The hybrid nature of the Eukaryota and a consilient view of life on Earth (original) (raw)
Martin, W. & Kowallik, K. Annotated English translation of Mereschkowsky's 1905 paper 'Über Natur und Ursprung der Chromatophoren imvPflanzenreiche'. Eur. J. Phycol.34, 287–295 (1999). Google Scholar
Wallin, I. E. The mitochondria problem. Am. Naturalist57, 255–261 (1923). Article Google Scholar
Alvarez-Ponce, D., Bapteste, E., Lopez, P. & McInerney, J. O. Gene similarity networks provide new tools for understanding eukaryote origins and evolution. Proc. Natl Acad. Sci. USA110, E1594–E1603 (2013). ArticlePubMedPubMed Central Google Scholar
Esser, C. et al. A genome phylogeny for mitochondria among α-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol. Biol. Evol.21, 1643–1660 (2004). ArticleCASPubMed Google Scholar
Kurland, C. G., Collins, L. J. & Penny, D. Genomics and the irreducible nature of eukaryote cells. Science312, 1011–1014 (2006). ArticleCASPubMed Google Scholar
López-García, P. & Moreira, D. Selective forces for the origin of the eukaryotic nucleus. Bioessays28, 525–533 (2006). ArticleCASPubMed Google Scholar
Pisani, D., Cotton, J. A. & McInerney, J. O. Supertrees disentangle the chimerical origin of eukaryotic genomes. Mol. Biol. Evol.24, 1752–1760 (2007). ArticleCASPubMed Google Scholar
Rivera, M. C. & Lake, J. A. The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature431, 152–155 (2004). ArticleCASPubMed Google Scholar
Stechmann, A. & Cavalier-Smith, T. The root of the eukaryote tree pinpointed. Curr. Biol.13, 665–666 (2003). ArticleCAS Google Scholar
Popper, K. R. The Logic of Scientific Discovery (Routledge, 1959). Google Scholar
Whewell, W. The Philosophy Of Inductive Sciences, Founded Upon Their History (John W. Parker, 1840). Google Scholar
Williams, T. A., Foster, P. G., Cox, C. J. & Embley, T. M. An archaeal origin of eukaryotes supports only two primary domains of life. Nature504, 231–236 (2013). ArticleCASPubMed Google Scholar
Fitzpatrick, D. A., Creevey, C. J. & McInerney, J. O. Genome phylogenies indicate a meaningful α-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales. Mol. Biol. Evol.23, 74–85 (2006). ArticleCASPubMed Google Scholar
Margulis, L. Archaeal–eubacterial mergers in the origin of Eukarya: phylogenetic classification of life. Proc. Natl Acad. Sci. USA93, 1071–1076 (1996). ArticleCASPubMedPubMed Central Google Scholar
Rinke, C., Schwientek, P., Sczyrba, A. & Ivanova, N. N. Insights into the phylogeny and coding potential of microbial dark matter. Nature499, 431–437 (2013). ArticleCASPubMed Google Scholar
Thiergart, T., Landan, G., Schenk, M., Dagan, T. & Martin, W. F. An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin. Genome Biol. Evol.4, 466–485 (2012). ArticleCASPubMedPubMed Central Google Scholar
Cavalier-Smith, T. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int. J. Syst. Evol. Microbiol.52, 297–354 (2002). ArticleCASPubMed Google Scholar
Hirt, R. P. et al. Microsporidia are related to Fungi: evidence from the largest subunit of RNA polymerase II and other proteins. Proc. Natl Acad. Sci. USA96, 580–585 (1999). ArticleCASPubMedPubMed Central Google Scholar
Roger, A. J. et al. A mitochondrial-like chaperonin 60 gene in Giardia lamblia: evidence that diplomonads once harbored an endosymbiont related to the progenitor of mitochondria. Proc. Natl Acad. Sci. USA95, 229–234 (1998). ArticleCASPubMedPubMed Central Google Scholar
Rodriguez-Ezpeleta, N. & Embley, T. M. The SAR11 group of α-proteobacteria is not related to the origin of mitochondria. PLOS ONE7, e30520 (2012). ArticleCASPubMedPubMed Central Google Scholar
Bapteste, E. et al. Evolutionary analyses of non-genealogical bonds produced by introgressive descent. Proc. Natl Acad. Sci. USA109, 18266–18272 (2012). ArticlePubMedPubMed Central Google Scholar
Gogarten, J. P. et al. Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes. Proc. Natl Acad. Sci. USA86, 6661–6665 (1989). ArticleCASPubMedPubMed Central Google Scholar
Brinkmann, H. & Philippe, H. Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies. Mol. Biol. Evol.16, 817–825 (1999). ArticleCASPubMed Google Scholar
Forterre, P. The origin of DNA genomes and DNA replication proteins. Curr. Opin. Microbiol.5, 525–532 (2002). ArticleCASPubMed Google Scholar
Van Valen, L. M. & Maiorana, V. C. The archaebacteria and eukaryotic origins. Nature287, 248–250 (1980). ArticleCASPubMed Google Scholar
Cotton, J. A. & McInerney, J. O. Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function. Proc. Natl Acad. Sci. USA107, 17252–17255 (2010). ArticlePubMedPubMed Central Google Scholar
