Evolution__3rd_Edition

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Molecular phylogenetics uses
statistical techniques
We establish the relation between
rooted and unrooted trees
CHAPTER 15 / The Reconstruction of Phylogeny 439
phylogeny is supported by 10 morphological characters and another by five other morphological
characters, the comparison is less straightforward. It is not easy to say what
amount of evolution in a knee bone is equivalent to any given change in a skull bone.
Although the phylogeny supported by five characters has less characters in support, the
evolution in those five characters may be somehow weightier, or more reliable. In
most phylogenetic inference, we have to weigh one set of characters against another a
because different characters sets will often support different phylogenies. However,
no general method exists for comparing evolution between different morphological
characters. Molecular characters are readily comparable and therefore easier to use.
These four properties of DNA and protein sequence data a the impossibility of any
deeper analysis of the character, the large amounts of evidence, the recognizability of
independent characters, and the comparability of evidence a have encouraged the
development of statistical techniques to infer phylogenies. The same techniques are in
principle just as applicable to morphological evidence, though here it is always tempting
to try to pre-empt statistical analysis and resolve the apparent conflicts by everdeepening
character analysis. Morphological data are also less readily divisible into
neat character states for statistical analysis.
15.9 Several statistical techniques exist to infer phylogenies
from molecular sequences
A full review of the statistical techniques that can be used to infer phylogenies from
molecular evidence would have to cover dozens of techniques. Instead we shall concentrate
on the basic principles of the three main classes of techniques that are currently in
use. But before we come to these three, we need to know about “unrooted” as opposed
to “rooted” trees.
15.9.1 An unrooted tree is a phylogeny in which the common ancestor
is unspecified
The phylogenies that we have been concerned with so far (such as Figure 15.1) are all
rooted trees. If you look at the phylogeny of species A–D in Figure 15.1 you can see the
common ancestor (or “root”) at the bottom of the tree. A rooted tree has a time axis on
it, and successively more distant ancestors are successively lower on the page. A rooted
tree is the goal of phylogenetic research. It is the way biologists think about the evolutionary
relationships between species.
However, most molecular phylogenetic techniques first work out what is called an
unrooted tree (Figure 15.10). An unrooted tree is like a rooted tree but with the time axis
taken off; it shows the branching relationships between a set of species, but not the location
of their common ancestor. Figure 15.10 illustrates the relation between a rooted
and unrooted tree for four species. An unrooted tree is a less informative statement
about phylogenetic relations. For four species, one unrooted tree is compatible with
five rooted trees. We need extra information (the location of the root) to say which