Common ancestry is a central feature of the theory of evolution, yet it is not clear what “common ancestry” actually means; nor is it clear how it is related to other terms such as “the Tree of Life” and “the last universal common ancestor”. I argue these terms describe three distinct hypotheses ordered in a logical way: that there is a Tree of Life is a claim about the pattern of evolutionary history, that there is a last universal common ancestor is an ontological claim about the existence of an entity of a specific kind, and that there is universal common ancestry is a claim about a causal pattern in the history of life. With these generalizations in mind, I argue that the existence of a Tree of Life entails a last universal common ancestor, which would entail universal common ancestry, but neither of the converse entailments hold. This allows us to make sense of the debates surrounding the Tree, as well as our lack of knowledge about the last universal common ancestor, while still maintaining the uncontroversial truth of universal common ancestry.
This is a preview of subscription content,to check access.
Access this article
When biologists claim that we know that “all life is related,” this does not require a precise definition of what counts as a living thing. However, it does require several clarifications. First, while viruses may or may not be alive, they are not being considering here. The origins of viruses are not at all clear. While it is possible that they all emerged out of cellular life, it is also possible that some viruses existed before cellular life and may or may not have originated independently of it (Forterre 2016; Nasir et al. 2017). Second, the claim is not necessarily about all life in the universe, but just the life on Earth that we have actually discovered and identified.
Of course lateral gene transfer is not the only process that causes gene histories to differ. For example, in sexual species, hybridization and incomplete lineage sorting also lead to gene tree incongruence (Maddison 1997).
Clarke (2010) lists thirteen different candidate definitions of individual or organism that have been defended in the literature.
In response to my claim that the Tree of Life must have a root, a number of audience members have pointed out at various talks that there are rooted and unrooted phylogenetic trees. But the Tree of Life is supposed to be a representation of evolutionary history and as such it must have a root. To see this, it is perhaps enough to note that on an unrooted phylogenetic tree, there is no distinction between a “clade” and its complement (all the tips not in that clade). To ensure that collections such as the “non-mammals” (which includes everything from lizards, the mosses, and E. coli) are not real groups requires a root.
A different story might be told utilizing the model of Doolittle and Booth’s (2017) “it’s the song not the singer” idea. Here, we could imagine a community where a song (a pattern of interactions such as metabolic, structural, or developmental interactions) gets preserved, replicated, and altered over time without the underlying physical lineages necessarily being the ancestors of the future lineages singing the song. Different singers (different taxa) can be recruited horizontally at different points during evolutionary history. This might also be called common ancestry without a LUCA.
A reader here may worry about the definition of “life” and how that is being used in the argument. If we want to answer the question “How many times did life begin?” we obviously need to know what qualifies as life. That problem is extremely tricky and may not even have a correct answer at all. But we do not have to answer the “what is life” question in order to answer the question of whether a given collection of entities has a common origin. For example, whether the LUCA in Weiss et al.’s (2016) story counts as alive or not is irrelevant since it is a causal bottleneck in the sense that living things can causally trace their properties back to the properties of LUCA.
