Evolution__3rd_Edition

454 PART 4 / Evolution and Diversity
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Africans
Non-Africans
Algorithms may be fooled by local
optima ...
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Ancestor
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Figure 15.18
Phylogenetic relations within Homo sapiens, as revealed by
mitochondrial DNA. Each of the 135 tips is a mitochondrial DNA
type; the 135 types came from 189 individual human beings. The
phylogeny suggests that humans originated in Africa and there
have been successive colonizations from that source. The
phylogeny is based on sequences of the control region within the
mitochondrion, which evolves 4–5 times as fast as the average for
the whole mitochondrion. The 135 types have the following
ethnic sources: Western Pygmies (1, 2, 37–48), Eastern Pygmies
(4–6, 30–2, 65–73), !Kung (7–22); African Americans (3, 27, 33,
35, 36, 59, 63, 100), Yorubans (24–6, 29, 51, 57, 60, 63, 77, 78, 103,
106, 107), Australian (49), Herero (34, 52–6, 105, 127), Asians
(23, 28, 58, 74, 75, 84–8, 90–3, 95, 98, 112, 113, 121–4, 126, 128),
Papua New Guineans (50, 79–82, 97, 108–10, 125, 129–35),
Hadza (61, 62, 64, 83), Naron (76), and Europeans (89, 94, 96, 99,
101, 102, 104, 111, 114–20). The computational procedures for
calculating the most parsimonious tree for 135 units are imperfect
and the tree shown is only one possibility among many. The tree
was inferred using PAUP and rooted using the chimpanzee. Arrows
indicate branches where changes are inferred to occur. Reprinted,
by permission, from Vigilant et al. (1991). © 1991 American
Association for the Advancement of Science.
algorithms are vulnerable to becoming trapped on “local optima” when they search
through the possible trees in a particular way. A local optimum is a tree that seems to be
the best possible, by comparison with the other trees that the algorithm investigates,
but is actually less parsimonious than other trees in a very different part of the space of
possible trees. One practical response to the problem is to run the algorithm several
times on a set of sequences, starting each run at a different starting point in the “tree
space.” If all the runs converge on the same answer, that strongly suggests it is the most
parsimonious tree. If they give conflicting results, however, it may suggest the evidence
is inadequate in some way.
A classic study of humans using mitochondrial DNA illustrates the problem
(Vigilant et al. 1991). Figure 15.18 is a branching diagram for 135 human mitochondrial
types. (A mitochondrial type is a particular mitochondrial sequence. Mitochondria
were sequenced from 189 individual humans, and because the study had 189 humans
and 135 mitochondrial types, each tip of the phylogeny represents one, or a few, individual
human beings.) The number of possible phylogenies with 135 tips is astronomic;
they cannot all be searched. The result in Figure 15.18 is the output after one run of a
parsimony algorithm, and it has a number of interesting properties. One is that the
deepest branch is African; it has African mitochondrial types to one side and a mix of
African and non-African mitochondrial types on the other, implying that the root of
the tree was an individual who lived in Africa. This is indeed part of the evidence that
modern humans have an African ancestry (though the main evidence comes from
fossils).
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