Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 30, 2013, Pages 12355-12360

  Shih, Patrick M ^a   Matzke, Nicholas J ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; ELONGATION FACTOR; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE;

ARTICLE; CALIBRATION; ENDOSYMBIONT; ENDOSYMBIOSIS; FOSSIL; GENE DUPLICATION; MOLECULAR CLOCK; NONHUMAN; PHANEROZOIC; PHYLOGENY; PLASTID; PRIORITY JOURNAL; PROTEROZOIC;

ADENOSINE TRIPHOSPHATASES; CALIBRATION; PHYLOGENY; SYMBIOSIS;

EID: 84880685461     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1305813110     Document Type: Article

References (57)

1. Brocks JJ, Logan GA, Buick R, Summons RE (1999) Archean molecular fossils and the early rise of eukaryotes. Science 285(5430):1033-1036.
2. Hoffman PF, Kaufman AJ, Halverson GP, Schrag DP (1998) A neoproterozoic snowball earth. Science 281(5381):1342-1346.
3. Cavalier-Smith T (2006) Cell evolution and Earth history: Stasis and revolution. Philos Trans R Soc Lond B Biol Sci 361(1470):969-1006.
4. Cavalier-Smith T (2010) Deep phylogeny, ancestral groups and the four ages of life. Philos Trans R Soc Lond B Biol Sci 365(1537):111-132.
5. Schopf JW, Kudryavtsev AB (2012) Biogenicity of Earth's earliest fossils: A resolution of the controversy. Gondwana Res 22(3-4):761-771.
6. Brasier MD, et al. (2002) Questioning the evidence for Earth's oldest fossils. Nature 416(6876):76-81.
7. Parham JF, et al. (2012) Best practices for justifying fossil calibrations. Syst Biol 61(2): 346-359.
8. Budd GE (2003) The cambrian fossil record and the origin of the phyla. Integr Comp Biol 43(1):157-165.
9. Diver W, Peat C (1979) On the interpretation and classification of Precambrian organic-walled microfossils. Geology 7(8):401-404.
10. Summons RE, Jahnke LL, Hope JM, Logan GA (1999) 2-Methylhopanoids as biomarkers for cyanobacterial oxygenic photosynthesis. Nature 400(6744):554-557.
11. Rashby SE, Sessions AL, Summons RE, Newman DK (2007) Biosynthesis of 2-methylbacteriohopanepolyols by an anoxygenic phototroph. Proc Natl Acad Sci USA 104(38): 15099-15104.
12. Welander PV, Coleman ML, Sessions AL, Summons RE, Newman DK (2010) Identification of a methylase required for 2-methylhopanoid production and implications for the interpretation of sedimentary hopanes. Proc Natl Acad Sci USA 107(19):8537-8542.
13. Zuckerkandl E, Pauling L (1965) Molecules as documents of evolutionary history. J Theor Biol 8(2):357-366.
14. Martin W, Gierl A, Saedler H (1989) Molecular evidence for pre-Cretaceous angiosperm origins. Nature 339(6219):46-48.
15. Doolittle RF (1992) Reconstructing history with amino acid sequences1. Protein Sci 1(2):191-200.
16. Roger AJ, Hug LA (2006) The origin and diversification of eukaryotes: Problems with molecular phylogenetics and molecular clock estimation. Philos Trans R Soc Lond B Biol Sci 361(1470):1039-1054.
17. Mulkidjanian AY, Makarova KS, Galperin MY, Koonin EV (2007) Inventing the dynamo machine: The evolution of the F-type and V-type ATPases. Nat Rev Microbiol 5(11): 892-899.
18. 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.
19. Gogarten JP, et al. (1989) Evolution of the vacuolar H+-ATPase: Implications for the origin of eukaryotes. Proc Natl Acad Sci USA 86(17):6661-6665.
20. Philippe H, Forterre P (1999) The rooting of the universal tree of life is not reliable. J Mol Evol 49(4):509-523.
21. Doolittle WF, Bapteste E (2007) Pattern pluralism and the Tree of Life hypothesis. Proc Natl Acad Sci USA 104(7):2043-2049.
22. Hilario E, Gogarten JP (1993) Horizontal transfer of ATPase genes-the tree of life becomes a net of life. Biosystems 31(2-3):111-119.
23. Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7(1):214.
24. Drummond AJ, Suchard MA, Xie D, Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29(8):1969-1973.
25. Falcón LI, Magallón S, Castillo A (2010) Dating the cyanobacterial ancestor of the chloroplast. ISME J 4(6):777-783.
26. Schirrmeister BE, Antonelli A, Bagheri HC (2011) The origin of multicellularity in cyanobacteria. BMC Evol Biol 11(1):45.
27. Tomitani A, Knoll AH, Cavanaugh CM, Ohno T (2006) The evolutionary diversification of cyanobacteria: Molecular-phylogenetic and paleontological perspectives. Proc Natl Acad Sci USA 103(14):5442-5447.
28. Schirrmeister BE, de Vos JM, Antonelli A, Bagheri HC (2013) Evolution of multicellularity coincided with increased diversification of cyanobacteria and the Great Oxidation Event. Proc Natl Acad Sci USA 110(5):1791-1796.
