Common descent

@article{bader1958similarity,
    author = "Bader, R. S.",
    title = "Similarity and Recency of Common Ancestry",
    year = "1958",
    journal = "Systematic Biology",
    url = "https://doi.org/10.2307/2411719",
    doi = "10.2307/2411719",
    number = "4",
    openalex = "W2078059327",
    pages = "184-187",
    volume = "7"
}

BACKGROUND: Since the reclassification of all life forms in three Domains (Archaea, Bacteria, Eukarya), the identity of their alleged forerunner (Last Universal Common Ancestor or LUCA) has been the subject of extensive controversies: progenote or already complex organism, prokaryote or protoeukaryote, thermophile or mesophile, product of a protracted progression from simple replicators to complex cells or born in the cradle of "catalytically closed" entities? We present a critical survey of the topic and suggest a scenario. RESULTS: LUCA does not appear to have been a simple, primitive, hyperthermophilic prokaryote but rather a complex community of protoeukaryotes with a RNA genome, adapted to a broad range of moderate temperatures, genetically redundant, morphologically and metabolically diverse. LUCA's genetic redundancy predicts loss of paralogous gene copies in divergent lineages to be a significant source of phylogenetic anomalies, i.e. instances where a protein tree departs from the SSU-rRNA genealogy; consequently, horizontal gene transfer may not have the rampant character assumed by many. Examining membrane lipids suggest LUCA had sn1,2 ester fatty acid lipids from which Archaea emerged from the outset as thermophilic by "thermoreduction," with a new type of membrane, composed of sn2,3 ether isoprenoid lipids; this occurred without major enzymatic reconversion. Bacteria emerged by reductive evolution from LUCA and some lineages further acquired extreme thermophily by convergent evolution. This scenario is compatible with the hypothesis that the RNA to DNA transition resulted from different viral invasions as proposed by Forterre. Beyond the controversy opposing "replication first" to metabolism first", the predictive arguments of theories on "catalytic closure" or "compositional heredity" heavily weigh in favour of LUCA's ancestors having emerged as complex, self-replicating entities from which a genetic code arose under natural selection. CONCLUSION: Life was born complex and the LUCA displayed that heritage. It had the "body "of a mesophilic eukaryote well before maturing by endosymbiosis into an organism adapted to an atmosphere rich in oxygen. Abundant indications suggest reductive evolution of this complex and heterogeneous entity towards the "prokaryotic" Domains Archaea and Bacteria. The word "prokaryote" should be abandoned because epistemologically unsound. REVIEWERS: This article was reviewed by Anthony Poole, Patrick Forterre, and Nicolas Galtier.

@article{doi10118617456150329,
    author = "Glansdorff, Nicolas and Xu, Ying and Labedan, Bernard",
    title = "The Last Universal Common Ancestor: emergence, constitution and genetic legacy of an elusive forerunner",
    year = "2008",
    journal = "Biology Direct",
    abstract = {BACKGROUND: Since the reclassification of all life forms in three Domains (Archaea, Bacteria, Eukarya), the identity of their alleged forerunner (Last Universal Common Ancestor or LUCA) has been the subject of extensive controversies: progenote or already complex organism, prokaryote or protoeukaryote, thermophile or mesophile, product of a protracted progression from simple replicators to complex cells or born in the cradle of "catalytically closed" entities? We present a critical survey of the topic and suggest a scenario. RESULTS: LUCA does not appear to have been a simple, primitive, hyperthermophilic prokaryote but rather a complex community of protoeukaryotes with a RNA genome, adapted to a broad range of moderate temperatures, genetically redundant, morphologically and metabolically diverse. LUCA's genetic redundancy predicts loss of paralogous gene copies in divergent lineages to be a significant source of phylogenetic anomalies, i.e. instances where a protein tree departs from the SSU-rRNA genealogy; consequently, horizontal gene transfer may not have the rampant character assumed by many. Examining membrane lipids suggest LUCA had sn1,2 ester fatty acid lipids from which Archaea emerged from the outset as thermophilic by "thermoreduction," with a new type of membrane, composed of sn2,3 ether isoprenoid lipids; this occurred without major enzymatic reconversion. Bacteria emerged by reductive evolution from LUCA and some lineages further acquired extreme thermophily by convergent evolution. This scenario is compatible with the hypothesis that the RNA to DNA transition resulted from different viral invasions as proposed by Forterre. Beyond the controversy opposing "replication first" to metabolism first", the predictive arguments of theories on "catalytic closure" or "compositional heredity" heavily weigh in favour of LUCA's ancestors having emerged as complex, self-replicating entities from which a genetic code arose under natural selection. CONCLUSION: Life was born complex and the LUCA displayed that heritage. It had the "body "of a mesophilic eukaryote well before maturing by endosymbiosis into an organism adapted to an atmosphere rich in oxygen. Abundant indications suggest reductive evolution of this complex and heterogeneous entity towards the "prokaryotic" Domains Archaea and Bacteria. The word "prokaryote" should be abandoned because epistemologically unsound. REVIEWERS: This article was reviewed by Anthony Poole, Patrick Forterre, and Nicolas Galtier.},
    url = "https://doi.org/10.1186/1745-6150-3-29",
    doi = "10.1186/1745-6150-3-29",
    openalex = "W2116103056"
}