Alexander DE (2015) On the wing: insects, pterosaurs, birds, bats and the evolution of animal flight. Oxford University Press, Oxford
Andam CP, Gogarten JP (2011) Biased gene transfer in microbial evolution. Nat Rev Microbiol 9:543–555
Arnoldt H, Strogatz SH, Timme M (2015) Toward the darwinian transition: switching between distributed and speciated states in a simple model of early life. Phys Rev E 92:052909
Baldauf SL, Palmer JD, Doolittle WF (1996) The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny. Proc Natl Acad Sci USA 93(15):7749–7754
Becerra A, Delaye L, Islas S, Lazcano A (2007) The very early stages of biological evolution and the nature of the last common ancestor of the three major cell domains. Annu Rev Ecol Evol Syst 38(1):361–379
Buller AR, Townsend CA (2013) Intrinsic evolutionary constraints on protease structure, enzyme acylation, and the identity of the catalytic triad. Proc Natl Acad Sci USA 110(8):E653–E661. https://doi.org/10.1073/pnas.1221050110
Ciccarelli FD, Doerks T, von Mering C, Creevey C, Snel B, Bork P (2006) Towards automatic reconstruction of a highly resolved Tree of Life. Science 311:1283–1287. https://doi.org/10.1126/science.1123061
Clarke E (2010) The problem of biological individuality. Biol Theor 5(4):312–325
Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284(5423):2124–2128
Doolittle WF (2005) If the Tree of Life fell, would we recognize the sound? In: Sapp J (ed) Microbial phylogeny and evolution: concepts and controversies. Oxford University Press, Oxford, pp 119–133
Doolittle WF (2009) The practice of classification and the theory of evolution, and what the demise of Charles Darwin’s Tree of Life hypothesis means for both of them. Philos Trans R Soc B Biol Sci 364(1527):2221–2228
Doolittle WF (2012) Population genomics: how bacterial species form and why they don’t exist. Curr Biol 22(11):R451–R453. https://doi.org/10.1016/j.cub.2012.04.034
Doolittle WF, Bapteste E (2007) Pattern pluralism and the Tree of Life hypothesis. Proc Acad Natl Sci USA 104:2043–2049
Doolittle WF, Booth A (2017) It’s the song, not the singer: an exploration of holobiosis and evolutionary theory. Biol Philos 32:5–24
Doolittle WF, Brunet TDP (2016) What is the Tree of Life? PLoS Genet 12(4):e1005912. https://doi.org/10.1371/journal.pgen.1005912
Doolittle WF, Boucher Y, Nesb\o CL, Douady CJ, Andersson JO, Roger AJ (2003) How big is the iceberg of which organellar genes in nuclear genomes are but the tip? Philos Trans B 358(1429):39–58
Ereshefsky M (2010) Microbiology and the species problem. Biol Philos 25:67–79
Forterre P, Filée, J, Myllykallio H (2004) Origin and evolution of DNA and DNA replication machineries. In: Ribas de Pouplana L (ed) The genetic code and the origin of life. Landes Bioscience, Austin, pp 145–168
Forterre P (2010) Defining life: the virus viewpoint. Orig Life Evol Biosph 40(2):151–160. https://doi.org/10.1007/s11084-010-9194-1
Forterre P (2016) To be or not to be alive: how recent discoveries challenge the traditional definitions of viruses and life. Stud Hist Philos Biol Biomed Sci 59:100–108
Galtier N, Daubin V (2008) Dealing with incongruence in phylogenetic analyses. Philos Trans R Soc Lond B Biol Sci 363:4023–4029
Gogarten JP, Olendzenski L (1999) The progenote. In: Creighton T (ed) Encyclopedia of molecular biology. Wiley, NY
Gogarten JP, Kibak H, Dittrich P, Taiz L, Bowman EJ, Bowman BJ, Manolson MF et al (1989) Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes. Proc Natl Acad Sci USA 86(17):6661–6665
Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, Butterfield CN, Hernsdorf AW, Amano Y, Ise K, Suzuki Y, Dudek N, Relman DA, Finstad KM, Amundson R, Thomas BC, Banfield JF (2016) A new view of the Tree of Life. Nat Microbiol. https://doi.org/10.1038/nmicrobiol.2016.48
Iwabe N, Kuma K, Hasegawa M, Osawa S, Miyata T (1989) Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc Natl Acad Sci USA 86(23):9355–9359
Koonin EV (2003) Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat Rev Microbiol 1(2):127–136
Land MF, Nilsson D-E (2002) Animal eyes. Oxford University Press, Oxford
Maddison W (1997) Gene trees in species trees. Syst Biol 46(3):523–536
Mindell DP (2013) The Tree of Life: metaphor, model, and heuristic device. Syst Biol 62(3):479–489
