A formal test of the theory of universal common ancestry. Nature

Department of Biochemistry, Brandeis University, Waltham, Massachusetts 01778, USA.
Nature (Impact Factor: 42.35). 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 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.
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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.
    Biological Journal of the Linnean Society 06/2014; 112(2). DOI:10.1111/bij.12300 · 2.54 Impact Factor
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    • "Although there is no proof or even strong hint on the possible life on Mars today (Cockell et al. 2012), if once it appeared there in the past, it had long time to adapt (facing to an environment getting more harsh as time passed by), and as a result of adaptation during long duration it could evolved towards a more complex state than commonly assumed (Gibson et al. 2009). The analysis of extreme tolerant communities instead of individual organisms (de la Vega et al. 2007) is twofold: (1) any possible Martian biota need not be composed of only one taxa (using the Earthrelated definition), and biologists are often using models with several organism groups when they are exploring the origin of life (LUCA is also taken to be a poorly defined, interconnected group of organisms (Glansdorff et al. 2008; Theobald 2010)); (2) the analysis of analogue communities (instead of single organism groups) could point to such behaviour that are important in the exploration of astrobiological issue in general. "
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    ABSTRACT: Tests on cyanobacteria communities embedded in cryptobiotic crusts collected in hot and cold deserts on Earth were performed under Mars-like conditions. The simulations were realized as a survey, to find the best samples for future research. During the tests organisms have to resist Mars-like conditions such as atmospheric composition, pressure, variable humidity (saturated and dry conditions) and partly strong UV irradiation. Organisms were tested within their original habitat inside the crust. Nearly half of the cryptobiotic samples from various sites showed survival of a substantial part of their coexisting organisms. The survival in general depended more on the nature of the original habitat and type of the sample than on the different conditions they were exposed to. The best survival was observed in samples from United Arab Emirates (Jebel Ali, 25 km SW of Dubai town) and from Western Australia (near the South edge of Lake Barley), by taxa: Tolypothrix byssoidea, Gloeocapsopsis pleurocapsoides, Nostoc microscopicum, Leptolyngbya or Symploca sp. At both places in salty desert areas members of the Chenopodiaceae family dominated among the higher plants and in the cryptobiotic crust cyanobacterial taxa Tolypothrix was dominant. These organisms were all living in salty locations with dry conditions most of the year. Among them Tolypothrix, Gloeocapsopsis and Symploca sp. were tested in Mars simulation chambers for the first time. The results suggest that extremophiles should be tested with taken into account the context of their original microenvironment, and also the importance to analyse communities of microbes beside single organisms.
    International Journal of Astrobiology 10/2013; 13(01):35-44. DOI:10.1017/S1473550413000323 · 0.83 Impact Factor
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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 · University of São Paulo
    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.