Archaea

In the two-domain system, the domain Archaea encompasses a diverse array of prokaryotic organisms distinguished by several key biochemical and genetic features that set them apart from Bacteria. Archaea possess unique ether-linked membrane lipids composed of isoprenoid chains attached to a glycerol-1-phosphate backbone, providing enhanced stability in extreme environments compared to the ester-linked fatty acid lipids typical of bacteria.^[42] Their transcription and translation machinery closely resembles that of eukaryotes, featuring a multi-subunit RNA polymerase and transcription factors such as TATA-binding protein (TBP) and transcription factor B (TFB), which enable complex gene regulation.^[22] Many archaea exhibit extremophile adaptations, including the ability to thrive in high-temperature, high-salinity, or acidic conditions; a prominent example is methanogenesis, a process exclusive to certain archaea that reduces carbon dioxide or acetate to methane using hydrogen or other substrates, facilitating energy conservation in anaerobic settings. The domain Archaea is organized into several major phyla, reflecting its phylogenetic diversity as revealed by genomic analyses. Prominent groups include Euryarchaeota, which encompasses methanogens and halophiles with versatile metabolisms; Crenarchaeota (now often classified within the broader Thermoproteota or TACK superphylum), featuring hyperthermophiles adapted to high-temperature aquatic environments; and the Asgard superphylum, which includes lineages like Heimdallarchaeota and Lokiarchaeota that harbor eukaryotic signature proteins.^[43] Additionally, the DPANN superphylum comprises ultrasmall archaea with reduced genomes (often <1 Mb) and parasitic or symbiotic lifestyles, such as Nanoarchaeota, which depend on host cells for metabolic functions due to their limited biosynthetic capabilities.^[44] These phyla highlight Archaea's ecological breadth, from free-living autotrophs to host-associated parasites. Within the two-domain framework, eukaryotes are integrated as a derived lineage within the Archaea domain, specifically emerging from the Asgard superphylum as a sister lineage to groups like Heimdallarchaeia. This placement positions eukaryotes alongside prokaryotic archaea, characterized by innovations such as a membrane-bound nucleus and mitochondria (acquired via endosymbiosis with alphaproteobacteria), while sharing core archaeal features in informational processes like transcription and translation.^[14] The Asgard archaea, in particular, encode actin-like proteins and other cytoskeletal elements that parallel eukaryotic structures, supporting the view of eukaryotes as an archaeal offshoot rather than a separate domain. Overall, Archaea encompasses approximately 20 phyla, as recognized by the Genome Taxonomy Database (GTDB) as of 2025, with Asgard representing the eukaryotic-adjacent branch amid broader prokaryotic diversity.^[14]^[36] As of 2025, the Genome Taxonomy Database (GTDB) provides a standardized classification for Archaea, integrating over 17,000 archaeal genomes and redefining traditional groupings based on phylogenomic markers. This taxonomy consolidates Asgardarchaeota as a distinct phylum and the closest prokaryotic sister to eukaryotes, while splitting former Euryarchaeota into multiple phyla (e.g., Methanobacteriota for methanogens) and recognizing DPANN as a basal, diverse superphylum; it abandons outdated ranks like Crenarchaeota in favor of monophyletic units derived from 120 conserved marker genes.^[45] This update, informed by recent metagenomic expansions, underscores Archaea's monophyly and the embedded position of eukaryotic ancestry within Asgard lineages.^[14] Ecologically, Archaea are ubiquitous and abundant, with an estimated global population of approximately 10²⁹ cells, predominantly in marine and subsurface environments where they outnumber bacteria in certain anoxic niches. They play pivotal roles in anoxic habitats, such as oxygen minimum zones and sediments, where methanogenic archaea generate methane—a potent greenhouse gas—and ammonia-oxidizing archaea (AOA) drive nitrification, influencing nutrient availability. In the global carbon cycle, archaea contribute significantly through chemolithoautotrophic CO₂ fixation in dark ocean conditions and anaerobic methane oxidation, which mitigates atmospheric CH₄ emissions and recycles organic carbon in sediments.^[46]

