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Reconstructing the Last Common Ancestor: Epistemological and Empirical Challenges

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Abstract

Reconstructing the genetic traits of the Last Common Ancestor (LCA) and the Tree of Life (TOL) are two examples of the reaches of contemporary molecular phylogenetics. Nevertheless, the whole enterprise has led to paradoxical results. The presence of Lateral Gene Transfer poses epistemic and empirical challenges to meet these goals; the discussion around this subject has been enriched by arguments from philosophers and historians of science. At the same time, a few but influential research groups have aimed to reconstruct the LCA with rich-in-detail hypotheses and high-resolution gene catalogs and metabolic traits. We argue that LGT poses insurmountable challenges for detailed and rich in details reconstructions and propose, instead, a middle-ground position with the reconstruction of a slim LCA based on traits under strong pressures of Negative Natural Selection, and for the need of consilience with evidence from organismal biology and geochemistry. We defend a cautionary perspective that goes beyond the statistical analysis of gene similarities and assumes the broader consequences of evolving empirical data and epistemic pluralism in the reconstruction of early life.

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Notes

  1. Eric Bapteste and John Dupré (2013) have called attention to the standard model or entities ontology and have argued in favor of a processual microbial ontology. Although their arguments are relevant for our proposal and for our emphasis on cellular processes, we have restricted ourselves to a tangential reference to their ideas.

  2. On the question of pluralism, also, “[a]universal Tree of Life (TOL) has long been a goal of molecular phylogeneticists, but reticulation at the level of genes and possibly at the levels of cells and species renders any simple interpretation of such a TOL, especially as applied to prokaryotes, problematic.” (Doolittle and Brunet 2016, p. 1).

  3. A progenote is “a hypothetical biological entity in which phenotype and genotype had an imprecise, rudimentary linkage relationship” (Woese and Fox 1977).

  4. By locating 355 protein families, Weiss et al. inferred a set of traits, including that the LCA (which equivocally for the authors is the same as the progenote) was anaerobic, CO2 fixing, H2 dependent with a Wood–Ljungdahl pathway, N2-fixing and thermophilic, among many other biochemical details. What drew the most pointed critique, however, was the speculation that this organism consisted of a cell-sized compartment bound by a mineral membrane, a hypothesis that revealed the lack of familiarity with current advances in the biochemistry of lipids and on the geochemistry of hydrothermal vents (the supposed environment of this organism). This membrane had an “underlying lipid bilayer added to provide a permeability barrier to ions such as Na+ and H+”. But, as Gogarten and Deamer point out, an obvious question was the source of the lipid forming the membrane, and the process by which it would adhere to the mineral surface.

    To this, they added a critique of the supposed ATP-ase and sodium–proton exchange mechanism embedded in the bilayer, finally concluding that “these biochemical systems and catalysts are characteristic of an advanced form of life having ribosomes, translation, genes and a genetic code, far beyond what most would imagine as the first form of life” (Gogarten and Deamer 2016).

  5. The complete methodological critique goes like this: “Weiss et al. propose a computational scheme that provides a shortcut to identify genes that may have been present in LUCA. This approach is subject to two types of error: False positives. The stated criterion for inclusion in the LUCA gene set is that the gene needs to be present in two archaeal and two bacterial groups. From the presented tables, it is clear that orders are considered as distinct groups. The criterion identifies a gene as present in LUCA if a single transdomain transfer occurred before the two ‘groups’ (that is, orders) in the receiving domain split, or if the transferred gene was subsequently transferred between the two groups. Given that gene transfer within domains occurs more frequently than transfer between domains, a large number of false positives are expected under the implemented scheme. False negatives, which are likely to be an even bigger problem. The authors correctly assume that gene transfer between the domains has occurred. Consequently, many genes that were present in LUCA will not be inferred as present. ATP synthases and aminoacyl-transfer RNA (tRNA) synthetases illustrate this point, because only one out of at least five ATP-synthase subunits was part of the inferred LUCA set, and only eight aminoacyl-tRNA synthetases, whereas LUCA appears to have used the full complement of today’s genetically encoded amino acids, and had a functional ATPase/ATP synthase. The consequence of these errors is that the inferred LUCA gene set is strongly biased toward genes that have a limited distribution and utility in today’s organisms'' (Gogarten and Deamer 2016, p. 1).

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Acknowledgements

A. Estrada thanks the Posgrado en Ciencias Biológicas at the Universidad Nacional Autónoma de México, as well as Consejo Nacional de Ciencia y Tecnología (CONACYT) for their support with fellowship No. 460604. I also thank Professor Daniel Piñero for his advice. We also acknowledge the invaluable help of Vivette García Deister and Luis Delaye for their insight on this paper.

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Scholarship No. 460604 to A.E. (CONACYT).

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Estrada, A., Suárez-Díaz, E. & Becerra, A. Reconstructing the Last Common Ancestor: Epistemological and Empirical Challenges. Acta Biotheor 70, 15 (2022). https://doi.org/10.1007/s10441-022-09439-1

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