Evolution__3rd_Edition

160 PART 2 / Evolutionary Genetics
Protein
sequence
…GLY GLY LEU… …GLY ALA LEU…
Rates of molecular evolution can be
measured ...
Species 1 Species 2
Common ancestor
Time
(years)
Figure 7.2
Imagine that some region of a protein has the illustrated
sequences in two species. The evolutionary change has happened
somewhere within the lineage connecting the two species via their
common ancestor. The simplest interpretation is that either an
alanine has been substituted for a glycine in the lineage leading to
species 2, or a glycine for an alanine in the lineage to species 1.
Either way, the amount of evolution is one change, and it has
taken place in twice the time from the species back to their
common ancestor; or, one change in 2t years. In practice,
particularly with DNA data, the method of maximum likelihood
is used to correct for multiple hits and the possibility that the
ancestor had none of the states present in the modern species
(Section 15.9.3, p. 442).
the approximate age of their common ancestor can be estimated from the fossil record.
The rate of protein evolution can then be calculated as the number of amino acid differences
between the protein of the two species divided by two times the time to their
common ancestor (Figure 7.2). For example, if the species are humans and mice, their
common ancestor probably lived about 80 million years ago. If we look at the sequence
of a 100 amino acid protein in the two species and it differs at 16 sites, then the rate of
evolution is estimated at 16/(100 × 160 × 10 6 ) ≈ 1 × 10 −9 per amino acid site per year.
Much the same calculation can be made per nucleotide site for the rate of DNA
evolution. But with DNA, a correction has to be made for “multiple hits.” For instance,
suppose that species 1 has nucleotide A at a certain site and species 2 has G at the equivalent
site. Using the reasoning of Figure 7.2, we could deduce that one change has taken
place in 2t years. However, more than one change may have occurred. The common
ancestor might have had nucleotide A (the same reasoning applies if it had G). In the
lineage leading to species 2, A changed to G. That requires at least one change, but there
may have been more. Up that lineage, A may first have evolved to T and then T to G. In
the lineage leading to species 1, A may have remained unchanged all the time.
Alternatively, A may have evolved into C and then C evolved to A again. We see only
one difference between the A and G in the modern species 1 and 2, but more than one
change may underlie it.
The problem a that more than one substitution may underlie one observed difference
between two species a is the problem of multiple hits. The problem is particularly
acute for DNA, because DNA has only four states: the four nucleotides A, C, G, and T.
Multiple evolutionary changes can easily end up leading to the same state in two
species. For amino acids in proteins, there are 20 states (the 20 main amino acids) and
multiple changes are less likely to result in the same state in two species. In Section
15.9.3 (p. 442) we look at how to correct for multiple hits in DNA data. Analogous
corrections can be made for protein data. In this chapter, we simply assume that the
necessary corrections have been made in estimates of evolutionary rates.
Table 7.1 gives some examples of evolutionary rate estimates, based on comparisons
between humans and mice. As can be seen, different proteins evolve at different rates.
Ribonuclease evolves slowly, albumin rapidly. Section 7.6 looks at why different
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