BACKGROUND: It is common belief that all cellular life forms on earth have a common origin. This view is supported by the universality of the genetic code and the universal conservation of multiple genes, particularly those that encode key components of the translation system. A remarkable recent study claims to provide a formal, homology independent test of the Universal Common Ancestry hypothesis by comparing the ability of a common-ancestry model and a multiple-ancestry model to predict sequences of universally conserved proteins. RESULTS: We devised a computational experiment on a concatenated alignment of universally conserved proteins which shows that the purported demonstration of the universal common ancestry is a trivial consequence of significant sequence similarity between the analyzed proteins. The nature and origin of this similarity are irrelevant for the prediction of "common ancestry" of by the model-comparison approach. Thus, homology (common origin) of the compared proteins remains an inference from sequence similarity rather than an independent property demonstrated by the likelihood analysis. CONCLUSION: A formal demonstration of the Universal Common Ancestry hypothesis has not been achieved and is unlikely to be feasible in principle. Nevertheless, the evidence in support of this hypothesis provided by comparative genomics is overwhelming.

@article{doi10118617456150564,
    author = "Koonin, Eugene V. and Wolf, Yuri I.",
    title = "The common ancestry of life",
    year = "2010",
    journal = "Biology Direct",
    abstract = {BACKGROUND: It is common belief that all cellular life forms on earth have a common origin. This view is supported by the universality of the genetic code and the universal conservation of multiple genes, particularly those that encode key components of the translation system. A remarkable recent study claims to provide a formal, homology independent test of the Universal Common Ancestry hypothesis by comparing the ability of a common-ancestry model and a multiple-ancestry model to predict sequences of universally conserved proteins. RESULTS: We devised a computational experiment on a concatenated alignment of universally conserved proteins which shows that the purported demonstration of the universal common ancestry is a trivial consequence of significant sequence similarity between the analyzed proteins. The nature and origin of this similarity are irrelevant for the prediction of "common ancestry" of by the model-comparison approach. Thus, homology (common origin) of the compared proteins remains an inference from sequence similarity rather than an independent property demonstrated by the likelihood analysis. CONCLUSION: A formal demonstration of the Universal Common Ancestry hypothesis has not been achieved and is unlikely to be feasible in principle. Nevertheless, the evidence in support of this hypothesis provided by comparative genomics is overwhelming.},
    url = "https://doi.org/10.1186/1745-6150-5-64",
    doi = "10.1186/1745-6150-5-64",
    openalex = "W2158197263",
    references = "doi1010160968000494901678, doi101038330401a0, doi10103890129, doi101038nrmicro751, doi10108010635150390235520, doi101126science1123061, doi101126science1123539, doi10118617456150329, doi10118617456150564"
}

@article{steel2010common,
    author = "Steel, Mike and Penny, David",
    title = "Common ancestry put to the test",
    year = "2010",
    journal = "Nature",
    url = "https://doi.org/10.1038/465168a",
    doi = "10.1038/465168a",
    number = "7295",
    pages = "168--169",
    volume = "465"
}

@article{theobald2010a,
    author = "Theobald, Douglas L.",
    title = "A formal test of the theory of universal common ancestry",
    year = "2010",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature09014",
    doi = "10.1038/nature09014",
    number = "7295",
    openalex = "W2068487992",
    pages = "219-222",
    volume = "465",
    references = "doi10108010635150390235520, doi101093molbevmsj030, doi1023071912557, doi1023072291091, doi1023073802723, doi105962bhltitle59991, doi105962bhltitle68064, doi105962bhltitle82303"
}

