Evolution__3rd_Edition

..
The root of a tree ...
. . . can be inferred by paralog
rooting
The method has been used to root
the angiosperms
CHAPTER 15 / The Reconstruction of Phylogeny 459
15.12 Paralogous genes can be used to root unrooted trees
The position of the root in an unrooted tree can be inferred by any of the cladistic
methods for determining character polarity (Section 15.6). Outgroup comparison is
the most widely used, but cannot be used in every case a we may be unsure which
species to use as an outgroup, or different outgroups may give different answers, or
evidence may be lacking as to the character states (or molecular sequences) of the outgroup.
In one case, the deep root of life, no outgroup exists. If we want to find the root
of the tree for the three domains of life (Archaea, Bacteria, Eukarya) a where all cellular
life is grouped a we cannot do it by outgroup comparison. (Viruses cannot be used as
an outgroup because they evolve too fast, and anyhow have probably evolved recently
a they do not belong to a deeper branch, below the common ancestor of the three
domains.)
Molecular phylogenetics has added a new method to root trees (and therefore to find
character polarities). Its beauty is that it works internally, within the unrooted tree
itself; it does not require us to find any external data, such as an outgroup. The method
is called paralog rooting.
The method works as follows (Figure 15.23). We need a gene that has duplicated
before the origin of the taxon we are studying. We then construct the unrooted gene
tree for all the copies of the gene. For a duplicated gene in four species, there are eight
tips to the unrooted gene tree (Figure 15.23b). Both genes in the duplicated pair have
evolved through the same tree, and the gene tree is likely to have a “mirror image”
shape. We can infer, from this tree alone, that the root lies in the long branch that connects
the two mirror-image subtrees. We now know where the root is in the species tree
(Figure 15.23c).
Paralog rooting was first applied to the problem of the deep root of all life (that is,
the Archaea–Bacteria–Eukarya tree). But that problem is hard to solve because of
saturation. The common ancestor of all cellular life lived 3,500–4,000 million years
ago. The molecular differences between Archaea, Bacteria, and Eukarya lie well into
the difficult region II or impossible region III of Figure 15.13. We can look at a more
successful application of paralog rooting, to the phylogeny of angiosperms (Mathews
& Donoghue 1999). Angiosperms are the group better known as flowering plants.
Outgroup comparison tends to produce ambiguous results for angiosperms. Figure 15.24
shows Mathews and Donoghue’s result using paralog rooting. The rooted tree has
Amborella (one species, living in New Caledonia) forming a branch by itself from the
root. The next deepest branch has the water lilies. Careful inspection of the two
mirror images shows a few small mismatches, but no more than would be expected
from the uncertainties of phylogenetic inference. In all, the two subtrees have impressively
similar branching orders. Paralog rooting has given a major new insight into
angiosperm phylogeny, and the method can be applied wherever molecular sequences
are available for duplicate genes (with appropriate amounts of divergence) in a group
of species.