Systematics and Evolution 145organisms, because the former have more genes in common than the latter). But since the
1990s, especially with the ability of the PCR (polymerase chain reaction) to produce lots of
copies of DNA, allowing us to read the DNA rapidly, we now have the full DNA sequence of
a number of organisms, including fruit flies, lab rats, mice, and rabbits, several domesticated
animals, the nematode worm Caenorhabditis elegans, and most of our ape relatives. The mito-
chondrial DNAs of many apes were sequenced as early as 1982, but the entire chimpanzee
nuclear DNA sequence was not completed until August 2005. Human nuclear DNA was
sequenced in 2001 by the Human Genome Project and also by Craig Venter’s lab. From all
these studies, we now have a powerful tool to compare the genetic codes of a wide range
of organisms. These data not only show us how we differ from other organisms but also
(especially in the case of human DNA) allow us to find out what genes code for what parts of
the body and where in the DNA the genes for inherited diseases occur. Many scientists hail
the decoding of human DNA as one of our greatest scientific achievements ever because of
its potential not only to answer scientific questions but also to cure many diseases.
Molecular approaches have been particularly useful where there isn’t much evidence
from the anatomy or the fossil record of organisms to determine their evolutionary relation-
ships. For example, the external form of most bacteria is pretty stereotyped, and most early
bacteriologists underestimated their diversity. With the advent of genetic analysis, however,
scientists such as Carl Woese have shown that there are several different kingdoms of bacte-
ria, including the most primitive organisms of all, the Archaebacteria, which mostly live in
extreme environments such as hot springs and anoxic conditions. Scientists have debated for
years about how animals, plants, fungi, and bacteria might be related, but molecular phy-
logeny has provided an answer that could never have been solved by traditional methods
(fig. 5.6). The relationships of the major groups of multicellular animals were also hotly
debated for over a century, but molecular techniques, in combination with newer ideas
about embryology and anatomy, have provided an answer that is no longer disputed
(fig. 5.7). Thus the molecular evidence provides an independent way of discovering the
family tree of life and, in many instances, has given us answers that could not have been
obtained by any other method.
This is not to say that every molecular study works perfectly or that molecular phy-
logenies are always superior to other methods. Like any other characters used in a phy-
logenetic analysis, molecular changes can be viewed as primitive and derived. But unlike
anatomical characters, most molecular changes are limited to the four nucleotides (adenine,
thymine, guanine, and cytosine), so there are only a limited number of possible changes.
Consequently, if a gene is going to change, it can very easily return to the primitive condi-
tion, since that is the only alternative. This generates some “noise” in the molecular signal.
In recent years, sophisticated methods have been used to detect this noise and filter it out.
Likewise, the “clocklike” mutation rate hypothesis sometimes fails, because some organisms
or taxonomic groups seem to have higher or lower than average rates of mutation, so there
are still debates when molecular clock estimates give ages of branching points in evolution
that are much too old to match the fossil record.
Still, there have been some remarkable successes. For years, paleoanthropologists
such as Elwyn Simons and David Pilbeam argued that Ramapithecus, a fossil from beds in
Pakistan that are 12 million years old, was the earliest member of our family Hominidae.
If that were true, then the ape-human split would be older than 12 million years ago. But
molecular biologists Vince Sarich and Allan Wilson of Berkeley looked at many different