Evolution__3rd_Edition

458 PART 4 / Evolution and Diversity
Figure 15.22
Mistaken phylogenetic
inference because of
comparison between
paralogous genes. Different
copies of the gene family have
been lost in different lineages.
The genes remaining in species
1 and 2 are orthologs and more
similar than either is to the
paralogous gene in species 3. In
species 1–3 we do not know that
the genes are a mix of orthologs
and paralogs. A similar problem
arises if the duplicate genes have
not been lost, but happen not to
have been sequenced; the
mistake is then due to absence
of data rather than gene loss.
(It is assumed that the two
copies of the duplicated gene
tend to evolve apart over time,
whereas the orthologs remain
more constant in different
species.)
Evolutionary
time
Species 1
Gene
loss
Gene
loss
Species 2
Ancestral gene
Gene duplication
the same as the history of the species. In phylogenetic inference we use genes trees to
infer species trees. In many, perhaps most, cases the method is reliable; but not in all, as
Figure 15.22 illustrates.
15.11.6 Conclusion: problems in molecular phylogenetics
Species 3
This section has concentrated on the problems of molecular phylogenetics. However,
this does not mean that molecular phylogenetics is a weak, or more uncertain than
average, research program. Indeed, it is because molecular phylogenetics is such a
flourishing research program that biologists are so interested in where it can go wrong.
Once the problem areas have been identified, we can do further research into how to fix
or avoid the problems a or not be deceived by deceptive results. The problems we have
looked at here are all tolerable problems that can cause local, temporary difficulties
within molecular phylogenetics. But they are not insidious general problems that
undermine the whole enterprise.
Gene
loss
Inferred
phylogeny
of species
..