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Evolution__3rd_Edition

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..<br />

Percentage difference in DNA of<br />

two species<br />

100<br />

0<br />

c.75%<br />

More than one substitution may<br />

underlie one base difference<br />

between two species<br />

I II III<br />

Multiple hits can be corrected for<br />

Time since common ancestor<br />

CHAPTER 15 / The Reconstruction of Phylogeny 443<br />

Figure 15.13<br />

As two species evolve apart over time, their DNA becomes<br />

increasingly different. Initially, each evolutionary change<br />

increases the difference between the two species and the line goes<br />

up. After a while, a second change may occur at a site where a<br />

change has already taken place; the second change then does not<br />

increase the difference between the two species. The line starts to<br />

level off. Eventually the two species are “saturated” with change<br />

and evolution has no average effect on the difference between<br />

them. The line is now flat. The line may flatten off at a 75%<br />

difference because there are four bases, but the exact figure may<br />

not be 75% for various reasons. See Figure 15.16 for examples.<br />

The regions I, II, and III correspond to regions where the<br />

molecular inference of phylogeny is (I) relatively easy, (II) possible<br />

but requires correction for multiple hits, and (III) impossible.<br />

distance between the species increases over time. The molecular distance increases<br />

because each successive change is likely to be at a different site in the 100-nucleotide<br />

stretch. After a while, a second change may occur at a site where a change has already<br />

occurred. Maybe the species with C evolves to have G. This evolutionary change will<br />

not increase the molecular distance between the species. When the first change happened,<br />

and one species had T and the other species had C, that produced a 1% difference.<br />

If the T or C now changes, the difference is still 1%. Thus, beyond a certain level,<br />

the molecular distance between the two species flattens off even though they continue<br />

to evolve apart. The later changes do not add the distance a there are multiple hits at<br />

the same site.<br />

The molecular distance between species is likely to level off at something like 75%<br />

(Figure 15.13) because DNA has four bases. Suppose the nucleotide is C at a site in<br />

one species. We then look at the equivalent site in a very different species a a species<br />

that is evolutionarily so distant that the site has changed many times and is effectively<br />

randomized. If we look at two random sequences of DNA, the chance of identity<br />

between the sequences at one site is approximately 25%. If the nucleotide at the site is<br />

C in one sequence, it could be C, G, T, or A in the other, chosen at random. Thus distance<br />

levels off at about 75% (and identity at 25%) for very different species. (These<br />

figures assume the base frequencies are equal. If C or G are more frequent than A or T in<br />

the species, molecular distance will level off at a figure below 75%.)<br />

Molecular distances can be corrected for multiple hits. We use a model of sequence<br />

evolution (Box 15.1). The simplest model assumes that the chance that any nucleotide<br />

will change (p) is the same. We can estimate the value of p from the sequence data for<br />

the species. We then use an appropriate statistical model (such as the Poisson distribution)<br />

to calculate how many changes underlie the observed sequence data. The calculation<br />

might, for instance, show that in a 100-nucleotide stretch of DNA in two species,<br />

30 sites have not changed, 30 have changed once, 20 have changed twice, 10 have<br />

changed three times, six have changed four times, and four have changed five times.<br />

We then add up the total number of changes: (30 × 1) + (20 × 2) + (10 × 3) + (6 × 4) +<br />

(4 × 5) = 144. This is the corrected number of evolutionary events. Compare it with<br />

the 70 sites that differ between the two sequences: we have corrected a raw number of

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