Evolution, 4th Edition

PHylogENy: THE UNITy ANd dIvERSITy of lIfE 409

Chapter 9). ILS is rampant among them, and until recently it was difficult to

determine their phylogeny with any confidence. Using several million base pairs

of DNA sequences, however, the evolutionary relations among the species can

now be resolved (FIGURE 16.9) [36].

INTRogRESSIoN A final culprit that makes estimating phylogenies difficult is

the introgression of genes between different species. In eukaryotes, introgression

happens most often by hybridization. Introgression also results from horizontal

gene transfer (HGT) between even very distantly related prokaryotes, in which

genes are exchanged by a variety of mechanisms (see Chapters 4 and 14). HGT

may have been so extensive during the early evolution of prokaryotes that their

evolutionary history more closely resembles braided hair than a simple branching

tree (FIGURE 16.10).

Whatever the mechanism, introgression causes some regions of the genome to

have an evolutionary history different from that of the species, and genes sampled

from those regions will give a misleading picture of the species tree. An extreme

case of introgression is seen in Anopheles mosquitoes, some of which transmit

malaria [12]. Hybridization has caused extensive genetic mixing, and many parts

of the genome have conflicting gene trees (FIGURE 16.11). Gene trees on the X

chromosome are deeper than those in other parts of the genome, suggesting that

they reflect the phylogeny of the species, while gene trees from other parts of the

genome reflect more recent hybridization. In Chapter 21 you will see there has

been hybridization in our own recent evolutionary past.

Methods for estimating phylogenies

Today, most phylogenies are based on DNA sequences. The data come from a

number of genes or even the entire genome. How are these data analyzed?

Futuyma Kirkpatrick Evolution, 4e

Sinauer Associates

Troutt Visual Services

Evolution4e_16.09.ai Date 01-02-2017

Harpagochromis

cf. serranus

Labrochromis

Pundamiliasp.“pink anal” sp. “stone”

Mbipia mbipi

Pundamilia nyererei

Paralabidochromis

sp. “rockribensis”

Neochromis

omnicaeruleus

Neochromis sp.

Neochromisrufocaudalis “unicuspid scraper”

Neochromis gigas

Paralabidochromis chilotes

“Haplochromis” cyaneus

Mbipia lutea

Lipochromis

melanopterus

Paralabidochromis

sp. “short snout

scraper”

Pundamilia

pundamilia

FIGURE 16.9 The cichlids of Lake

Victoria are a spectacular example of

an adaptive radiation. The phylog-

eny of 16 representative species was

recently resolved by using a very large

data set of several million DNA bases.

Each species is represented by several

individuals, shown by dots of the same

color. Because this tree was construct-

ed without an outgroup, it has no root.

(From [36].)

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