Evolution__3rd_Edition

..
When two species are very
different, phylogenetic inference is
impossible
Phylogenies can be inferred on the
assumption that change is rare
CHAPTER 15 / The Reconstruction of Phylogeny 445
differences of about 70 to an inferred number of events of 144. The increase is due to
the unobservability of multiple hits. (The numbers here are for illustration only. A real
example would be more complex, and the numbers could look very different from
those here.)
Figure 15.13 divides into three regions. For small amounts of change, the observed
molecular distances accurately reflect the amount of evolution and no correction for
multiple hits is needed. In the second region, we should correct for multiple hits. The
corrected molecular distances are the figures to use in phylogenetic inference. Finally,
in the third region, evolution has effectively randomized the sequences and, once the
line has gone flat, we cannot recover the real amount of evolutionary change making
correction for multiple hits impossible. Phylogenetic inference is impossible for
sequences that have evolved this far apart. (The process by which changes occur at an
increasing fraction of the sites in the sequences of two species as they evolve apart over
time is referred to as saturation. When practically all the sites have changed, we are in
region III of Figure 15.13 and the two sequences are referred to as “saturated,” and are
no longer any use for phylogenetic inference.)
The art of molecular phylogenetics consists in finding molecules that have evolved
the right distance apart. For all techniques of molecular phylogenetics, inference is
relatively easy in region I, becoming more difficult as we move through region II, and
is impossible in region III. Section 15.10 looks at some examples to illustrate the point.
15.9.4 A second class of phylogenetic techniques uses the principle
of parsimony
In phylogenetic inference, parsimony refers to the principle that the phylogeny
requiring the fewest evolutionary changes is the best estimate of the true phylogeny. In
a simplified case, we proceed as follows (Figure 15.14). First, write out all the possible
unrooted trees for the species. Then count the smallest number of evolutionary events
implied by each unrooted tree, given the observed data. The best estimate of the true
phylogeny is the one that produces the lowest count.
How can the parsimony principle be justified? Why is a phylogeny requiring less evolutionary
events a more plausible inference than one requiring more? The parsimony
principle is reasonable because evolutionary change is improbable. Suppose we know
that a modern species and one of its ancestors both have the same character state
(Figure 15.15). Parsimony suggests that all the intermediate stages in the continuous
lineage between ancestor and modern species possessed that same character state. As
we have seen, an indefinitely large number of changes a indeed an infinite number a
could logically have occurred between ancestor and descendant. However, a change
followed by a reversal of that change is unlikely. Each change requires a gene (or set of
genes) to arise by mutation and then to be substituted, either by drift if the change is
neutral or by selection; both these processes are improbable. It is much more likely that
the same character would have been continuously passed on, in much the same form,
from ancestor to descendant by simple inheritance. We know that this is plausible
because it happens every time a parent produces an offspring a the parental characters
are passed on.