29. Sato N (2006) Origin and Evolution of Plastids: Genomic View on the Unification and Diversity of Plastids. The Structure and Function of Plastids, Advances in Photosynthesis and Respiration, eds Wise R, Hoober JK (Springer, The Netherlands), Vol 23, pp 75-102.
30. Douzery EJP, Snell EA, Bapteste E, Delsuc F, Philippe H (2004) The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils? Proc Natl Acad Sci USA 101(43):15386-15391.
31. Parfrey LW, Lahr DJG, Knoll AH, Katz LA (2011) Estimating the timing of early eukaryotic diversification with multigene molecular clocks. Proc Natl Acad Sci USA 108(33):13624-13629.
32. Yoon HS, Hackett JD, Ciniglia C, Pinto G, Bhattacharya D (2004) A molecular timeline for the origin of photosynthetic eukaryotes. Mol Biol Evol 21(5):809-818.
33. Johnston DT, Wolfe-Simon F, Pearson A, Knoll AH (2009) Anoxygenic photosynthesis modulated Proterozoic oxygen and sustained Earth's middle age. Proc Natl Acad Sci USA 106(40):16925-16929.
34. Canfield DE, Teske A (1996) Late Proterozoic rise in atmospheric oxygen concentration inferred from phylogenetic and sulphur-isotope studies. Nature 382(6587):127-132.
35. Criscuolo A, Gribaldo S (2011) Large-scale phylogenomic analyses indicate a deep origin of primary plastids within cyanobacteria. Mol Biol Evol 28(11):3019-3032.
36. Turner S, Pryer KM, Miao VPW, Palmer JD (1999) Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. J Eukaryot Microbiol 46(4):327-338.
37. Shih PM, et al. (2013) Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc Natl Acad Sci USA 110(3):1053-1058.
38. Schopf JW (1993) Microfossils of the Early Archean Apex chert: New evidence of the antiquity of life. Science 260(5108):640-646.
39. Schopf JW (2012) The Fossil Record of Cyanobacteria. Ecology of Cyanobacteria II: Their Diversity in Space and Time, ed Whitton BA (Springer, The Netherlands), pp 15-36.
40. Hofmann HJ (1976) Precambrian microflora, Belcher Islands, Canada; significance and systematics. J Paleontol 50(6):1040-1073.
41. Zwickl DJ, Hillis DM (2002) Increased taxon sampling greatly reduces phylogenetic error. Syst Biol 51(4):588-598.
42. Wertheim JO, Sanderson MJ (2011) Estimating diversification rates: How useful are divergence times? Evolution 65(2):309-320.
43. Brown JR, Doolittle WF (1995) Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc Natl Acad Sci USA 92(7):2441-2445.
44. Keeling PJ, Fast NM, McFadden GI (1998) Evolutionary relationship between translation initiation factor eIF-2? and selenocysteine-specific elongation factor SELB: Change of function in translation factors. J Mol Evol 47(6):649-655.
45. Mathews S, Clements MD, Beilstein MA (2010) A duplicate gene rooting of seed plants and the phylogenetic position of flowering plants. Philos Trans R Soc Lond B Biol Sci 365(1539):383-395.
46. Katoh K, Kuma K-i, Toh H, Miyata T (2005) MAFFT version 5: Improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33(2):511-518.
47. Abascal F, Zardoya R, Posada D (2005) ProtTest: Selection of best-fit models of protein evolution. Bioinformatics 21(9):2104-2105.
48. R Development Core Team (2012) R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna, Austria).
49. Rambaut A, Drummond AJ (2007) Tracer version 1.5. Available at http://beast.bio.ed. ac.uk/Tracer.
50. Smith SA, Beaulieu JM, Donoghue MJ (2010) An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants. Proc Natl Acad Sci USA 107(13):5897-5902.
51. Berbee ML, Taylor JW (2010) Dating the molecular clock in fungi-how close are we? Fungal Biol Rev 24(1-2):1-16.
52. Sanderson MJ, Thorne JL, Wikström N, Bremer K (2004) Molecular evidence on plant divergence times. Am J Bot 91(10):1656-1665.
53. Wellman CH, Gray J (2000) The microfossil record of early land plants. Philos Trans R Soc Lond B Biol Sci 355(1398):717-731, discussion 731-732.
54. Doyle JA (1998) Molecules, morphology, fossils, and the relationship of angiosperms and Gnetales. Mol Phylogenet Evol 9(3):448-462.
55. Kopp RE, Kirschvink JL, Hilburn IA, Nash CZ (2005) The Paleoproterozoic snowball Earth: A climate disaster triggered by the evolution of oxygenic photosynthesis. Proc Natl Acad Sci USA 102(32):11131-11136.
56. Cohen BA, Swindle TD, Kring DA (2000) Support for the lunar cataclysm hypothesis from lunar meteorite impact melt ages. Science 290(5497):1754-1756.
57. Rambaut A, Drummond A (2007) Tracer v1.4. Available at http://beast.bio.ed.ac.uk/Tracer.