@article{theobald2010reply,
    author = "Theobald, D. L.",
    title = "Theobald reply",
    year = "2010",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature09483",
    doi = "10.1038/nature09483",
    number = "7326",
    pages = "E10--E10",
    volume = "468"
}

@article{yonezawa2010universal,
    author = "Yonezawa, Takahiro and Hasegawa, Masami",
    title = "Was the universal common ancestry proved?",
    year = "2010",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature09482",
    doi = "10.1038/nature09482",
    number = "7326",
    pages = "E9--E9",
    volume = "468"
}

@article{theobald2011universal,
    author = "Theobald, Douglas L.",
    title = "On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence",
    year = "2011",
    journal = "Biology Direct",
    url = "https://doi.org/10.1186/1745-6150-6-60",
    doi = "10.1186/1745-6150-6-60",
    number = "1",
    pages = "60",
    volume = "6"
}

Douglas Theobald recently developed an interesting test putatively capable of quantifying the evidence for a Universal Common Ancestry uniting the three domains of life (Eukarya, Archaea and Bacteria) against hypotheses of Independent Origins for some of these domains. We review here his model, in particular in relation to the treatment of Horizontal Gene Transfer (HGT) and to the quality of sequence alignment.

@article{doi104081eb2012e5,
    author = "de Oliveira Martins, Leonardo and Posada, David",
    title = "Proving universal common ancestry with similar sequences",
    year = "2012",
    journal = "Trends in Evolutionary Biology",
    abstract = "Douglas Theobald recently developed an interesting test putatively capable of quantifying the evidence for a Universal Common Ancestry uniting the three domains of life (Eukarya, Archaea and Bacteria) against hypotheses of Independent Origins for some of these domains. We review here his model, in particular in relation to the treatment of Horizontal Gene Transfer (HGT) and to the quality of sequence alignment.",
    url = "https://doi.org/10.4081/eb.2012.e5",
    doi = "10.4081/eb.2012.e5",
    number = "1",
    openalex = "W2099175457",
    pages = "5",
    volume = "4",
    references = "doi101007bf00160154, doi101007bf01734359, doi10108010635150390235520, doi10108010635150490522304, doi101093bioinformaticsbtg180, doi101093bioinformaticsbtr088, doi101093sysbiosyq085, doi101126science1065889"
}

@misc{theobald2012evidences,
    author = "Theobald, Douglas L.",
    title = "29+ Evidences for Macroevolution: The Scientific Case for Common Descent",
    year = "2012",
    url = "https://talkorigins.org/faqs/comdesc/",
    howpublished = "TalkOrigins Archive, version 2.89"
}

@article{deoliveiramartins2014testing,
    author = "de Oliveira Martins, Leonardo and Posada, David",
    title = "Testing for Universal Common Ancestry",
    year = "2014",
    journal = "Systematic Biology",
    url = "https://doi.org/10.1093/sysbio/syu041",
    doi = "10.1093/sysbio/syu041",
    number = "5",
    openalex = "W2164044732",
    pages = "838-842",
    volume = "63",
    references = "doi10108010635150500433722, doi101093molbevmsn067, doi101093molbevmsp098, doi101093nar22224673, doi101093nargkh340, doi101093sysbiosyq085, doi101126science1151532, doi1023072291091, doi104081eb2012e5, martins2012proving"
}

Abstract The common ancestry of life is supported by an enormous body of evidence and is universally accepted within the scientific community. However, some potential sources of data that can be used to test the thesis of common ancestry have not yet been formally analyzed. We developed a new test of common ancestry based on nucleotide sequences at amino acid invariant sites in aligned homologous protein coding genes. We reasoned that since nucleotide variation at amino acid invariant sites is selectively neutral and, thus, unlikely to be due to convergent evolution, the observation that an amino acid is consistently encoded by the same codon sequence in different species could provide strong evidence of their common ancestry. Our method uses the observed variation in codon sequences at amino acid invariant sites as a test statistic, and compares such variation to that which is expected under three different models of codon frequency under the alternative hypothesis of separate ancestry. We also examine hierarchical structure in the nucleotide sequences at amino acid invariant sites and quantified agreement between trees generated from amino acid sequence and those inferred from the nucleotide sequences at amino acid invariant sites. When these tests are applied to the primate families as a test case, we find that observed nucleotide variation at amino acid invariant sites is considerably lower than nucleotide variation predicted by any model of codon frequency under separate ancestry. Phylogenetic trees generated from amino-acid invariant site nucleotide data agree with those generated from protein-coding data, and there is far more hierarchical structure in amino-acid invariant site data than would be expected under separate ancestry. We definitively reject the separate ancestry of the primate families, and demonstrate that our tests can be applied to any group of interest to test common ancestry.

