Biology Reference
In-Depth Information
to use as many different genes as possible rather than just a few hundred bp of
a single protein-coding gene. Furthermore,
Quental and Marshall (2010)
argue
that it is important to include the fossil record (if possible) in phylogenetic anal-
yses to document change through time because molecular assumptions may be
unrealistic (uniform changes in time may not occur). Assumptions made for fos-
sils are that correct taxonomy and stratigraphy have been applied.
12.3.2 The Molecular Clock
Until the 1960s, the analysis of fossils was the only way to estimate the
time
when ancestors of extant organisms lived. Molecular studies in the 1960s pro-
vided a concept called the
molecular clock
that could be used to estimate the
evolutionary history and time of divergence of organisms. The molecular clock
was particularly useful for living species that have a poor fossil record, which
includes a very high proportion of extant species.
The molecular-clock hypothesis was proposed after
Zuckerkandl and Pauling
(1965)
examined amino-acid substitutions in hemoglobin and cytochrome c pro-
teins from different vertebrates. They found the rate of molecular evolution
was approximately constant over time in all vertebrate lineages examined and
concluded that amino-acid sequences could be used to measure the evolution-
ary distance (time) between organisms by counting the number of accumulated
changes (mutations).
The molecular clock is based on the assumption that basic processes such as
DNA replication, transcription, protein synthesis, and metabolism are remark-
ably similar in all living organisms and the proteins and RNAs that carry out key
“housekeeping functions” are highly conserved. Of course, over time, muta-
tions in housekeeping genes occurred and DNA and protein sequences changed,
although the changes tended to preserve the
function
of the gene rather than
modify or improve it. Thus, changes in these fundamental genes should have
minimal, or no, effect on function. For example, because the genetic code is
degenerate, the third base in a codon often can be altered without affecting
which amino acid is designated. Changes in the code also can occur without
changing protein function if amino-acid changes occur in region(s) that do not
affect function, or if one amino acid is replaced by a similar amino acid. The
molecular-clock hypothesis assumes that mutations in the housekeeping genes
that constitute the clock occur at a
constant
rate, thus providing a reliable
method for measuring time.
Unfortunately, subsequent analyses of different protein sequences suggest
that the rates of change
can
vary between proteins and lineages, indicating that
