. "The Superoxide Dismutase Molecular Clock Revisited." Tempo and Mode in Evolution: Genetics and Paleontology 50 Years After Simpson. Washington, DC: The National Academies Press, 1995.
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TABLE 1 Paleontological dates and numbers of replacements
Amino acid differences
Sister groups
Mya
Replacements
Observed SOD
Simulated
D. nebulosa–D. melanogaster
55 ± 5
33
18 ± 2
18 ± 2
D. hydei–D. melanogaster
60 ± ?
36
19 ± 3
20 ± 4
Chymomyza–D. melanogaster
65 ± ?
39
23 ± 2
20 ± 4
Homo sapiens–Bos taurus
70 ± 10
42
27 ± 2
22 ± 4
Ceratitis–D. melanogaster
100 ± ?
60
31 ± 2
28 ± 3
Monocot–dicot
125 ± ?
74
28 ± 3
31 ± 5
Angiosperm–gymnosperm
220 ± ?
132
29 ± 7
42 ± 5
Frog–mammals
350 ± 10
210
49 ± 2
53 ± 6
Fish–tetrapods
400 ± 20
240
44 ± 4
56 ± 7
Yeast–Neurospora
?
46 ± 1
Insect–vertebrate
580 ± 20
348
59 ± 3
60 ± 6
Fungi–metazoans
1000 ± ?
600
67 ± 4
66 ± 7
Replacements refer to the number of replacements used in the simulation, which is equivalent to six replacements every 10 Myr. Observed is the average number of amino acid differences observed between members of the two sister groups shown. The sister group names (e.g., Drosophila nebulosa–Drosophila melanogaster) should be understood as indicating the groups to which these species belong and not just two individual species. Simulated is the observed number of amino acid differences obtained after the number of replacements shown had been incorporated. The plus/minus values are crude estimates of error for Mya but are SDs for observed and simulated differences. The simulated values are based on 40 simulated instances for each entry. See Methods for details of the simulation. D. stands for Drosophila.
number of differences. It was soon recognized that changes could occur at positions where changes had already occurred. Margoliash and Smith (1965) introduced a correction as follows
where r is the number of replacements, n is the number of variable positions in the sequence, and d is the number of divergent positions (differences). It is interesting that Margoliash and Smith contemplated the possibility of invariable positions so early, even though the concern that this might be an important consideration was not present in the field for nearly 20 years, except for Fitch (Fitch and Markowitz, 1970; Shoemaker and Fitch, 1989).
1
The equation they said they used was r = n In(n/d), which would be incorrect, but their results are those obtained by the correct equation shown.
