Estimating the timing of early eukaryotic diversification with multigene molecular clocks

Parfrey, Laura Wegener; Lahr, Daniel J. G.; Knoll, Andrew H.; Katz, Laura A.

doi:10.1073/pnas.1110633108

Cited by 811 publications

(737 citation statements)

References 72 publications

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“…Accession numbers and additional details are provided in Supplementary Tables 1 and 2. REVIEW RESEARCH years ago 20 . These data are consistent with molecular dating analyses that place the last common ancestor of eukaryotes at between 1.9 and 1.7 billion years ago 76 . An earlier origin for eukaryotes had been suggested on the basis of the presence of sterane biomarkers in 2.7-billion-year-old rocks 77 , but these were subsequently shown to be contaminants from younger rocks 78,79 .…”

Section: The Origin Of Eukaryotes In Light Of Other Datasupporting

confidence: 89%

An archaeal origin of eukaryotes supports only two primary domains of life

Williams

Foster

Cox

et al. 2013

Nature

446

367

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The discovery of the Archaea and the proposal of the three-domains 'universal' tree, based on ribosomal RNA and core genes mainly involved in protein translation, catalysed new ideas for cellular evolution and eukaryotic origins. However, accumulating evidence suggests that the three-domains tree may be incorrect: evolutionary trees made using newer methods place eukaryotic core genes within the Archaea, supporting hypotheses in which an archaeon participated in eukaryotic origins by founding the host lineage for the mitochondrial endosymbiont. These results provide support for only two primary domains of life-Archaea and Bacteria-because eukaryotes arose through partnership between them.S ince their discovery by Carl Woese and his co-workers in 1977, the Archaea have figured prominently in hypotheses for eukaryotic origins 1,2 . Although similar to Bacteria in terms of cell structure, molecular phylogenies for ribosomal RNA and a small core of genes, that mainly have essential roles in protein translation 3 , suggested that the Archaea were more closely related to the eukaryotic nuclear lineage; that is, to the host cell that acquired the mitochondrion 4 . The idea that Archaea and eukaryotes are more closely related to each other than either is to Bacteria depends on analyses suggesting that the root of the tree should be placed on the bacterial stem, or within the Bacteria 5-12 , implying that the prokaryotes-cells that lack a nucleus-are a paraphyletic group 13 . The main question now debated is whether core components of the eukaryotic nuclear lineage descend from a common ancestor shared with Archaea, as in the three-domains tree 14 (Fig. 1), which is also often called the 'universal tree' or 'tree of life' 15-17 , or from within the Archaea, as proposed by archaeal-host hypotheses for eukaryotic origins 2 . The archaeal-host scenario with the greatest phylogenetic support is the eocyte hypothesis 18 , which proposes a sister-group relationship between eukaryotes and the eocytes (or Crenarchaeota 14 ), one of the major archaeal divisions (Fig. 1). However, the three-domains-eocyte debate remains controversial because different phylogenetic methods have delivered different results, often from the same data 19 . This disagreement is due, at least in part, to the difficulties associated with resolving ancient divergences in phylogenetic trees. Challenges of reconstructing ancient relationshipsA major issue in reconstructing ancient relationships is the strength and quality of historical signal remaining after the millions of years since the divergence of Archaea and eukaryotes. The earliest fossils identified as eukaryotic appeared by about 1.8 billion years ago 20 ; over this enormous span of time, the accumulation of multiple substitutions in DNA and protein sequences might have erased any signal that would allow the relationship between archaeal and eukaryotic core genes to be established 21 . However, more recent simulations and empirical studies suggest that there are reasons to be cautiously optimistic ...

