Root of the Eukaryotic Tree of Life

While it has become quite clear that the last eukaryotic common ancestor (LECA) was a bikont, i.e. had two anterior cilia to move around (as I wrote previously), it now seems that the LECA wasn't only a bikont, but also an excavate. Excavates are one of the five main groups of eukaryotes (Adl et al.2012) having ancestrally two cilia and a ventral feeding groove. Excavates include for example Trichomonas (Parabasalia), Giardia (Fornicata), Euglenozoa (e.g. Euglena, Trypanosoma), Heterolobosea, Jakobida (latter three belonging to Discoba), and Malawimonas, but it has turned out that they might not form a monophyletic group that seemed quite likely in 2009 (Hampl et al. 2009). In my previous post I treated excavates as monophyletic and avoided discussing them, although I was aware of some problems. Particularly, Malawimonas, which is structurally a typical excavate (possessing two cilia with a characteristic ciliary apparatus and a ventral feeding groove; Simpson, 2003) did not want to group very well with other excavates in phylogenomic analyses (Rodríguez-Ezpeletaet al. 2007; Derelle & Lang, 2012; Zhao et al. 2013; Brown et al. 2013). I thought perhaps the data was incomplete to make a big deal about this. Now it looks pretty clear (Cavalier-Smith et al. 2014; 2015; Derelle et al. 2015) that Malawimonas is more closely related to unikont/Opimoda branch (amoebae, animals, fungi and others; Fig. 1) than to (most) other excavates. Interestingly, phylogenomic analyses by Cavalier-Smith et al. (2014; 2015) reveal that excavate groups Parabasalia, Fornicata, and Preaxostyla might also be more closely related to unikonts than to Discoba (Euglenozoa, Heterolobosoa, and Jakobida). Parabasalia, Fornicata, and Preaxostyla are classified under Metamonada, who are all anaerobic or microaerophilic and lack typical respiratory mitochondria. Many of them are parasites or symbionts of animals. Unfortunately most of them are fast evolving, making it difficult to place them in phylogenetic analyses, particularly Trichomonas and Giardia for which full genomes are available. It would be necessary to obtain additional genome scale data for more slowly evolving free-living species from groups like Dysnectes and Carpediemonas (Takishita et al. 2012) to place representatives of Metamonada among eukaryotes more reliably.

Figure 1. Phylogeny of eukaryotes updated from my previous post mainly on the basis of Cavalier-Smith et al. (20142015) and Derelle et al. (2015) papers. Although since 2010, Cavalier-Smith prefers to root the tree between Euglenozoa (member of Discoba) and other eukaryotes, the rooting found by Derelle et al. (2015) is more reliable, because it is based on large number of mitochondrial and other bacterial genes for which there are closer out-groups available than for genes of archaeal origin (see for example the rooting found by Lasek-Nesselquist& Gogarten, 2013 which fits Cavalier-Smith's scenario). Cavalier-Smith (20102013) lists some genomic characters that appear to be ancestral (i.e. shared with prokaryotes) in Euglenozoa but derived in other eukaryotes. The problem is that full genome sequences are available only for few fast evolving and mostly parasitic Euglenozoa and other excavates, which makes these kinds of lists highly speculative.

If the rooting of the eukoryote tree (Fig. 1) is correct, then it really seems that the LECA might have been quite similar to a typical excavate like Malawimonas or a jakobid (e.g. Jakoba, Reclinomonas, Andalucia). This scenario finds support also from some alveolates (e.g. Colponema) that are structurally quite similar to excavates (Tikhonenkov et al. 2014; Cavalier-Smith et al. 2014). Apparently, Colponema, Acavomonas and many other similar undescribed groups (Janouškovecet al. 2013; Tikhonenkov et al. 2014) are phylogenetically diverse bunch that are variously related to, but clearly outside of the three main groups of alveolates (ciliates, apicomplexans, and dinoflagellates).

