Robert J. Brooker - Genetica
Esperimento di genetica 26.1
Scientists Can Analyze Ancient DNA
to Examine the Relationships Between
Living and Extinct Flightless Birds
The majority of phylogenetic trees have been constructed from molecular data using DNA samples collected from living species. With
this approach, we can infer the prehistoric changes that gave rise to
present-day DNA sequences. As an alternative, scientists have discovered that it is occasionally possible to obtain DNA sequence information from species that have lived in the past. In 1984, the first
successful attempt at determining DNA sequences from an extinct
species was accomplished by groups at the University of California at
Berkeley and the San Diego Zoo, including Russell Higuchi, Barbara
Bowman, Mary Freiberger, Oliver Ryder, and Allan Wilson. They
obtained a sample of dried muscle from a museum specimen of the
quagga (Equus quagga), a zebralike species that became extinct in
1883. This piece of muscle tissue was obtained from an animal that
had died 140 years ago. A sample of its skin and muscle had been
preserved in salt in the Museum of Natural History at Mainz, Germany. The researchers extracted DNA from the sample, cloned pieces
of it into vectors, and then sequenced hybrid vectors containing the
quagga DNA. This pioneering study opened the field of ancient
DNA analysis, also known as molecular paleontology.
Since the mid-1980s, many researchers have become excited about
the information that might be derived from sequencing DNA obtained
from older specimens. Currently there is debate concerning how long
DNA can remain significantly intact after an organism has died. Over
time, the structure of DNA is degraded by hydrolysis and the loss of
purines. Nevertheless, under certain conditions (e.g., cold temperature,
low oxygen), DNA samples may remain stable for as long as 50,000 to
100,000 years and perhaps longer.
In most studies involving prehistoric specimens (in particular, those
that are much older than the salt-preserved quagga sample), the ancient
DNA is extracted from bone, dried muscle, or preserved skin. These
samples are often obtained from museum specimens that have been gathered by archaeologists. However, it is unlikely that enough DNA can be
extracted to enable a researcher to directly clone the DNA into a vector.
Since 1985, however, the advent of PCR technology, described in Chapter 18, has made it possible to amplify very small amounts of DNA using
PCR primers that flank a region within the 12S rRNA gene, a slowly
changing gene. In recent years, this approach has been used to elucidate
the phylogenetic relationships between modern and extinct species.
In the experiment described in Figure EG26.1.1, Alan Cooper,
Starting material: Tissue samples from four extinct species of moas were obtained from museum specimens. Tissue samples were
also obtained from three species of kiwis, one emu, one cassowary, one ostrich, and two species of rhea.
FIGURE EG26 .1.1 DNA analysis reveals phylogenetic relationships among extinct and modern flightless birds.
© 2010 The McGraw-Hill Companies, S.r.l. - Publishing Group Italia
Robert J. Brooker - Genetica
Cécile Mourer-Chauviré, Geoffrey Chambers, Arndt von Haeseler,
Allan Wilson, and Svante Pääbo investigated the evolutionary relationships among some extinct and modern species of flightless
birds. Two groups of flightless birds, the moas and the kiwis, existed in New Zealand during the Pleistocene era. The moas are now
extinct, although 11 species were formerly present. In this study, the
researchers investigated the phylogenetic relationships among four
extinct species of moas that were available as museum samples,
three kiwis of New Zealand, and several other (nonextinct) species
of flightless birds. These included the emu and the cassowary
(found in Australia and New Guinea), the ostrich (found in Africa
and formerly Asia), and two rheas (found in South America).
The samples from the various species were subjected to PCR to
amplify the 12S rRNA gene. This provided enough DNA to subject
the gene to DNA sequencing. The sequences of the genes were
aligned using computer programs described in Chapter 21.
THE GOAL
Because DNA is a relatively stable molecule, it can be amplified by
PCR from a preserved sample of a deceased organism and subjected
to DNA sequencing. A comparison of these DNA sequences with
modern species may help elucidate the phylogenetic relationships
between extinct and modern species.
THE DATA
© 2010 The McGraw-Hill Companies, S.r.l. - Publishing Group Italia
Robert J. Brooker - Genetica
INTERPRETING THE DATA
The data of Figure 26.15 illustrate a multiple sequence alignment of
the amplified DNA sequences. The first line shows the DNA sequence of one extinct moa species, and underneath it are the sequences of the other species. When the other sequences are identical
to the first sequence, a dot is placed in the corresponding position.
When the sequences are different, the nucleotide base (A, T, G, or
C) is placed there. In a few regions, the genes are different lengths.
In these cases, a dash is placed at the corresponding position.
As you can see from the large number of dots, the sequences among
these flightless birds are very similar. To establish evolutionary
relationships, researchers focus on the few differences that occur.
Some surprising results were obtained. The sequences from the kiwis (a New Zealand species) are actually more similar to the sequence from the ostrich (an African species) than they are to those
of the moas, which were once found in New Zealand. Likewise, the
kiwis are more similar to the emu and cassowary (found in Australia and New Guinea) than they are to the moas. Contrary to their
original expectations, the authors concluded that the kiwis are more
closely related to Australian and African flightless birds than they
are to the moas. They proposed that New Zealand was colonized
twice by ancestors of flightless birds. As shown in Figure 26.16,
the researchers constructed a new evolutionary tree to illustrate the
relationships among these modern and extinct species.
Since these early studies, sequences of ancient DNA have been derived from a variety of species. Figure 26.17 shows some extinct
organisms from which DNA sequences have been determined
Many of these samples were tens of thousands of years old. For
example, the sample of a Neanderthal man was approximately
30,000 years old. The oldest samples are likely to be in the range of
50,000 to 100,000 years old.
FIGURE EG26.1.2 A revised phylogenetic tree of moas, kiwis,
emus, cassowaries, ostriches, and rheas.
FIGURE EG26.1.3 Extinct organisms from which DNA sequences
have been obtained. Right panel, from bottom right to top right:
quagga, marsupial wolf, sabre-toothed cat, moa, mammoth, cave bear,
blue antelope, giant ground sloth, and Aurochs. Left panel, from bottom
left to top right: mastodon, New Zealand coot, South Island piopio,
Steller’s sea cow, Neanderthal man, South Island adzebill (Aptornis
defossor), hasta ground sloth, pig-footed bandicoot, moa-nalo, and
Balearic Islands cave goat (Myotragus balearicus). (Adapted from Hofreiter et al. [2001], “Ancient DNA,” Nature Reviews Genetics, vol. 2, p.
357.)
© 2010 The McGraw-Hill Companies, S.r.l. - Publishing Group Italia