Evolution__3rd_Edition

..
. . . as happened in one study of
human phylogeny
A set of species may have too
little ...
. . . or too much change for
phylogenetic inference
CHAPTER 15 / The Reconstruction of Phylogeny 455
Another interesting result is that the mitochondrial types do not fall into the groupings
that might have been expected. Look, for instance, at the Yorubans. The caption
reveals which numbers in the picture are Yoruban mitochondrial types, and they are
scattered through the phylogeny, even though all Yorubans live in Nigeria; likewise,
Papua New Guineans do not form a discrete group. This might be because our naive
expectations are incorrect a but it is more likely to be because the tree is unreliable. The
tree is a “local optimum.” It appears to be the most parsimonious tree, because it has
only been compared with trees that are similar to itself and not with very different trees.
When the program was rerun, starting in different regions of the tree space, many more
trees were found that were more parsimonious than the one in Figure 15.18. Some had
African deep roots, and others did not, and the different trees showed all sorts of groupings
of human populations (Templeton 1993).
In summary, when the number of species (or other taxa) at the tips of the phylogeny
is large, the number of possible phylogenies may be too high for all of them to be
searched. The algorithms that are used to search among the trees are often reliable,
but not infallible. The main danger is that an algorithm will become stuck on a local
optimum a a tree that on local comparisons seems to be the best estimate of the true
tree, but is not in fact the best estimate among all the possible trees.
15.11.3 Species in a phylogeny may have diverged too little or too much
We saw above (Sections 15.9.3 and 15.10.1) how we need a molecule that has evolved
an appropriate amount for the phylogeny under analysis. Molecular phylogenetics can
run into difficulties if the molecules have not yet evolved far enough apart between the
species, or if they have evolved apart too much and all the sites are “saturated” with
change. In terms of Figure 15.13, the amount of change should not be so small that the
data are all near the origin, and it should not be so large that the data are in the “leveled
off ” part of the graph (region III).
Vigilant et al.’s (1991) data illustrate the problem of too little evolutionary change.
Figure 15.18 has 135 tips, but only 119 changes that can distinguish between alternative
trees. The relations between human populations are better resolved by more rapidly
evolving parts of our DNA (Cavalli-Sforza 2000).
The opposite problem, of too much change, arises in rapidly evolving life forms
such as RNA viruses. It is probably impossible to recover the phylogeny of different
kinds of RNA viruses, such as HIV, influenza virus, and polio virus. We can find the
phylogeny of different strains of HIV, or of influenza virus, but the relations between
these major types are more uncertain (Holmes et al. 1996). Likewise, the phylogeny of
life forms that had common ancestors in the deep past are difficult to recover. No
molecules evolve slow enough to reveal the 3,000 million-year-old relations between
the three major domains of life a Archaea, Bacteria, and Eukarya. In this case there is a
further problem of horizontal gene transfer. Genes seem to move relatively readily
between bacteria, and even between archaeans and bacteria. The Archaea, Bacteria, and
Eukarya may not have a normal tree-like phylogeny. Some bacterial genes may be closer
to archaeans, and other bacterial genes may be closer to eukaryotes. The true phylogeny
would then be an anastomizing network rather than a branching tree (Figure 15.19).