Evolution__3rd_Edition

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Figure 15.15
The same character is found in
both a descendant species and
one of its ancestors. It is more
likely (a) that the character has
remained constant and has
been passed on by inheritance
than (b) that it has changed and
reverted to its original state a
number of times between the
ancestor and descendant.
The probability of a tree can be
computed, given data and a model
of evolution
CHAPTER 15 / The Reconstruction of Phylogeny 447
(a) Likely inference (b) Unlikely inference
a
Descendant species
Ancestral species
Character a
Character
a
Descendant species
Ancestral species
conclusion, it is more likely that a character will be shared by common descent than by
independent, convergent evolution. For any set of species, a phylogeny requiring less
evolutionary change is more plausible than one requiring more.
15.9.5 A third class of phylogenetic techniques uses the principle of
maximum likelihood
The final technique we shall look at uses a statistical framework called maximum
likelihood. The detailed calculations, when fully spelled out, are quite laborious, even
for a simple case. (Box 15.2 works through the calculations for one nucleotide site in
a four-species tree.) The basic procedure is to calculate (using a model of sequence
evolution) the probability of observing the sequence data for a set of species, for all possible
phylogenies. The most likely phylogeny is the one that has the highest probability
of having produced the observed sequences.
Maximum likelihood is a computationally more demanding technique than parsimony.
The method not only has to work through all possible phylogenies (just as
parsimony has to), but also has to make detailed estimates and calculations for all the
phylogenies. Maximum likelihood was little used until recently because it could only be
implemented with small numbers of species. The advantage of maximum likelihood is
that it can readily exploit information about rates of evolution. In the simple model
used in Box 15.2, the chance of any evolutionary change was the same, p. But the same
procedure can be used with more complicated models that have several parameters
to describe evolution. Phylogenetic analysis with maximum likelihood can also use
other information: the rate of evolution may vary between species, or between genes,
or over time. Maximum likelihood is a very broad framework. It also has some other
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