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Section: The Origin Of Eukaryotes In Light Of Other Datasupporting

confidence: 89%

An archaeal origin of eukaryotes supports only two primary domains of life

Williams

Foster

Cox

et al. 2013

Nature

446

367

View full text Add to dashboard Cite

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“…This suite of genes includes sterol 24-C-methyltransferase (SMT), which allows for the methylation of sterol side chains and the biosynthesis of canonical C 26 -C 30 eukaryotic sterols. Our analysis dates the origin of LECA between ~1.30-2.17 Gyr ago, while multi-gene molecular clocks have estimated LECA between 0.95 and 1.87 Gyr ago (Berney and Pawlowski, 2006;Douzery et al, 2004;Parfrey et al, 2011). Subsequently, there is broad consensus that LECA evolved prior to the Neoproterozoic, and that it was capable of producing 24-methyl steroids.…”

Section: Genetic Evidence For Early Sterol Biosynthesis and The Recomentioning

confidence: 78%

Paleoproterozoic sterol biosynthesis and the rise of oxygen

Gold

Caron

Fournier

et al. 2017

Nature

108

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The Record of Precambrian Steroidal HydrocarbonsThe record of sterane and triterpane hydrocarbon biomarkers in Archean and Proterozoic sedimentary rocks has come under extremely thorough scrutiny in recent times. Concerns about contamination, and doubts about reports of steroidal hydrocarbons in the 2.7 billion year-old Fortescue Group sediments of the Pilbara Craton (Brocks et al., 1999), were initially raised in 2003(Brocks et al., 2003. These potential problems became increasingly difficult to dismiss when new and improved types of geochemical analyses were devised and applied. For example, Brocks and colleagues showed that a selection of rock and sediment samples from a range of localities were ubiquitously contaminated with petroleum-and plastic-derived organic compounds . Analyses of thin slices of sediment core showed that spatial distributions of hydrocarbons could be used to distinguish indigenous hydrocarbons from surface contaminants in Archean shales (Brocks, 2011). In another example, the carbon isotopic data values of in situ and insoluble kerogen and pyrobitumen in rock formations that had previously yielded biomarkers were discrepant from those of the extractable hydrocarbons, meaning that the latter could not be indigenous (Rasmussen et al., 2008).

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“…Ancestral sequence reconstruction may help overcome uncertainties of historical information obtained primarily from fossil inferences (Benner, Sassi, & Gaucher, 2007; Felsenstein, 1981; Kacar, 2016; Kumar & Hedges, 1998; Parfrey, Lahr, Knoll, & Katz, 2011; Pauling & Zuckerkandl, 1963). This approach utilizes phylogenetic models of sequence evolution to computationally reconstruct ancestral gene and protein sequences.…”

Section: Introductionmentioning

confidence: 99%

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree

et al. 2017

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Ribulose 1,5‐bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO, or Rubisco) catalyzes a key reaction by which inorganic carbon is converted into organic carbon in the metabolism of many aerobic and anaerobic organisms. Across the broader Rubisco protein family, homologs exhibit diverse biochemical characteristics and metabolic functions, but the evolutionary origins of this diversity are unclear. Evidence of the timing of Rubisco family emergence and diversification of its different forms has been obscured by a meager paleontological record of early Earth biota, their subcellular physiology and metabolic components. Here, we use computational models to reconstruct a Rubisco family phylogenetic tree, ancestral amino acid sequences at branching points on the tree, and protein structures for several key ancestors. Analysis of historic substitutions with respect to their structural locations shows that there were distinct periods of amino acid substitution enrichment above background levels near and within its oxygen‐sensitive active site and subunit interfaces over the divergence between Form III (associated with anoxia) and Form I (associated with oxia) groups in its evolutionary history. One possible interpretation is that these periods of substitutional enrichment are coincident with oxidative stress exerted by the rise of oxygenic photosynthesis in the Precambrian era. Our interpretation implies that the periods of Rubisco substitutional enrichment inferred near the transition from anaerobic Form III to aerobic Form I ancestral sequences predate the acquisition of Rubisco by fully derived cyanobacterial (i.e., dual photosystem‐bearing, oxygen‐evolving) clades. The partitioning of extant lineages at high clade levels within our Rubisco phylogeny indicates that horizontal transfer of Rubisco is a relatively infrequent event. Therefore, it is possible that the mutational enrichment periods between the Form III and Form I common ancestral sequences correspond to the adaptation of key oxygen‐sensitive components of Rubisco prior to, or coincident with, the Great Oxidation Event.

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Estimating the timing of early eukaryotic diversification with multigene molecular clocks

Cited by 811 publications

References 72 publications

An archaeal origin of eukaryotes supports only two primary domains of life

An archaeal origin of eukaryotes supports only two primary domains of life

Paleoproterozoic sterol biosynthesis and the rise of oxygen

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree

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