@misc{doi101101035915,
    author = "Bontrager, Martin and Larget, Bret and Ané, Cécile and Baum, David",
    title = "Statistical Evidence for Common Ancestry: Testing for Signal in Silent Sites",
    year = "2016",
    booktitle = "bioRxiv (Cold Spring Harbor Laboratory)",
    abstract = "Abstract The common ancestry of life is supported by an enormous body of evidence and is universally accepted within the scientific community. However, some potential sources of data that can be used to test the thesis of common ancestry have not yet been formally analyzed. We developed a new test of common ancestry based on nucleotide sequences at amino acid invariant sites in aligned homologous protein coding genes. We reasoned that since nucleotide variation at amino acid invariant sites is selectively neutral and, thus, unlikely to be due to convergent evolution, the observation that an amino acid is consistently encoded by the same codon sequence in different species could provide strong evidence of their common ancestry. Our method uses the observed variation in codon sequences at amino acid invariant sites as a test statistic, and compares such variation to that which is expected under three different models of codon frequency under the alternative hypothesis of separate ancestry. We also examine hierarchical structure in the nucleotide sequences at amino acid invariant sites and quantified agreement between trees generated from amino acid sequence and those inferred from the nucleotide sequences at amino acid invariant sites. When these tests are applied to the primate families as a test case, we find that observed nucleotide variation at amino acid invariant sites is considerably lower than nucleotide variation predicted by any model of codon frequency under separate ancestry. Phylogenetic trees generated from amino-acid invariant site nucleotide data agree with those generated from protein-coding data, and there is far more hierarchical structure in amino-acid invariant site data than would be expected under separate ancestry. We definitively reject the separate ancestry of the primate families, and demonstrate that our tests can be applied to any group of interest to test common ancestry.",
    url = "https://doi.org/10.1101/035915",
    doi = "10.1101/035915",
    openalex = "W2263396908",
    references = "deoliveiramartins2014testing, larget2016statistical"
}

Since Darwin, biologists have come to recognize that the theory of descent from common ancestry (CA) is very well supported by diverse lines of evidence. However, while the qualitative evidence is overwhelming, we also need formal methods for quantifying the evidential support for CA over the alternative hypothesis of separate ancestry (SA). In this article, we explore a diversity of statistical methods using data from the primates. We focus on two alternatives to CA, species SA (the separate origin of each named species) and family SA (the separate origin of each family). We implemented statistical tests based on morphological, molecular, and biogeographic data and developed two new methods: one that tests for phylogenetic autocorrelation while correcting for variation due to confounding ecological traits and a method for examining whether fossil taxa have fewer derived differences than living taxa. We overwhelmingly rejected both species and family SA with infinitesimal P values. We compare these results with those from two companion papers, which also found tremendously strong support for the CA of all primates, and discuss future directions and general philosophical issues that pertain to statistical testing of historical hypotheses such as CA.

@article{doi101111evo12934,
    author = "Baum, David and Ané, Cécile and Larget, Bret and Solís‐Lemus, Claudia and Ho, Lam Si Tung and Boone, P L and Drummond, Chloe P. and Bontrager, Martin and Hunter, Steven and Saucier, William",
    title = "Statistical evidence for common ancestry: Application to primates",
    year = "2016",
    journal = "Evolution",
    abstract = "Since Darwin, biologists have come to recognize that the theory of descent from common ancestry (CA) is very well supported by diverse lines of evidence. However, while the qualitative evidence is overwhelming, we also need formal methods for quantifying the evidential support for CA over the alternative hypothesis of separate ancestry (SA). In this article, we explore a diversity of statistical methods using data from the primates. We focus on two alternatives to CA, species SA (the separate origin of each named species) and family SA (the separate origin of each family). We implemented statistical tests based on morphological, molecular, and biogeographic data and developed two new methods: one that tests for phylogenetic autocorrelation while correcting for variation due to confounding ecological traits and a method for examining whether fossil taxa have fewer derived differences than living taxa. We overwhelmingly rejected both species and family SA with infinitesimal P values. We compare these results with those from two companion papers, which also found tremendously strong support for the CA of all primates, and discuss future directions and general philosophical issues that pertain to statistical testing of historical hypotheses such as CA.",
    url = "https://doi.org/10.1111/evo.12934",
    doi = "10.1111/evo.12934",
    openalex = "W2345386884",
    references = "deoliveiramartins2014testing, larget2016statistical"
}