Margulis, L., Bermudes, D. & Obar, R. Symbiosis in evolution: status of the hypothesis of the spirochete origin of undulipodia. Orig. Life Evol. Biosph.16, 319 (1986). Article Google Scholar
Lake, J. A., Henderson, E., Oakes, M. & Clark, M. W. Eocytes: a new ribosome structure indicates a kingdom with a close relationship to eukaryotes. Proc. Natl Acad. Sci. USA81, 3786–3790 (1984). ArticleCASPubMedPubMed Central Google Scholar
Williams, T. A., Foster, P. G., Nye, T. M. W., Cox, C. J. & Embley, T. M. A congruent phylogenomic signal places eukaryotes within the Archaea. Proc. Biol. Sci.279, 4870–4879 (2012). ArticleCASPubMedPubMed Central Google Scholar
Lake, J. A., Servin, J. A., Herbold, C. W. & Skophammer, R. G. Evidence for a new root of the tree of life. Systemat. Biol.57, 835–843 (2008). ArticleCAS Google Scholar
Dagan, T., Roettger, M., Bryant, D. & Martin, W. Genome networks root the tree of life between prokaryotic domains. Genome Biol. Evol.2, 379–392 (2010). ArticleCASPubMedPubMed Central Google Scholar
Ciccarelli, F. D. et al. Toward automatic reconstruction of a highly resolved tree of life. Science311, 1283–1287 (2006). ArticleCASPubMed Google Scholar
Lasek-Nesselquist, E. & Gogarten, J. P. The effects of model choice and mitigating bias on the ribosomal tree of life. Mol. Phylogenet. Evol.69, 17–38 (2013). ArticlePubMed Google Scholar
Creevey, C. J., Doerks, T., Fitzpatrick, D. A., Raes, J. & Bork, P. Universally distributed single-copy genes indicate a constant rate of horizontal transfer. PLOS ONE6, e22099 (2011). ArticleCASPubMedPubMed Central Google Scholar
Gouy, M. & Li, W. H. Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree. Nature339, 145–147 (1989). ArticleCASPubMed Google Scholar
Tourasse, N. J. & Gouy, M. Accounting for evolutionary rate variation among sequence sites consistently changes universal phylogenies deduced from rRNA and protein-coding genes. Mol. Phylogenet. Evol.13, 159–168 (1999). ArticleCASPubMed Google Scholar
Gribaldo, S., Poole, A. M., Daubin, V., Forterre, P. & Brochier-Armanet, C. The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse? Nature Rev. Microbiol.8, 743–752 (2010). ArticleCAS Google Scholar
Woese, C. R., Kandler, O. & Wheelis, M. L. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl Acad. Sci. USA87, 4576 (1990). ArticleCASPubMedPubMed Central Google Scholar
Baldauf, S. L., Palmer, J. D. & Doolittle, W. F. The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny. Proc. Natl Acad. Sci. USA93, 7749–7754 (1996). ArticleCASPubMedPubMed Central Google Scholar
Keane, T. M., Creevey, C. J., Pentony, M. M., Naughton, T. J. & McLnerney, J. O. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol. Biol.6, 29 (2006). ArticleCASPubMedPubMed Central Google Scholar
Cox, C., Foster, P., Hirt, R. & Harris, S. The archaebacterial origin of eukaryotes. Proc. Natl Acad. Sci. USA105, 20356–20361 (2008). ArticlePubMedPubMed Central Google Scholar
Foster, P. G., Cox, C. J. & Embley, T. M. The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods. Phil. Trans. R. Soc. Lond. B Biol. Sci.364, 2197–2207 (2009). Article Google Scholar
Lartillot, N., Lepage, T. & Blanquart, S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics25, 2286–2288 (2009). ArticleCASPubMed Google Scholar
Guy, L. & Ettema, T. J. The archaeal 'TACK' superphylum and the origin of eukaryotes. Trends Microbiol.19, 580–587 (2011). ArticleCASPubMed Google Scholar
Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics22, 2688–2690 (2006). ArticleCASPubMed Google Scholar
Makarova, K. S., Yutin, N., Bell, S. D. & Koonin, E. V. Evolution of diverse cell division and vesicle formation systems in Archaea. Nature Rev. Microbiol.8, 731–741 (2010). ArticleCAS Google Scholar
Mojzsis, S. J. et al. Evidence for life on Earth before 3,800 million years ago. Nature384, 55–59 (1996). ArticleCASPubMed Google Scholar
Wacey, D., Kilburn, M. R., Saunders, M., Cliff, J. & Brasier, M. D. Microfossils of sulphur-metabolizing cells in 3.4-billion-year-old rocks of Western Australia. Nature Geosci.4, 698–702 (2011). ArticleCAS Google Scholar
Knoll, A. H., Javaux, E. J., Hewitt, D. & Cohen, P. Eukaryotic organisms in Proterozoic oceans. Phil. Trans. R. Soc. Lond. B Biol. Sci.361, 1023 (2006). ArticleCAS Google Scholar
Brocks, J. J., Logan, G. A., Buick, R. & Summons, R. E. Archean molecular fossils and the early rise of eukaryotes. Science285, 1033–1036 (1999). ArticleCASPubMed Google Scholar
Knoll, A. H. Paleobiological perspectives on early eukaryotic evolution. Cold Spring Harb. Perspect. Biol.6, a016113.