Nasir A, Kim KM, Caetano-Anollés G (2017) Phylogenetic tracings of proteome size support the gradual accretion of protein structural domains and the early origin of viruses from primordial cells. Front Microbiol 8:1178. https://doi.org/10.3389/fmicb.2017.01178
Ouzounis CA, Kunin V, Darzentas N, Goldovsky L (2006) A minimal estimate for the gene content of the last universal common ancestor—exobiology from a terrestrial perspective. Res Microbiol 157:57–68
Penny D, Poole A (1999) The nature of the last universal common ancestor. Curr Opin Genet Dev 9(6):672–677
Penny D, Foulds LR, Hendy MD (1982) Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences. Nature 297(5863):197–200
Philippe H, Forterre P (1999) The rooting of the universal Tree of Life is not reliable. J Mol Evol 49:509–523
Puigbò P, Wolf YI, Koonin EV (2009) Search for a Tree of Life in the thicket of the phylogenetic forest. J. Biol 8:59. https://doi.org/10.1186/jbiol159 PMID: 19594957
Puigbò P, Wolf YI, Koonin EV (2013) Seeing the Tree of Life behind the phylogenetic forest. BMC Biol 11:46. https://doi.org/10.1186/1741-7007-11-46 PMID: 23587361
Sage RF (2004) The evolution of C4 photosynthesis. New Phytol 161:341–370. https://doi.org/10.1111/j.1469-8137.2004.00974.x
Sober E (2008) Evidence and evolution: the logic behind the science. Cambridge University Press, Cambridge
Sober E, Steel M (2002) Testing the hypothesis of common ancestry. J Theor Biol 218(4):395–408
Spang A, Saw JH, Jorgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, van Eijk R, Schleper C, Guy L, Ettema TJ (2015) Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521:173–179
Syvanen M (2002) On the occurrence of horizontal gene transfer among an arbitrarily chosen group of 26 genes. J Mol Evol 54:258–266. https://doi.org/10.1007/s0023901-0007-z
Syvanen M (2005) The last universal common ancestor. The panda’s thumb. https://pandasthumb.org/archives/2005/08/the-last-univer.html. Accessed 30 August 2005
Theobald DL (2010) A formal test of the theory of universal common ancestry. Nature 465:219–222
Velasco JD (2012) The future of systematics: tree thinking without the tree. Philos Sci 79:624–636
Velasco JD (2013) The Tree of Life. In: Ruse M (ed) The Cambridge encyclopedia of darwin and evolutionary thought. Cambridge University Press, Cambridge, pp 340–345
Vetsigian K, Woese C, Goldenfeld N (2006) Collective evolution and the genetic code. Proc Natl Acad Sci 103(28):10696–10701
Weiss MC, Sousa FL, Mrnjavac N, Neukirchen S, Roettger M, Nelson-Sathi S, Martin WF (2016) The physiology and habitat of the last universal common ancestor. Nat Microbiol, vol 1. https://doi.org/10.1038/nmicrobiol.2016.116
Wells J (2006) The politically incorrect guide to darwinism and intelligent design. Regnery Publishing Inc, Washington, DC
Williams TA, Foster PG, Cox CJ, Embley TM (2013) An archaeal origin of eukaryotes supports only two primary domains of life. Nature 504:231–236
Woese CR (1983) The primary lines of descent and the universal ancestor. In: Bendall DS (ed) Evolution from molecules to men. Cambridge University Press, Cambridge, pp 209–233
Woese CR (1987) Bacterial evolution. Microbiol Mol Biol Rev 51(2):221–271
Woese C (1998) The universal ancestor. Proc Acad Natl Sci USA 95(12):6854–6859
Woese CR, Fox GE (1977) The concept of cellular evolution. J Mol Evol 10(1):1–6. https://doi.org/10.1007/BF01796132
Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Acad Natl Sci USA 87(12):4576–4579
Zaremba-Niedzwiedzka K, Careres EF, Saw JH, Backstrom D, Juzokaite L, Vancaester E, Seitz KW, Anantharaman K, Starnawski P, Kjeldsen KU, Stott MB, Nunoura T, Banfield JF, Schramm A, Baker BJ, Spang A, Ettema TJ (2017) Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541:353–358
Zhaxybayeva O, Gogarten P (2004) Cladogenesis, coalescence and the evolution of the three domains of life. Trends Genet 20(4):182–187
I would like to thank Ford Doolittle, Maureen O’Malley, Jeremy Schwartz, Elliott Sober, Quayshawn Spencer, several anonymous referees, and audiences at the University of Pennsylvania and the 2016 Philosophy of Science Association meeting for helpful comments and discussion.
About this article
Cite this article
Velasco, J. Universal common ancestry, LUCA, and the Tree of Life: three distinct hypotheses about the evolution of life. Biol Philos 33, 31 (2018). https://doi.org/10.1007/s10539-018-9641-3