Evolution__3rd_Edition

456 PART 4 / Evolution and Diversity
Archaea Eukarya Bacteria
Figure 15.20
Long branch attraction. (a) The
lineages leading to species 3
and 4 have evolved rapidly.
The marks through those two
lineages indicate a large number
of evolutionary changes, such
that all sites are saturated with
multiple hits. The sequences in
species 3 and 4 will be
approximately 25% similar by
chance (see Figure 15.13). The
lineages leading to species 1 and
2 have changed little. In cases
such as this, many methods of
phylogenetic inference are
liable in conclude (b) that
species 3 and 4 are more closely
related than in (c) the true tree.
Most of the similarity between
species 1 and 2 is ancestral
and ignored in phylogenetic
inference: if we exclude the
ancestral G states, species 1 and
2 have zero similarity. Species 3
and 4 show 25% similarity.
Application of parsimony (see
Figure 15.14), for instance,
will show that (b) is more
parsimonious than (c).
Figure 15.19
Horizontal gene transfer between lineages means that no unique
phylogenetic tree exists. Some genes in eukaryotes have a more
recent common ancestor with genes in Bacteria than in Archaea;
other genes in eukaryotes have a more recent common ancestor
with genes in Archaea than in Bacteria. Biologists disagree about
the extent of gene transfer between the main domains of life,
and about how clear-cut a tree exists for these three domains.
15.11.4 Different lineages may evolve at different rates
Molecular phylogenetics is most reliable for molecules that evolve at a fairly constant
rate, in the manner of a molecular clock. Phylogenetic inference becomes more difficult
if some lineages evolve fast, and others evolve slowly. The statistical methods then
become confused by two, related problems. One we met in the lizard–bird–crocodile
case (see Figure 15.6): lineages that retain many ancestral homologies may be put
together in the phylogeny, even though they are unrelated. This is mainly a problem
for distance methods that do not distinguish ancestral from derived similarities.
Parsimony and maximum likelihood should not be confused by ancestral similarity.
However, they can suffer from the second problem, called long branch attraction
(Figure 15.20). Two long branches will be 25% similar on average, and by chance could
be more than 25% similar. They may be more similar than shorter branches, and are
then put together in the phylogeny. The problem can be dealt with by discarding
species in which evolution has been exceptionally rapid, or by analyzing new species
that “break up” the long branches (Hillis 1996).
(a) Pattern of evolution (b) Inferred tree (c) True tree
CCCCCCCC TTTTTTCC
3 4 3 1
1 2
AGGGGGGG GGGGGGAG
Ancestral state
GGGGGGGG
4
2
3 2
1 4
..