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are many controversies as systematists try to find agreement on disputed parts of the tree of life. In some cases, the shape of the tree is clear because each node is diagnosed by many apomorphies, but in others the clades and nodes are hard to pinpoint. Perhaps in those cases, evolution happened so fast that apo-morphies were not established, or perhaps they have been overwritten in time.

The molecular revolution

The second approach in reconstructing the tree of life is based on comparison of molecules. With the birth of molecular biology in the 1950s and 1960s, it became clear that homologous proteins share similar structures in different organisms. For example, many animals share the molecule hemoglobin, a protein that carries oxygen in the blood, and that makes the blood red. Structurally, the hemoglobin of all organisms that possess it is very similar because it has to perform its oxygen-carrying function - but there are subtle differences. So, the hemoglobin of humans and chimps is identical, but their hemoglobin differs a little from that of a horse or cow, and a great deal from the hemoglobin of a shark or a salmon.

Comparisons of molecules allow analysts to do two things: to draw up trees of relationships and to estimate time. Trees of relationships can be based on a simple comparison of the amount of difference between protein sequences, and a best-fitting dendrogram, or branching diagram, is drawn. Identifying specific amino acid changes, and treating them as synapomorphies, allows the dendrogram to be treated as a molecular cladogram.

Time estimation comes from the concept of the molecular clock. The amount of difference in the fine structure of a protein between any pair of species is proportional to the time since they last shared a common ancestor. Differences have been documented in the primary structure of proteins, the sequence of amino acids from end to end of the unfurled protein backbone. There are some 20 amino acids, and their sequence determines the shape and function of a protein. Small changes in the amino acid sequence of hemoglobin occurred every few million years, somewhat at random, and the rate of change allows a time scale to be calibrated against the molecular tree.

Since 1990, attention has shifted almost entirely from sequencing proteins to sequencing the nucleic acids such as DNA and RNA. These are the molecules in the nucleus that comprise the genetic code, and they may be sequenced in a semiautomated manner using a process called the polymerase chain reaction (PCR). PCR is a means of cloning, or duplicating, small samples of nucleic acid, and then of determining the exact sequence of base pairs, the four components of the nucleic acid strand, adenine, cytosine, guanine and thymine (or uracil), abbreviated as A, C, G and T (or U). DNA and RNA may be sequenced from the nucleus or the mitochondria of cells (see p. 186), and molecular biologists generate huge sequences of such information each year. Indeed, the human genome project was one of many examples of international programs to determine the entire DNA sequence of all the chromosomes of a single species. The PCR method has also opened up the possibility of sequencing the genetic material of extinct organisms (Box 5.6).

Box 5.6 Fossil proteins: the real Jurassic Park?

Proteins were extracted from fossils in the 1960s and 1970s, but most of these were decay materials, the proteins of bacteria that decomposed the original tissues. Even in cases of exceptional preservation where soft tissues are preserved (see p. 60), the proteins have usually long vanished. Until 1985, the oldest DNA, recovered in tiny quantities, came from Egyptian mummies, 2400 years old.

Then came Jurassic Park! In the book by Michael Crichton (1990), and in the film by Steven Spielberg (1993), a scenario was developed where molecular biologists extracted dinosaur DNA from blood retained in the stomach of a mosquito preserved in amber. The fragments of dinosaur DNA were cloned and inserted into the living cells of a modern frog (an odd choice when the nearest living relatives of dinosaurs are birds), and the whole dinosaur genetic code was somehow reconstructed and living dinosaurs recreated. Amazingly, science then followed the fiction for a time.

Michael Crichton was wise to choose amber as the means of preservation (see p. 63). Insects in amber are trapped instantly, usually overwhelmed by the sticky resin, and no decay takes place; the amber excludes oxygen and water so that no physical or chemical changes should occur during subsequent millennia. A series of scientific reports were published in high-profile journals through the 1990s, announcing original DNA from a termite in Oligocene-Miocene amber, a weevil in Early Cretaceous amber, Miocene leaves, and even supposed dinosaur DNA in 1994. These reports col lapsed like a pack of cards soon after. The "dinosaur" DNA turned out to be human: the PCR technique is so sensitive that the tiniest fragment of DNA, in this case from sweat or sneezed mucus of a lab assistant, can be amplified. Careful study showed that DNA is highly labile and breaks down in even hundreds of years, and is pretty well all gone by 40,000 years, even in the most exceptional preservation.

The most convincing studies of the DNA of fossil species come from ice age mammals such as the cave bear, giant Irish deer, Neandertal man, woolly rhino and woolly mammoth. In a rush of enthusiasm, three labs independently sequenced and published the complete mitochondrial genome of the woolly mammoth in early 2006 (Krause et al. 2006; Poinar et al. 2006; Rogaev et al. 2006). These studies gave conflicting results: it is still not clear whether the closest living relative of the mammoth is the Asian elephant Elephas maximus or the African elephant, Loxodonta africana (Fig. 5.11). All studies though confirm that modern elephants and the mammoth are about as closely related to each other as humans are to chimps, and that the species split apart 5-6 Ma.

Read more at http://www.blackwellpublishing.com/paleobiology/.

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—Mammuthus primigenus 1.0, 0.88,

Elephas maximus A

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Elephas maximus B

Loxodonta africana A

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Loxodonta africana B

—Mammuthus primigenus 1.0, 0.88,

Elephas maximus A

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Elephas maximus B

Loxodonta africana A

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Loxodonta africana B

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