Article

Theobald, D. L. A formal test of the theory of universal common ancestry. Nature 465, 219-222

Department of Biochemistry, Brandeis University, Waltham, Massachusetts 01778, USA.
Nature (Impact Factor: 41.46). 05/2010; 465(7295):219-22. DOI: 10.1038/nature09014
Source: PubMed

ABSTRACT

Universal common ancestry (UCA) is a central pillar of modern evolutionary theory. As first suggested by Darwin, the theory of UCA posits that all extant terrestrial organisms share a common genetic heritage, each being the genealogical descendant of a single species from the distant past. The classic evidence for UCA, although massive, is largely restricted to 'local' common ancestry-for example, of specific phyla rather than the entirety of life-and has yet to fully integrate the recent advances from modern phylogenetics and probability theory. Although UCA is widely assumed, it has rarely been subjected to formal quantitative testing, and this has led to critical commentary emphasizing the intrinsic technical difficulties in empirically evaluating a theory of such broad scope. Furthermore, several researchers have proposed that early life was characterized by rampant horizontal gene transfer, leading some to question the monophyly of life. Here I provide the first, to my knowledge, formal, fundamental test of UCA, without assuming that sequence similarity implies genetic kinship. I test UCA by applying model selection theory to molecular phylogenies, focusing on a set of ubiquitously conserved proteins that are proposed to be orthologous. Among a wide range of biological models involving the independent ancestry of major taxonomic groups, the model selection tests are found to overwhelmingly support UCA irrespective of the presence of horizontal gene transfer and symbiotic fusion events. These results provide powerful statistical evidence corroborating the monophyly of all known life.

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    • "It indicated that life is divided into three different domains: the archaea, the bacteria, and the eucarya [5] [6] [8]. Later studies using other molecular sequences placed the root of the tree, corresponding to the last universal common ancestor, somewhere between the bacteria and archaea [9] [10] [11] [12] [13], roughly 3.5 − 3.8 billion years ago. The nature of the last universal common ancestor, however, remains unresolved: Was it prokaryotic or eukaryotic? "
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    ABSTRACT: It has been hypothesized that in the era just before the last universal common ancestor emerged, life on earth was fundamentally collective. Ancient life forms shared their genetic material freely through massive horizontal gene transfer (HGT). At a certain point, however, life made a transition to the modern era of individuality and vertical descent. Here we present a minimal model for stochastic processes potentially contributing to this hypothesized "Darwinian transition." The model suggests that HGT-dominated dynamics may have been intermittently interrupted by selection-driven processes during which genotypes became fitter and decreased their inclination toward HGT. Stochastic switching in the population dynamics with three-point (hypernetwork) interactions may have destabilized the HGT-dominated collective state and essentially contributed to the emergence of vertical descent and the first well-defined species in early evolution. A systematic nonlinear analysis of the stochastic model dynamics covering key features of evolutionary processes (such as selection, mutation, drift and HGT) supports this view. Our findings thus suggest a viable direction out of early collective evolution, potentially enabling the start of individuality and vertical Darwinian evolution.
    Full-text · Article · Nov 2015 · Physical Review E
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    • "It indicated that life is divided into three different domains: the Archaea, the Bacteria and the Eucarya [5] [6] [8]. Later studies using other molecular sequences placed the root of the tree, corresponding to the last universal common ancestor, somewhere between the Bacteria and Archaea [9] [10] [11] [12] [13], roughly 3.5 − 3.8 billion years ago. The nature of the last universal common ancestor, however, remains unresolved: Was it prokaryotic or eukaryotic? "
    [Show abstract] [Hide abstract]
    ABSTRACT: It has been hypothesized that in the era just before the last universal common ancestor emerged, life on earth was fundamentally collective. Ancient life forms shared their genetic material freely through massive horizontal gene transfer (HGT). At a certain point, however, life made a transition to the modern era of individuality and vertical descent. Here we present a minimal model for this hypothesized "Darwinian transition." The model suggests that HGT-dominated dynamics may have been intermittently interrupted by selection-driven processes during which genotypes became fitter and decreased their inclination toward HGT. Stochastic switching in the population dynamics with three-point (hypernetwork) interactions may have destabilized the HGT-dominated collective state and led to the emergence of vertical descent and the first well-defined species in early evolution. A nonlinear analysis of a stochastic model dynamics covering key features of evolutionary processes (such as selection, mutation, drift and HGT) supports this view. Our findings thus suggest a viable route from early collective evolution to the start of individuality and vertical Darwinian evolution, enabling the emergence of the first species.
    Full-text · Article · Jan 2015
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    • "Moreover, some researchers have cast doubt on a single origin (Doolittle, 2000; but see also Doolittle, 2009). Nonetheless, monophyly of all extant life on Earth is widely accepted (Theobald, 2010). According to this view, the universal common ancestor, or progenitor of superdomain Biota, is estimated to have been created, seeded or spontaneously generated approximately 3.8 billion years ago (Lane, 2009: 8). "
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    ABSTRACT: An introduction and overview are provided for a special issue of the Biological Journal of the Linnean Society concerning the role of behaviour in evolution. Conceptual separation of the process of living from the process of evolution has heuristic value, with the potential to ask better questions about both. Following a short account of the origin of this collection of essays, the first main part of the paper assesses current ideas about the nature of living systems. Becausee all known taxa apparently constitute a single, monophyletic group (superdomain Biota), life can only be characterized, not defined. The second part reviews the ten papers that, collectively, comprise this special issue. It is concluded that we need to acknowledge both the ‘processes of life’ and the ‘processes’ of evolution and we need to explore the consequences that flow from making this distinction. Behaviour, in its broadest sense, is seen as both the expression and mediator of organismic agency, and must therefore play a key role in the processes of evolution. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112, 219–241.
    Full-text · Article · Jun 2014 · Biological Journal of the Linnean Society
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Questions & Answers about this publication

