Biology Reference
In-Depth Information
the molecular clock may tick at different rates in different lineages (
Rodriguez-
Trelles et al. 2001, Lanfear et al. 2010
). For example, cytochrome c has an
acceptable clockwise behavior for the original organisms studied. However, cop-
per-zinc superoxide dismutase (SOD) behaves like an erratic clock (
Ayala 1986
).
The average rate of amino-acid substitutions in SOD per 100 residues per 100
million years is a minimum of 5.5 when fungi and animals are compared. The
rate of substitutions in SOD is 9.1 amino acids/100 residues/100 million years
when comparisons are made between insects and mammals, and 27.8 when
mammals are compared with each other (
Ayala 1986, Fitch and Ayala 1994
).
Thus, the molecular clock should be calibrated with data that are independently
derived, and preferably with fossil evidence, if the absolute time of divergence
is desired.
Wilson et al. (1987)
pointed out that analyses by both morphological
and molecular techniques of species with abundant fossil records have reduced
the uncertainty in estimating the time of divergence by several orders of
magnitude. However, the molecular clock is thought by some to be more use-
ful in calculating
relative
times rather than absolute times of divergence, espe-
cially if fossil data are unavailable to validate the dates.
Arbogast et al. (2002)
reviewed the methods of estimating divergence times from molecular data and
emphasized the importance of model testing and appropriate statistical tests.
Warnock et al. (2012)
explored the effect of using different methods for esti-
mating divergence time using Bayesian methods and showed that calibration is
important.
The molecular-clock approach was used by
Moran et al. (1993)
to determine
when endosymbiont bacteria (
Buchnera
) colonized their aphid hosts.
Moran
et al. (1993)
compared 16S ribosomal DNA sequences of aphids and
Buchnera
and found the clock was approximately constant. These symbiotic bacteria live
within specialized aphid cells, are maternally inherited, and are essential for
growth and reproduction of their hosts, indicating a long and intimate relation-
ship. The 16S ribosomal DNA (rDNA) sequences indicate that the symbionts in
diverse aphids are distinct and concordant with the phylogeny of their hosts,
suggesting that the current distribution of
Buchnera
is due to vertical transfer
from an ancestral aphid. The data also indicate that cospeciation occurred, with
the aphids and their endosymbionts radiating synchronously.
Moran et al. (1993)
estimated the aphid and bacterial radiations occurred at a relatively constant
rate, with 0.01-0.02 substitutions per site per 50 million years, suggesting that
the association between aphids and endosymbionts began
≈
160-280 million
years ago (mya).
Nardi et al. (2010)
evaluated the timing of the domestication of olive fly and a
host shift to cultivated olives by using complete mitochondrial genomes.
