Tempo and Mode in Evolution Genetics and Paleontology 50 Years After Simpson (1995) / Chapter Skim
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The Superoxide Dismutase Molecular Clock Revisited
The Superoxide Dismutase Molecular Clock Revisited
Pages 235-250
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From page 235... ...
Key lecture, spoke on the enormous difference between the way one might expect a molecular clock to work and the way Cu,Zn superoxide dismutase (SOD) seems to have evolved since the last common ancestor of the metazoans and fungi (Ayala, 1986~.
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From page 236... ...
The divergence times can have any value but, to test the possibility that the SOD data can arise by the simulated clock, the replacements must be in the same proportion as the paleontological time estimates. The time estimates we used are given in Table 1.
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From page 237... ...
The most parsimonious tree we have found requires 1940 nucleotide substitutions; the tree in Figure 1 requires 1984. The sequences used were amino acid sequences, back translated into ambiguous codons so that the changes are in substitutions rather than replacements, although nearly all substitutions are replacement substitutions.
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From page 238... ...
African clawed toad 1~.5 29.4 ~ African clawed toad-B ~4 ~ African clawed toad-A sheep bovine 4.4 - L _ ~, horse s.2 rat-1 - rabbit swordfish I 9 mouse FIGURE 1 Superoxide dismutase tree. The amino acid sequences (back translated to ambiguous codons)
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From page 239... ...
mimica 11.6 ~ D busckii 7 ~ Zaprionus tuberculatus ' '> Ceratitis capitata SY.1 polyhedrosis virus 2,~ garden petunia 2 ~ ~ tomato-2 8.2 ~ spinach-2 25.9 y 7 garden pea-2 73.b , I scots pine-2 Is.3 ~ Arabidopsis thaliana l—T white cabbage 4.1 2 / ~ tomato-1 sweet potatoes 6.4 1l ~ spinach-1 s.u garden pea-1 //~.2 maize ~ .
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From page 240... ...
The average is obtained by weighing equally each bifurcating branch irrespective of the number of subsequent branchings. The y intercept yields the estimate of the fraction of invariable codons in a single species and is 0.826.
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From page 241... ...
. It is interesting that Margoliash and Smith contemplated the possibility of invariable positions so early, even though the concern J ~ J .
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From page 242... ...
The y intercept is the estimated fraction of codons that are not covarions. The vertical bars represent 1 SD of the estimate of the fraction of invariable codons.
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From page 243... ...
The fixation of this number reduces the number of parameters that are free to change in order to get a good fit to the SOD observations. In a complementary vein, the 11 clades for which paleontological dates were estimated constitute a large extent of variant data, all of which must be fit to demonstrate that the SOD observations could arise via a perfect clock.
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From page 244... ...
Ayala positions present only in the liverfluke, nematode, and/or bacteria but not in the other sequences. If all 44 unvaried sites were permanently invariable sites within the plant-animal-fungal sequences, then 162 44 = 118 were potentially variable.
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From page 245... ...
, it may then be necessary to take into account that the variable positions are not the same in different lineages. Any estimate of divergence time, where the covarion process has not been taken into account, is in danger of significant error.
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From page 246... ...
This is biologically reasonable, although an alternative possibility is that the paleontological dates are either systematically underestimated for the early dates or overestimated for the intermediate dates. This would make it easier to obtain a better fit for both regions, simply by assuming a somewhat larger or smaller replacement rate respectively.
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From page 247... ...
The flip side of the observation just made is that inferences of divergence time between lineages derived from a particular clock cannot be assumed to be correct unless the relevant components of the clock have been ascertained. The apparent rate of SOD divergence observed among mammals or flies would yield grossly erroneous time estimates when simply extrapolated to the differences observed between the vertebrate classes (fish versus tetrapod or amphibian versus mammal)
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From page 248... ...
the inference that a given gene is a bad clock may sometimes arise through a failure to take all the relevant biology into account and (ii) one should examine the possibility that different subsets of amino acids are evolving at different rates, because otherwise the assumption of a clock may yield erroneous estimates of divergence times on the basis of the observed number of amino acid differences.
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From page 249... ...
(1989) Evolution of CuZn Superoxide dismutase and the Greek key beta-barrel structural motif.
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