Adl SM, Simpson AGB, Lane CE, Lukeš J, Bass D, Bowser SS, Brown MW, Burki F, Dunthorn M, Hampl V, Heiss A, Hoppenrath M, Lara E, Gall L le, Lynn DH, McManus H, Mitchell E a D, Mozley-Stanridge SE, Parfrey LW, Pawlowski J, Rueckert S, Shadwick L, Schoch CL, Smirnov A, Spiegel FW (2012) The revised classification of eukaryotes. The Journal of eukaryotic microbiology 59 (5): 429–514. doi: 10.1111/j.1550-7408.2012.00644.x
Brown MW, Sharpe SC, Silberman JD, Heiss AA, Lang BF, Simpson AGB, Roger AJ (2013) Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads. Proceedings. Biological sciences / The Royal Society 280 (1769): 20131755. doi: 10.1098/rspb.2013.1755
Cavalier-Smith T (2010) Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree. Biology letters 6: 342–345. doi: 10.1098/rsbl.2009.0948
Cavalier-Smith T (2013) Early evolution of eukaryote feeding modes, cell structural diversity, and classification of the protozoan phyla Loukozoa, Sulcozoa, and Choanozoa. European journal of protistology 49 (2): 115–178. doi: 10.1016/j.ejop.2012.06.001
Cavalier-Smith T, Chao EE, Snell E a, Berney C, Fiore-Donno AM, Lewis R (2014) Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts (animals, fungi, choanozoans) and Amoebozoa. Molecular phylogenetics and evolution 81: 71–85. doi: 10.1016/j.ympev.2014.08.012
Cavalier-Smith T, Chao EE, Lewis R (2015) Multiple origins of Heliozoa from flagellate ancestors: New cryptist subphylum Corbihelia, superclass Corbistoma, and monophyly of Haptista, Cryptista, Hacrobia and Chromista. Molecular phylogenetics and evolution. doi: 10.1016/j.ympev.2015.07.004
Derelle R, Lang BF (2012) Rooting the Eukaryotic Tree with Mitochondrial and Bacterial Proteins. Molecular biology and evolution 29: 1277–1289. doi: 10.1093/molbev/msr295
Derelle R, Torruella G, Klimeš V, Brinkmann H, Kim E, Vlček Č, Lang BF, Eliáš M (2015) Bacterial proteins pinpoint a single eukaryotic root. Proceedings of the National Academy of Sciences 112: E693–E699. doi: 10.1073/pnas.1420657112
Hampl V, Hug L, Leigh JW, Dacks JB, Lang BF, Simpson AGB, Roger AJ (2009) Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”. Proceedings of the National Academy of Sciences of the United States of America 106: 3859–3864. doi: 10.1073/pnas.0807880106
Janouškovec J, Tikhonenkov D V, Mikhailov K V, Simdyanov TG, Aleoshin V V, Mylnikov AP, Keeling PJ (2013) Colponemids represent multiple ancient alveolate lineages. Current biology 23: 2546–2552. doi: 10.1016/j.cub.2013.10.062
Lasek-Nesselquist E, Gogarten JP (2013) The effects of model choice and mitigating bias on the ribosomal tree of life. Molecular phylogenetics and evolution 69: 17–38. doi: 10.1016/j.ympev.2013.05.006
Rodríguez-Ezpeleta N, Brinkmann H, Burger G, Roger AJ, Gray MW, Philippe H, Lang BF (2007) Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans. Current Biology 17: 1420–1425. doi: 10.1016/j.cub.2007.07.036
Simpson AGB (2003) Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota). International Journal of Systematic and Evolutionary Microbiology 53: 1759–1777. doi: 10.1099/ijs.0.02578-0
Takishita K, Kolisko M, Komatsuzaki H, Yabuki A, Inagaki Y, Cepicka I, Smejkalová P, Silberman JD, Hashimoto T, Roger AJ, Simpson AGB (2012) Multigene Phylogenies of Diverse Carpediemonas-like Organisms Identify the Closest Relatives of ‘Amitochondriate’ Diplomonads and Retortamonads. Protist 163: 344–355. doi: 10.1016/j.protis.2011.12.007
Tikhonenkov DV, Janouškovec J, Mylnikov AP, Mikhailov KV, Simdyanov TG, Aleoshin VV, Keeling PJ (2014) Description of Colponema vietnamica sp.n. and Acavomonas peruviana n. gen. n. sp., Two New Alveolate Phyla (Colponemidia nom. nov. and Acavomonidia nom. nov.) and Their Contributions to Reconstructing the Ancestral State of Alveolates and Eukaryotes. PloS one 9: e95467. doi: 10.1371/journal.pone.0095467
Zhao S, Shalchian-Tabrizi K, Klaveness D (2013) Sulcozoa revealed as a paraphyletic group in mitochondrial phylogenomics. Molecular phylogenetics and evolution 69 (3): 462–468. doi: 10.1016/j.ympev.2013.08.005