BACKGROUND: The evidence for universal common ancestry (UCA) is vast and persuasive. A phylogenetic test has been proposed for quantifying its odds against independently originated sequences based on the comparison between one versus several trees. This test was successfully applied to a well-supported homologous sequence alignment, which was however criticized on the basis of simulations showing that alignments without any phylogenetic structure could mislead its conclusions. RESULTS: Here we present a simplified version of this same counterexample, which can be interpreted as a tree with arbitrarily long branches, and where the UCA test fails again. We also present another case whereby any sufficiently similar alignment will favour UCA irrespective of the true independent origins for the sequences. Finally, we present a class of frequentist tests that perform better than the purportedly formal UCA test. CONCLUSION: Despite claims to the contrary, we show that the counterexamples successfully detected a drawback of the original UCA test, of relying on sequence similarity. In light of our own simulations, we therefore conclude that the UCA test as originally proposed should not be trusted unless convergence has already been ruled out a priori.

@article{doi101186s130620160120y,
    author = "Martins, Leonardo and Posada, David",
    title = "Infinitely long branches and an informal test of common ancestry",
    year = "2016",
    journal = "Biology Direct",
    abstract = "BACKGROUND: The evidence for universal common ancestry (UCA) is vast and persuasive. A phylogenetic test has been proposed for quantifying its odds against independently originated sequences based on the comparison between one versus several trees. This test was successfully applied to a well-supported homologous sequence alignment, which was however criticized on the basis of simulations showing that alignments without any phylogenetic structure could mislead its conclusions. RESULTS: Here we present a simplified version of this same counterexample, which can be interpreted as a tree with arbitrarily long branches, and where the UCA test fails again. We also present another case whereby any sufficiently similar alignment will favour UCA irrespective of the true independent origins for the sequences. Finally, we present a class of frequentist tests that perform better than the purportedly formal UCA test. CONCLUSION: Despite claims to the contrary, we show that the counterexamples successfully detected a drawback of the original UCA test, of relying on sequence similarity. In light of our own simulations, we therefore conclude that the UCA test as originally proposed should not be trusted unless convergence has already been ruled out a priori.",
    url = "https://doi.org/10.1186/s13062-016-0120-y",
    doi = "10.1186/s13062-016-0120-y",
    openalex = "W2323017461",
    references = "deoliveiramartins2014testing, doi104081eb2012e5, martins2012proving"
}

While there is no doubt among evolutionary biologists that all living species, or merely all living species within a particular group (e.g., animals), share descent from a common ancestor, formal statistical methods for evaluating common ancestry from aligned DNA sequence data have received criticism. One primary criticism is that prior methods take sequence similarity as evidence for common ancestry while ignoring other potential biological causes of similarity, such as functional constraints. We present a new statistical framework to test separate ancestry versus common ancestry that avoids this pitfall. We illustrate the efficacy of our approach using a recently published large molecular alignment to examine common ancestry of all primates (including humans). We find overwhelming evidence against separate ancestry and in favor of common ancestry for orders and families of primates. We also find overwhelming evidence that humans share a common ancestor with other primate species. The novel statistical methods presented here provide formal means to test separate ancestry versus common ancestry from aligned DNA sequence data while accounting for functional constraints that limit nucleotide base usage on a site-by-site basis.

