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Evolution__3rd_Edition

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Ribosomal RNA genes are widely<br />

used in molecular phylogenetics<br />

The origin of HIV has been dated<br />

CHAPTER 15 / The Reconstruction of Phylogeny 451<br />

Ribosomal RNA genes are particularly valuable in phylogenetic reconstruction because<br />

they are found in almost all species: they are present in both mitochondrial and nuclear<br />

DNA. The mitochondrial genes evolve more rapidly than the nuclear (Figure 15.16a<br />

and b), and mitochondrial rRNA genes are useful for resolving phylogenetic problems<br />

in the 10–100 million year range, whereas the slowly evolving nuclear rRNA genes are<br />

useful in the hundreds of millions of years range.<br />

Thus when Milinkovitch et al. (1993) wished to resolve the phylogeny of dolphins<br />

and whales, which the fossil record suggests to have originated less than 35–40 million<br />

years ago, the mitochondrial rRNA genes were appropriate (Figure 15.16c).<br />

By contrast, Figure 15.16d shows the results of a study by Lake (1990) on the major<br />

groups in the animal kingdom. These groups originated about 1,000 million years ago<br />

(Section 18.4, p. 535) and the nuclear rRNA genes were the appropriate molecule for<br />

the problem. Some of the branch patterns in Lake’s result have since been challenged,<br />

but the main point here is that slowly evolving molecules are needed to infer phylogenetic<br />

relations of this degree of antiquity.<br />

15.10.2 Molecular phylogenies can now be produced rapidly, and are<br />

used in medical research<br />

Human populations are recurrently infected with new, or apparently new, diseases.<br />

Many of the diseases are caused by viruses. Molecular phylogenetics has become, in the<br />

past decade, a key part of the medical research program to identify each new disease<br />

and where it came from. For example, HIV emerged as a mysterious new disease in the<br />

early 1980s. Since then, many copies of the virus, and other related viruses, have been<br />

sequenced. Figure 15.17 shows a phylogeny of HIV, which strongly suggests that HIV-1<br />

entered human populations, perhaps more than once, from chimpanzees and HIV-2<br />

came from sooty mangabeys. The molecular clock can be used to estimate the date<br />

when the virus moved between species, and Korber et al. (2000) estimate that HIV-1<br />

moved from chimpanzees to humans in the 1930s.<br />

The viruses that cause new diseases are now almost routinely sequenced, and the<br />

sequence run through a phylogeny program. We can identify the source, and something<br />

of the nature, of each new disease virus within months, or even weeks, after the<br />

disease breaks out.<br />

15.11 Several problems have been encountered in<br />

molecular phylogenetics<br />

Molecular phylogenetics is now among the most, perhaps the most, active areas of<br />

research in evolutionary biology. A number of problems have come up in this research<br />

program. None of them are insuperable, and in this section we shall look at five of the<br />

main problems and how they are being dealt with.

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