  1. Nice post, Marko. Great summary of the current state of the LECA. Could you help me understand a few things?

    1. Why is the LECA thought to be a protist when it would most likely be more similar to lokiarchaeota or another archaeon? If the latter is true, then shouldn't the LECA be talked about as a nucleated archaeon rather than a protist similar to Malawimonas?

    2. What are the data suggesting eukaryotes share one common ancestor and not many (like bacteria)? Is it not a more plausible scenario that multiple nucleated archaea gave rise to various eukaryotic lineages which are represented in the different supergroups? Is there evidence against this scenario?

    If you happen to find the time to read and reply - thanks so much!

  2. Hi Alex,

    I'll answer the second question first.

    2. Genetic (phylogenies of universal genes) and cellular data (e.g. presence of nucleus, mitochondria, Golgi apparatus etc. and details of these structures) clearly suggest that eukaryotes have single origin. 50-60 years ago when most of that data was missing, it was seriously considered that eukaryotes might be polyphyletic, that different groups might have originated from different prokaryotes. Today there is no evidence for that. Although eukaryote specific cellular structures suggest monophyly (single origin) of this group, they do not really pinpoint from which prokaryotic group eukaryotes evolved, because there almost are no comparable structures in prokaryotes. Phylogenies estimated from universal genes (mainly transcription and translation related) clearly show eukaryote monophyly and their origin from Archaea. Phylogenies estimated from mitochondrial genes also support eukaryote mononphyly (all eukaryotes had or have had mitochondria) and their origin from Alphaproteobacteria. In these gene trees all eukaryotes are very closely related (protein sequences of some of these genes are hardly different between animals and plants for example) compared to the diversity within prokaryotes. Specific similarities with certain prokaryotes in some eukaryotes (e.g. plastids from cyanobacteria and horizontally transferred single genes) are all later acquisitions after eukaryotes already had nucleus, mitochondria etc. Anyway, I think no researcher nowadays seriously suggests that eukaryotes evolved multiple times from prokaryotes.

    1. Considering the monophyly of eukaryotes, it is parsimonious to assume that last eukaryotic common ancestor (LECA) had the characters that all eukaryotes now have. There are no good reasons to suggest in case of monophyly that nucleus etc. evolved independently in different eukaryotes. First eukaryotic common ancestor (FECA) is a different thing. If eukaryotes originated in a merger of Archaea and Bacteria, then FECA would be a bacterium (ancestor of mitochondrion) inside an archaeon without any eukaryote specific characters (this scenario seems most likely to me in light of recent literature). Or if some prokaryote gradually evolved to become eukaryote and only later picked up mitochondrion, then FECA would simply be some kind of prokaryote.

    Hope it helped.

    For example Nick Lane has written about these things in his recent book "The Vital Question". Worth reading, not just because of interesting topics, but also because he is a good writer.