@misc{larget2016statistical,
    author = "Larget, Bret and Ané, Cécile and Bontrager, Martin and Hunter, Steve and Stenz, Noah and Baum, David A.",
    title = "Statistical evidence for common ancestry: New tests of universal ancestry",
    year = "2016",
    abstract = "While there is no doubt among evolutionary biologists that all living species, or merely all living species within a particular group (e.g., animals), share descent from a common ancestor, formal statistical methods for evaluating common ancestry from aligned DNA sequence data have received criticism. One primary criticism is that prior methods take sequence similarity as evidence for common ancestry while ignoring other potential biological causes of similarity, such as functional constraints. We present a new statistical framework to test separate ancestry versus common ancestry that avoids this pitfall. We illustrate the efficacy of our approach using a recently published large molecular alignment to examine common ancestry of all primates (including humans). We find overwhelming evidence against separate ancestry and in favor of common ancestry for orders and families of primates. We also find overwhelming evidence that humans share a common ancestor with other primate species. The novel statistical methods presented here provide formal means to test separate ancestry versus common ancestry from aligned DNA sequence data while accounting for functional constraints that limit nucleotide base usage on a site-by-site basis.",
    url = "https://doi.org/10.1101/036327",
    doi = "10.1101/036327",
    openalex = "W2288243766",
    references = "deoliveiramartins2014testing, doi101093bioinformaticsbtg412, doi101093bioinformaticsbtq706, doi101093bioinformaticsbtu033, doi1012019780429246593, doi101371journalpgen1001342, doi105962bhltitle59991, doi105962bhltitle68064, openalexw3217097258"
}

The nature of the last universal common ancestor (LUCA), its age and its impact on the Earth system have been the subject of vigorous debate across diverse disciplines, often based on disparate data and methods. Age estimates for LUCA are usually based on the fossil record, varying with every reinterpretation. The nature of LUCA's metabolism has proven equally contentious, with some attributing all core metabolisms to LUCA, whereas others reconstruct a simpler life form dependent on geochemistry. Here we infer that LUCA lived ~4.2 Ga (4.09-4.33 Ga) through divergence time analysis of pre-LUCA gene duplicates, calibrated using microbial fossils and isotope records under a new cross-bracing implementation. Phylogenetic reconciliation suggests that LUCA had a genome of at least 2.5 Mb (2.49-2.99 Mb), encoding around 2,600 proteins, comparable to modern prokaryotes. Our results suggest LUCA was a prokaryote-grade anaerobic acetogen that possessed an early immune system. Although LUCA is sometimes perceived as living in isolation, we infer LUCA to have been part of an established ecological system. The metabolism of LUCA would have provided a niche for other microbial community members and hydrogen recycling by atmospheric photochemistry could have supported a modestly productive early ecosystem.

@article{doi101038s41559024024611,
    author = "Moody, Edmund R. R. and Álvarez-Carretero, Sandra and Mahendrarajah, Tara and Clark, James and Betts, Holly C. and Dombrowski, Nina and Szánthó, Lénárd L. and Boyle, Richard A. and Daines, Stuart J. and Chen, Xi and Lane, Nick and Yang, Ziheng and Shields, Graham and Szöllősi, Gergely J. and Spang, Anja and Pisani, Davide and Williams, Tom A. and Lenton, Timothy M. and Donoghue, Philip C. J.",
    title = "The nature of the last universal common ancestor and its impact on the early Earth system",
    year = "2024",
    journal = "Nature Ecology \& Evolution",
    abstract = "The nature of the last universal common ancestor (LUCA), its age and its impact on the Earth system have been the subject of vigorous debate across diverse disciplines, often based on disparate data and methods. Age estimates for LUCA are usually based on the fossil record, varying with every reinterpretation. The nature of LUCA's metabolism has proven equally contentious, with some attributing all core metabolisms to LUCA, whereas others reconstruct a simpler life form dependent on geochemistry. Here we infer that LUCA lived 	extasciitilde 4.2 Ga (4.09-4.33 Ga) through divergence time analysis of pre-LUCA gene duplicates, calibrated using microbial fossils and isotope records under a new cross-bracing implementation. Phylogenetic reconciliation suggests that LUCA had a genome of at least 2.5 Mb (2.49-2.99 Mb), encoding around 2,600 proteins, comparable to modern prokaryotes. Our results suggest LUCA was a prokaryote-grade anaerobic acetogen that possessed an early immune system. Although LUCA is sometimes perceived as living in isolation, we infer LUCA to have been part of an established ecological system. The metabolism of LUCA would have provided a niche for other microbial community members and hydrogen recycling by atmospheric photochemistry could have supported a modestly productive early ecosystem.",
    url = "https://doi.org/10.1038/s41559-024-02461-1",
    doi = "10.1038/s41559-024-02461-1",
    openalex = "W4400589084",
    references = "theobald2010a"
}