Evolution__3rd_Edition

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Variable evolutionary rates upset
distance methods
Cladists prefer parsimony
15.9.6 Distance, parsimony, and maximum likelihood methods are all
used, but their popularity has changed over time
Distance methods, parsimony, and maximum likelihood, in that order, require
increasing amounts of data, and increasing computer power, in order for them to be
used. Partly for this reason, the historic trend in phylogenetic research has been from
using distance methods, which were used in the pioneering years of the late 1960s
through to the early 1980s, to increasing use of parsimony, from the late 1970s to the
1990s, to an increasing use of maximum likelihood through the 1990s and into the
twenty-first century. Maximum likelihood is likely now the most widely used method
of molecular phylogenetics.
However, many biologists still use, and defend the use of, parsimony and distance
methods. Some biologists think that molecules evolve in a basically clock-like manner,
meaning that distance methods will usually give the right answer, and the sophistications
of parsimony and maximum likelihood are unnecessary. But if some lineages
evolve faster than others, distance methods misbehave a for much the same reason
that simple phenetic similarity gives the wrong answer when comparing birds,
crocodiles, and lizards (see Figure 15.6). Parsimony and maximum likelihood are less
likely to go wrong.
Parsimony has a particularly close relation with the methods of cladistics. The cladistic
methods we looked at in the first part of this chapter are logically almost identical to
the principle of parsimony. Parsimony counts evolutionary events, and each event generates
a new derived character state. The use of homologies rather than homoplasies,
and of derived rather than ancestral homologies, correspond to the principle of parsimony.
Methods such as outgroup comparison (Section 15.6.1) are simple applications
of parsimony. It is therefore no coincidence that the use of parsimony in phylogenetic
inference, and of cladistics in systematics, rose hand-in-hand from about 1980
onwards. (Chapter 16 considers cladistic systematics further.)
The sheer quantity of DNA data that are available now, along with increased computer
power, makes maximum likelihood (arguably) the most powerful method in
modern biology. However, the use of maximum likelihood is still seriously limited by
the power of computers (for reasons we return to in Section 15.11.2).
15.10 Molecular phylogenetics in action
CHAPTER 15 / The Reconstruction of Phylogeny 449
15.10.1 Different molecules evolve at different rates and molecular
evidence can be tuned to solve particular phylogenetic
problems
Different proteins, and stretches of DNA, evolve at different rates (Table 7.1, p. 161,
and Table 7.6, p. 177), and they can be used like clocks with hands that revolve at
different rates. If you use a rapidly evolving molecule for an ancient group, the
molecule will have “turned over” many times during the phylogeny, and once multiple