  • Fabio Andrade Machado added an answer in Ecology and Evolution:
    Theory of evolution
    Is the theory of evolution scientific? According to inductive logic, if the mathematical probability about a theory is high, it is scientific. If it is little or tends to zero, it is not.
    Fabio Andrade Machado
    Dear Carmen,

    I was not trying to diss your question. I'm pretty sure that we can evaluate the validity of a theory in a way very similar to the one that you are proposing. The problem is that we have to confront it with another scientific idea in order to actually test it. So the hole thing became circular if we think only in statistical terms ("a scientific theory can only be evaluated when confronted with another scientific theory").

    That's why i think that we can evaluate theories in statistical terms, but not access their scientific status through statistics. It becomes pointless to do so.

    I'm sending bellow a illustrative example of a formal test of universal common ancestry theory. It is interesting to notice that the author had to devise an alternative model, or models, to confront this theory, in order to obtain probability ratios. Namely, he proposed various hypothesis of independent origin for various taxa (including humans, a test that I found particularly funny). The results show that UCA theory is in fact the best theory to explain the (molecular) data.

    Saludos,
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      [Show abstract] [Hide abstract]
      ABSTRACT: Universal common ancestry (UCA) is a central pillar of modern evolutionary theory. As first suggested by Darwin, the theory of UCA posits that all extant terrestrial organisms share a common genetic heritage, each being the genealogical descendant of a single species from the distant past. The classic evidence for UCA, although massive, is largely restricted to 'local' common ancestry-for example, of specific phyla rather than the entirety of life-and has yet to fully integrate the recent advances from modern phylogenetics and probability theory. Although UCA is widely assumed, it has rarely been subjected to formal quantitative testing, and this has led to critical commentary emphasizing the intrinsic technical difficulties in empirically evaluating a theory of such broad scope. Furthermore, several researchers have proposed that early life was characterized by rampant horizontal gene transfer, leading some to question the monophyly of life. Here I provide the first, to my knowledge, formal, fundamental test of UCA, without assuming that sequence similarity implies genetic kinship. I test UCA by applying model selection theory to molecular phylogenies, focusing on a set of ubiquitously conserved proteins that are proposed to be orthologous. Among a wide range of biological models involving the independent ancestry of major taxonomic groups, the model selection tests are found to overwhelmingly support UCA irrespective of the presence of horizontal gene transfer and symbiotic fusion events. These results provide powerful statistical evidence corroborating the monophyly of all known life.
      Preview · Article · May 2010 · Nature