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Evolution__3rd_Edition

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452 PART 4 / <strong>Evolution</strong> and Diversity<br />

Figure 15.17<br />

Tree for human<br />

immunodeficiency virus (HIV)<br />

and other related viruses (SIV)<br />

that infect other primate<br />

species. The tree was<br />

constructed using 38 amino<br />

acid sequences of the pol gene,<br />

by a phylogenetic method called<br />

neighbor joining. (Tree<br />

courtesy of Dr D. Robertson.<br />

See Holmes (2000a) for a<br />

similar tree, and further<br />

discussion.)<br />

Tree for viruses (HIV/SIV) Primate hosts<br />

0.1 substitutions/site<br />

SIVcpz<br />

HIV-1/O<br />

SIVcpz<br />

HIV-1/N<br />

HIV-1/M<br />

SIVagmTAN<br />

SIVagmGRI<br />

SIVagmVER<br />

SIVmnd<br />

HIV-2/A<br />

HIV-2/B<br />

15.11.1 Molecular sequences can be difficult to align<br />

SIVsyk<br />

When we compare a DNA sequence from two species, and count how many<br />

nucleotides have changed, we need to be sure that each site in one species corresponds<br />

to the same site in the other species. The two sequences need to be correctly aligned.<br />

Alignment is not simply a matter of putting the two sequences next to each other. With<br />

normal length sequences of more than 100 nucleotides, regions will usually have been<br />

deleted during evolution in some species and added to others, such that the sequences<br />

of the different species do not simply align, with nucleotide number 39 of species 1 corresponding<br />

to nucleotide 39 of the other species. There are ways of dealing with the<br />

problem, but they can sometimes go wrong. (See the references in the further reading<br />

section at the end of the chapter.)<br />

15.11.2 The number of possible trees may be too large for them all<br />

to be analyzed<br />

In Section 15.9.4 and 15.9.5, we saw that it is necessary to search through all the possible<br />

trees in order to find the most likely, or the most parsimonious, tree. The problem is<br />

that the number of possible trees may be impossibly large. With four species, three<br />

bifurcating unrooted trees are possible meaning it is not difficult to count the number<br />

SIVsm<br />

SIVlhoest<br />

SIVsun<br />

SIVcol<br />

Chimpanzee<br />

Human<br />

Chimpanzee<br />

Human<br />

Human<br />

Tantalus monkey<br />

Grivet monkey<br />

Vervet monkey<br />

Sykes’ monkey<br />

Human<br />

Human<br />

Sooty mangabey<br />

Mandrill<br />

L’Hoest monkey<br />

Sun-tailed monkey<br />

Colobus monkey<br />

..

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