Tempo and Mode in Evolution Genetics and Paleontology 50 Years After Simpson (1995) / Chapter Skim
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Tempo, Mode, the Progenote, and the Universal Root
Tempo, Mode, the Progenote, and the Universal Root
Pages 3-24
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From page 3... ...
In this article, we focus on the period of early cellular evolution, between the appearance of the first self-replicating informational macromolecule and the deposition of the first microfossils, by all accounts already modern cells (Schopf, 1994~. We ask whether major shifts in predominant mode occurred during this period, and (since the answer is of course yes)
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From page 4... ...
If divergences that established the major lineages of contemporary living things occurred before completion of the period of progressive Darwinian evolution, then we would expect that the information processing systems of these lineages would differ from each other—the earlier the divergence, the more profound the difference. That is, components of the replication, transcription, and translation machineries that were still experiencing progressive Darwinian evolution at the time of divergence should be differently refined or altogether separately fashioned (nonhomologous)
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From page 5... ...
Tempo, Mode, the Progenote, and the Universal Root / 5 o i_ ~ 0 _ _ u, ~ cd 0 ~ ~ _ ~~ ~ u, 0 ~ o o _ _ u, `w cat ~ 0 ~ set i_ ._ ~ s 0 a, _ as O environment-driven diversification multicellularity complex cells transcriptional specificity gene regulation ~j ~ ~ gene organization translational specificity ~ transcription I DNA genomes ~ at_ RNA genomes / ~ ribosomal proteins / D / ribozymes ~/ RNA processing /^ ~ 'd exons primitive translation self-replicating RNAs _ oligonucleotides, peptides bases, sugars, amino acids prebiotic chemistry FIGURE 1 Fanciful interpretation of early evolution. The underlying assumption is that some contemporary processes and molecules had to appear before others and that the evolution of the information processing system involved interactions between separately evolving components.
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From page 6... ...
concluded, from the evident homology of DNA (or RNA) polymerases in the three domains, that the transition from RNA to DNA genomes had itself already been made by that last common ancestor, whatever its residual reliance on ribozymology (Benner et al., 1989~.
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From page 7... ...
constrained the biology and molecular biology of the 1960s, 1970s, and early 1980s, providing the framework within which all of the results of biochemists, geneticists, and evolutionists were interpreted (Figure 2~. In typical text books from this era, genes in Escherichia cold are compared and contrasted to their counterparts in yeast, mouse, and man, with differences interpreted either in terms of the relatively advanced and complex state of the latter or the admirably streamlined features of the former.
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From page 8... ...
Brown /~< BY OTIS ~\~ _~5 0' :~ Go' ~5 / FIGURE 2 Prevalent evolutionary view between 1970 and 1977. The eukaryotic nuclear lineage arose from within the already characterized prokaryotes (eubacteria, perhaps a mycoplasma)
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From page 9... ...
cytoplasmic small-subunit rRNA, was not demonstrably related to any specific, previously characterized prokaryotic lineage (Figure 3~. This was not expected: the endosymbiont hypothesis saw the endosymbiotic host arising within the bacteria, the descendant of some otherwise typical prokaryote that had lost its cell wall and acquired the ability to engulf other cells.
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From page 10... ...
lineages from which the eukaryotic nuclear lineage was thought to have evolved were entirely separate from that lineage. Distinct properties of rRNAs suggested that the r~bosome of the last common ancestor was a primitive r~bosome and that the last common ancestral cell was a primitive "progenote," still experiencing progressive Darwinian evolution.
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From page 11... ...
Eukaryotic nuclear genomes are after all very messy structures, with vast amounts of seemingly unneccesary "junk" DNA, difficult-torationalize complexities in mechanisms of transcription and mRNA modification and processing, and needless scattering of genes that often in prokaryotes would be neatly arranged into operons. It might be easiest to see nuclear genomes as in a primitive state of organization, which prokaryotes, by dint of vigorous selection for economy and efficiency ("streamlining")
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From page 12... ...
These include unique isopranyl ether lipids (and the absence of acyl ester lipids found in eubacteria and eukaryotes) ; characteristic genetic organization, sequence, and function of RNA polymerase subunits; structural and functional characteristics of ribosomes and modification patterns of tRNAs; varied but unique cell-envelope polymers; and distinctive antibiotic sensitivities and insensitivities (Zillig et al., 1993~.
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From page 13... ...
. With either data set, rooted trees showing archaebacteria and eukaryotic nuclear genomes to be sister groups were obtained; eubacteria represented the earliest divergence from the universal tree (Figure 6~.
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From page 14... ...
Although not rootable, these data too seemed to support a specific archaebacterial/eukaryotic affinity (Ramirez et al., 1993~. In 1990, Woese, Kandler and Wheelis incorporated the Iwabe rooting in a new and broader exegesis on the significance of the tripartite division of the living world (Woese et al., 1990~.
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From page 15... ...
rooting and renaming by Woese and collaborators of three primary kingdoms as domains (1990~. Microsporidia and Giardia are archezoans thought to have diverged from the rest of the eukaryotic nuclear lineage before the acquisition of mitochondria or plastics through endosymbiosis.
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From page 16... ...
Even the eubacteria have not been plumbed in depth newly discovered deeply branching lineages like Aquifex and the Thermotogales remain almost completely unknown in molecular or biochemical terms. Implications of the Rooting for an Understanding of Tempo and Mode in Early Cellular Evolution The Iwabe rooting and the renaming of the three domains as Bacteria, Archaea, and Eukarya (Figure 6)
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From page 17... ...
Proteins were assigned to a particular topology based on the two domains determined to be closest after calculation of interdomain distances. Interdomain distances were estimated from the means of multiple pairwise comparisons between different species of each domain by using the program PROTDIST of the P~P version 3.5 package James R
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From page 18... ...
The genome of this cell, the cenancestor, would have been as far as its organization is concerned—remarkably like that of a modern eubacterium, and we would have no hope of recreating the period of progressive Darwinian evolution by the comparative method. There is a consolation, however, if this is true.
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From page 19... ...
As well, other characteristic features of eukaryotic nuclear molecular biology, such as multiple RNA polymerases and complex mRNA processing and intron splicing, must have appeared since this divergence. We simply do not know how soon after the nuclear divergence these changes were wrought.
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From page 20... ...
Along with the ATPase and elongation factor gene duplication analyses, it has become common to stress the similarity in sequence of archaebacterial and eukaryotic RNA polymerase subunits or (certain) ribosomal proteins.
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From page 21... ...
If there have been lateral transfers of related or physically linked genes, then we might be able to see them. If transfer has so scrambled genomes that we can no longer talk sensibly about the early evolution of cellular lineages but only of lineages of genes, then that too should be apparent, as would the need to change the very language with which we address an evolutionary process so radically different in both tempo and mode.
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From page 22... ...
At the same time, protein data will increasingly supplement rRNA sequences rRNAs may mislead us when they show base compositional biases, and there is anyway no single molecule which defines a cellular lineage, once lateral transfer is admitted. Molecular evolution is maturing, which means that the arguments of molecular evolutionists are becoming more pluralistic and subtler.
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From page 23... ...
Cold Spring Harbor Symp. Quant.
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From page 24... ...
(1981) A microplasma-like archaebacterium possibly related to the nucleus and cytoplasm of eukaryotic cells.
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