Evolution, 4th Edition

410 CHAPTER 16

Many methods are used to estimate phylogenies from DNA sequences. The sim-

plest is parsimony, which we described above. The example in FIGURE 16.12 shows

how parsimony works when the data are complicated by homoplasy. We wish to

determine the relationships among species 1, 2, and 3. Their true evolutionary his-

tory is shown in tree A, but in reality, we do not know that. To estimate the phylog-

eny, we note that the sequences of the outgroup species suggest that the ancestral

sequence was very likely AAA. Under the hypothesis that tree A is correct, at least

4 changes are needed to account for the sequences in the living species. One of the

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Chloroplasts

Mitochondria

Other

bacteria

Proteobacteria

Cyanobacteria Crenarchaeota

Euryarchaeota

Bacteria Archaea Eukarya

FIGURE 16.10 An imaginative portrayal Animals Fungi Plants Algae Ciliates

of horizontal gene transfer (HGT) during

the early history of life. HGT makes the

evolutionary relations among species

resemble a network rather than a simple

branching tree. The early evolution of the

Bacteria and Archaea may have involved

massive HGT, which continues at a lower

rate today. HGT was also responsible for

the origin of the eukaryotes and the origin

of plants.

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3L

G M A

M G A

A G M

11%

62%

27%

7%

87%

6%

4%

92%

4%

12%

79%

9%

67%

23%

10%

0 Mb 10 20 30 40 50 60

2L 2La inversion

2R

3R

X

FIGURE 16.11 Gene trees from different parts of the genome

give conflicting evidence about the phylogenetic relations of

three mosquito species that are important malaria vectors. The

different gene trees result from a long history of hybridization,

as well as incomplete lineage sorting. Left: The three possible

gene trees showing the relations among the species Anoph-

eles gambiae (G), A. melas (M), and A. arabiensis (A). Right: The

horizontal panels represent the major chromosome elements of

the mosquito’s genome: the left and right arms of chromosome 2,

the left and right arms of chromosome 3, and the X chromosome.

Each chromosome is divided into many 10-kilobase (kb) windows,

and the color of each vertical line shows the gene tree for a given

window, with colors corresponding to the gene trees at left. On

the left arm of chromosome 3, for example, 92 percent of the

gene trees suggest that A. gambiae is most closely related to A.

arabiensis. Gene trees on the X chromosome are deeper (older)

than those on the autosomes, which strongly suggests that they

reflect the history of speciation. The conclusion is that A. melas

and A. arabiensis are sister species, as shown in the phylogeny at

the top left. (From [12].)

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