Rasmussen, B., Fletcher, I. R., Brocks, J. J. & Kilburn, M. R. Reassessing the first appearance of eukaryotes and cyanobacteria. Nature455, 1101–1104 (2008). ArticleCASPubMed Google Scholar
Brocks, J. J. & Banfield, J. Unravelling ancient microbial history with community proteogenomics and lipid geochemistry. Nature Rev. Microbiol.7, 601–609 (2009). ArticleCAS Google Scholar
Parfrey, L. W., Lahr, D. J. G., Knoll, A. H. & Katz, L. A. Estimating the timing of early eukaryotic diversification with multigene molecular clocks. Proc. Natl Acad. Sci. USA108, 13624–13629 (2011). ArticleCASPubMedPubMed Central Google Scholar
Shih, P. M. & Matzke, N. J. Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins. Proc. Natl Acad. Sci. USA110, 12355–12360 (2013). ArticlePubMedPubMed Central Google Scholar
Timmis, J. N., Ayliffe, M. A., Huang, C. Y. & Martin, W. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nature Rev. Genet.5, 123–135 (2004). ArticleCASPubMed Google Scholar
Jain, R., Rivera, M. C. & Lake, J. A. Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl Acad. Sci. USA96, 3801 (1999). ArticleCASPubMedPubMed Central Google Scholar
Alvarez-Ponce, D. & McInerney, J. O. The human genome retains relics of its prokaryotic ancestry: human genes of archaebacterial and eubacterial origin exhibit remarkable differences. Genome Biol. Evol.3, 782–790 (2011). ArticleCASPubMedPubMed Central Google Scholar
Poole, A. M. & Penny, D. Evaluating hypotheses for the origin of eukaryotes. Bioessays29, 74–84 (2007). ArticlePubMed Google Scholar
Naor, A. & Gophna, U. Cell fusion and hybrids in Archaea: prospects for genome shuffling and accelerated strain development for biotechnology. Bioengineered4, 126–129 (2013). ArticlePubMed Google Scholar
Naor, A., Lapierre, P., Mevarech, M., Papke, R. T. & Gophna, U. Low species barriers in halophilic archaea and the formation of recombinant hybrids. Curr. Biol.22, 1444–1448 (2012). ArticleCASPubMed Google Scholar
Wachtershauser, G. From pre-cells to Eukarya — a tale of two lipids. Mol. Microbiol.47, 13–22 (2003). ArticleCASPubMed Google Scholar
Shimada, H. & Yamagishi, A. Stability of heterochiral hybrid membrane made of bacterial _sn_-G3P lipids and archaeal _sn_-G1P lipids. Biochemistry50, 4114–4120 (2011). ArticleCASPubMed Google Scholar
Nelson-Sathi, S. et al. Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. Proc. Natl Acad. Sci. USA109, 20537–20542 (2012). ArticlePubMedPubMed Central Google Scholar
Muller, M. et al. Biochemistry and evolution of anaerobic energy metabolism in eukaryotes. Microbiol. Mol. Biol. Rev.76, 444–495 (2012). ArticleCASPubMedPubMed Central Google Scholar
Moran, N. A. Microbial minimalism: genome reduction in bacterial pathogens. Cell108, 583–586 (2002). ArticleCASPubMed Google Scholar
Forterre, P. Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain. Proc. Natl Acad. Sci. USA103, 3669–3674 (2006). ArticleCASPubMedPubMed Central Google Scholar
Forterre, P. The origin of viruses and their possible roles in major evolutionary transitions. Virus Res.117, 5–16 (2006). ArticleCASPubMed Google Scholar