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we can extrapolate the approximate dates of speciation for other species,
for which no fossil dates are available (Crisci et al. 2000). In order to test
the molecular clock hypotheses, three tests are available: the likelihood ra-
tio test, the dispersion index, and the relative rate test (Page and Holmes
1998).
As analyses from several taxa began to accumulate in the 1970s, it be-
came apparent that the molecular clock is not always a good model for the
process of molecular evolution (Rutschmann 2006). If the null hypothesis of
a constant rate is rejected or if we have evidence that rates vary across the
tree, we may have to use methods that correct for rate heterogeneity (Ram-
baut and Bromham 1998) or that estimate divergence times by incorporating
rate heterogeneity (Kishino et al. 2001; Sanderson 2002).
Some problems associated with molecular methods include the
stochastic nature of molecular substitution, the assumption of rate con-
stancy among lineages when such constancy is absent, and the link
between substitution rate and elapsed time on the branches of a cladogram
(Magallón 2004). Calibration made by reference to geological events runs
the risk of circular reasoning because the clock is used to test biogeographic
hypotheses that involve an event potentially caused by a geological process
(Crisci et al. 2000). Bromham and Woolfit (2004) noted that sometimes mo-
lecular date estimates are notoriously at odds with other lines of evidence
(e.g., the “Cambrian explosion” of Metazoan phyla and the ordinal-level radi-
ations of mammals and birds are almost twice as old as the available fossils
suggest). This discrepancy may have occurred because systematic biases
in the fossil record left particular taxa, regions, or periods unrecorded or be-
cause explosive radiations could speed the molecular clock, causing dates
for these radiations to be overestimated consistently. Magallón (2004) and
Benton and Donoghue (2007) clarified the relationship of the fossil record
and molecular dating methods, the former documenting first appearances of
morphological features and the latter dating splits of molecular lineages ( fig.
7.9 ) .
Heads (2005a) offered some criticisms of molecular calibrations:
• Calibration based on fossils: Taking the fossil record at face value and
equating the age of the oldest known fossil with the age of the taxon is
simplistic and misleading. Although it is recognized that the age of fos-
silization is less or much less than the age of the taxon, in the practice
some authors take the age of the fossil as absolute, not minimum.
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