Evolution__3rd_Edition

..
Ribosomal RNA genes are widely
used in molecular phylogenetics
The origin of HIV has been dated
CHAPTER 15 / The Reconstruction of Phylogeny 451
Ribosomal RNA genes are particularly valuable in phylogenetic reconstruction because
they are found in almost all species: they are present in both mitochondrial and nuclear
DNA. The mitochondrial genes evolve more rapidly than the nuclear (Figure 15.16a
and b), and mitochondrial rRNA genes are useful for resolving phylogenetic problems
in the 10–100 million year range, whereas the slowly evolving nuclear rRNA genes are
useful in the hundreds of millions of years range.
Thus when Milinkovitch et al. (1993) wished to resolve the phylogeny of dolphins
and whales, which the fossil record suggests to have originated less than 35–40 million
years ago, the mitochondrial rRNA genes were appropriate (Figure 15.16c).
By contrast, Figure 15.16d shows the results of a study by Lake (1990) on the major
groups in the animal kingdom. These groups originated about 1,000 million years ago
(Section 18.4, p. 535) and the nuclear rRNA genes were the appropriate molecule for
the problem. Some of the branch patterns in Lake’s result have since been challenged,
but the main point here is that slowly evolving molecules are needed to infer phylogenetic
relations of this degree of antiquity.
15.10.2 Molecular phylogenies can now be produced rapidly, and are
used in medical research
Human populations are recurrently infected with new, or apparently new, diseases.
Many of the diseases are caused by viruses. Molecular phylogenetics has become, in the
past decade, a key part of the medical research program to identify each new disease
and where it came from. For example, HIV emerged as a mysterious new disease in the
early 1980s. Since then, many copies of the virus, and other related viruses, have been
sequenced. Figure 15.17 shows a phylogeny of HIV, which strongly suggests that HIV-1
entered human populations, perhaps more than once, from chimpanzees and HIV-2
came from sooty mangabeys. The molecular clock can be used to estimate the date
when the virus moved between species, and Korber et al. (2000) estimate that HIV-1
moved from chimpanzees to humans in the 1930s.
The viruses that cause new diseases are now almost routinely sequenced, and the
sequence run through a phylogeny program. We can identify the source, and something
of the nature, of each new disease virus within months, or even weeks, after the
disease breaks out.
15.11 Several problems have been encountered in
molecular phylogenetics
Molecular phylogenetics is now among the most, perhaps the most, active areas of
research in evolutionary biology. A number of problems have come up in this research
program. None of them are insuperable, and in this section we shall look at five of the
main problems and how they are being dealt with.