Evolution__3rd_Edition

..
Figure 15.11
Distance methods. (a) The data
consist of a matrix of distances
between species. Here we have
four species (A, B, C, and D)
and the matrix shows pairwise
distances between all the
species. If distance is measured
as percent difference between
the DNA of two species, for
example, then the DNA of
species A and B would differ by
4%. The shaded region of the
matrix is either meaningless or
redundant. (b) Each species is
grouped with the other species
that it has the shortest distance
to. The numbers on the
branches are the implied
amounts of evolutionary
change, and add up to the
total distances in (a).
Molecular distances between
species can be measured
Species
CHAPTER 15 / The Reconstruction of Phylogeny 441
(a) Molecular distances (b) Phylogenetic inference
Species
A B C D
A 4 10 10
B
C
D
10 10
4
Species
A B C D
2 2 2 2
be the same at some sites and different at others. Maybe it is the same at 96 sites and different
at four. The two sequences are then 4% different. This figure is a simple example
of a molecular distance. The simplest kind of molecular phylogenetic inference uses the
matrix of molecular distances between species to infer the phylogeny. The species with
shorter distances between them are inferred to be more closely related (Figure 15.11).
This is a quick and dirty method of phylogenetic inference. The method assumes a
“molecular clock” (Section 7.3, p. 164). 3 If the molecular distances between species
increases constantly with time, the species pairs with shorter distances will indeed share
more recent common ancestors.
Some classic molecular phylogenetic inferences have been made by what are essentially
“distance” methods. For example, the molecular distance between two whole
DNA molecules, from two species, can be measured by DNA hybridization. This
method begins with DNA from a number of species. The DNA of any pair of species is
“denatured”: the double-stranded molecule is made into two single strands, usually by
heating the molecule up. The single strands of DNA from the two species are allowed to
join up and form double-stranded hybrid DNA. This hybrid molecule is then in turn
denatured by heating it up. The crucial measurement is how hot you have to make the
hybrid DNA before it will separate into its two single strands. The more similar the
DNA of the two species is, the stronger the bond between them, and the higher the temperature
required to separate them. The same procedure is followed for all pairs of
species, producing a matrix of distances for all the species. The matrix is turned into a
phylogeny, assuming that species with more similar DNA have more recent common
ancestors (Figure 15.12).
3 This is a key assumption. When looking at cladistic techniques earlier in the chapter, I pointed out that
simple phenetic similarity (or phenetic distance) between species is not thought to reveal phylogenetic relations.
Rates of phenetic evolution are so erratic that we need to break down phenetic similarity, to find the
component due to shared derived characters. Chapter 16 will make much the same point. However, if molecular
evolution is divergent and has a fairly constant rate, molecular distances can be used and cladistic analysis is
unnecessary. In more advanced work, the molecular clock may not be a crucial assumption. If molecules, or
lineages, with weird rates of evolution can be identified, they can be either corrected for or removed from the
analysis.
6