Comparisons and Implications

Differences from the three-domain system

The three-domain system, proposed by Carl Woese and colleagues in 1990, classifies all cellular life into three equal domains—Bacteria, Archaea, and Eukarya—based primarily on small subunit ribosomal RNA (16S/18S rRNA) sequences, emphasizing a fundamental divide between prokaryotic (Bacteria and Archaea) and eukaryotic (Eukarya) forms of life. This model portrays the domains as distinct lineages diverging from a common ancestor, with Archaea and Eukarya often depicted as sister groups in rooted phylogenetic trees. In contrast, the two-domain system critiques the three-domain model as an artifact of methodological limitations, such as horizontal gene transfer (HGT) affecting early rRNA-based phylogenies and errors in rooting the universal tree of life.^[1] Phylogenomic analyses using supergene trees—concatenated alignments of hundreds of universal protein-coding genes—consistently place Eukarya as a derived lineage nested within the Archaea, specifically as a sister group to the TACK (Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota) superphylum or the more recently identified Asgard archaea.^[47]^[1] This nesting implies that Archaea are paraphyletic, rendering Eukarya an archaeal offshoot rather than a separate domain, and challenges the equal status of the three domains by showing eukaryogenesis occurred within archaeal diversification.^[48] Visually, the three-domain model is often represented by rooted trees where Bacteria branches early, leaving Archaea and Eukarya as a "crown" clade of sister groups, emphasizing their shared informational genes.^[48] The two-domain model, however, features unrooted or differently rooted trees (with the root placed within Euryarchaeota), where Eukarya emerges internally from Archaea, eliminating the distinct crown and highlighting Bacteria as the sole outgroup domain.^[1]^[48] Recent analyses from 2023 to 2025 indicate a growing consensus toward the two-domain system for understanding cellular evolution, with several phylogenomic studies robustly supporting this topology using expanded genomic datasets, while retaining the three-domain view for informational gene phylogenies like rRNA due to lower HGT rates in those markers. For example, a 2025 study in Philosophical Transactions of the Royal Society supports the two-domain hypothesis through historical tree reconstructions.^[3]^[5]^[5] Educational resources, including updated oceanography texts, now discuss the two-domain model as increasingly favored based on this evidence.^[49] A key flaw in the three-domain system is its implication that prokaryotes (Bacteria plus Archaea) form a paraphyletic group, as genomic and fossil records show early microbial life diverging into monophyletic bacterial and archaeal lineages without encompassing all non-eukaryotes.^[50]

Impacts on evolutionary and ecological understanding

The two-domain system simplifies the tree of life by positioning eukaryotes as a derived lineage within Archaea, thereby reducing the number of primary domains from three to two and highlighting Archaea as the innovative group that gave rise to complex cellular structures. This framework emphasizes archaeal contributions to evolutionary complexity, such as the development of eukaryotic features like the nucleus and cytoskeleton, which originated through endosymbiotic events involving archaeal hosts and bacterial endosymbionts. By integrating eukaryotes into the archaeal domain, the model positions eukaryogenesis, estimated at approximately 2.5–1.8 billion years ago, within archaeal diversification, aligning it with geological evidence of rising atmospheric oxygen levels that may have facilitated such transitions. Ecologically, the two-domain perspective elevates Archaea's centrality in the biosphere, portraying them not as marginal extremophiles but as key players in global biogeochemical cycles, with implications for refining climate models that account for methanogen contributions to greenhouse gas dynamics. For instance, recognizing archaeal methanogens as more integral to anaerobic environments underscores their role in carbon cycling and methane production, influencing predictions of climate feedback loops in wetlands and oceans. In microbiome studies, this system encourages viewing eukaryotic microbes—such as protists—as "archaeal" derivatives, prompting integrated analyses of host-microbe interactions that blur traditional prokaryote-eukaryote boundaries and reveal novel symbiotic networks in health and environmental contexts. The adoption of the two-domain system drives research shifts toward culturing Asgard archaea to experimentally recreate archaeal-eukaryotic transitions, while synthetic biology efforts aim to engineer hybrid systems mimicking these evolutionary innovations for applications in biotechnology. This model has implications for astrobiology, including models of life on exoplanets. Broader implications challenge outdated "prokaryotic" paradigms in medicine and biotechnology, urging a reevaluation of antimicrobial strategies and genetic engineering tools that previously overlooked archaeal-eukaryotic affinities.

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