Footnotes and extra appendixes
transferred away from the PhD manuscript for the lack of space
of the problems associated with the evolutionary Molecular clock/Mutation Clock
Originally the Kimura’s neutrality theory (1968) predicted, as mathematically
formulated from the hypothesis of Zuckerland & Pauling (1965), that
molecular evolution behaves like a stochastic clock. Now that we have even
too much of the data at hand it seems, however, that the number of amino
acid replacement in a given protein do not appear to change linearly with
time, after all.
This phenomenon is called erratic overdispersion, and when Rodriguez-Trelles
et al (2001) studied glycerol-3-phosphate dehydrogenase, suproxide dismutase,
and xanthine dehydrogenase from a total of 78 species of plants, fungi,
and mamals, they ended up tabulating divergence times, respectively, as
follows: 41, 46, and 53 Mryrs between Drosophila groups; 60, 60,
and 60 Mryrs between Drosophila subgenera; 142, 74, and 65 Mryrs
between drosophilid genera; 455, 110, and 90 Mryrs between dipteran families;
400, 105, and 38 Mryrs between mammalian orders; 3890, 374, and 364 Mryrs
between animal phyla; 6699, 276, and 130 Mryrs between fungi; and 7045,
451, and 398 Mryrs between kingdoms. (When aplying the rate of Drosophila
subgenera to other organisms.)
Regarding the clocks at the multicellular divergence dates, Michael
Lee (1999) summarizes:
"Even if one makes the bold assumption that molecular
clock models have little error, there seems little objective reason for
accepting as sacrosanct a few fossil dates used in calibrations and rejecting
as unreliable the much more numerous fossil dates that contradict the resultant
molecular estimates… Unfortunately, molecular clocks studies have yet to
provide a set of rigorous criteria for justifying which fossil dates are
to be used in calibrations and which are to be treated with scepticism."
Lee concludes his evaluation by stating:
"Many molecular studies argue persuasively for the gross
inadequacy of he fossil record, but it has been insufficintly acknowledged
that their inferences, too, are ultimately based on this same record and
should therefore be treated with similar caution."
The assumption, really, is bold after tabulation of metazoan (common animal)
divergence for 22 important nuclear proteins with a variation between 1,600-274
(weighted average 851± 81) Mryrs (based directly on mammal-bird
divergence of 310 Mryrs on fossil record), or 1,375-594 (weighted average
830±55) Mryrs (based on metazoan-fungus divergence of 1,100 Mryrs,
but ultimately only on the former one). Lee calibrates these already "internally"
or "externally" calibrated published dates by four corrections: 0.93 (based
on mammal-bird divergence of 288 Mryrs), 0.85 or 0.65 (based on primate-rodent
divergence of 85 or 65 Mryrs), and 0.548 (based on metazoan-fungus divergence
of 603 Mryrs) upon revised and "direct" evidence from the fossil record.
Lee ends up at the figure of 791-528 Mryr for the metazoan divergence,
because he rejects the metazoan-fungal fossil dates leading to 455 Mryr,
which comes late to the dates with the scenario of Neoproterozoic-Cambrian
radiation, popularly called as the cambrian explosion. Lee also acknowledges
other data series starting at divergence of over 1,000 Mryrs, that he is
able to recalibrate nearly by half.
Lee MSY (1999) Molecular Clock Calibrations and Metazoan Divergence Dates. J Mol Evol 49, 385-91
Kimura M (1968) Evolutionary rate at the molecular level.
Kimura M (1983) The neutral theory of molecular evolution.
Cambridge Univ. Press, UK.
Rodriguez-Trelles F, Tarrio R & Ayala FJ (2001) Erratic
overdispersion of three molecular clocks: GPDH, SOD, and XDH. Proc Natl
Acad Sci 98, 11405-10
Zuckerland E & Pauling L (1965) in Evolving Genes
and Proteins, eds. Bryson V & Vogel HJ. Academic, New York pp.