The topic of ancient DNA, indeed the very existence of it, sparks both public
imagination and scientific controversy. Although molecular genetic research on
this topic has gone on since the mid 1980s, research using ancient remains has
been conducted on mummies, plant remains, and fossils since the 1930s (2,4). Some
of the early work was focused on determining food preferences of ancient
populations and genetics of human populations. A symposium (Beyond Jurassic
Park: Accessing Genetic Information Hidden in Herbaria and Archival Plant,
Microbe, and Insect Specimens) held at the 1998 American Phytopathological
Society’s annual meeting discussed what information is being gleaned from
Recent efforts at analyzing ancient materials began with the cloning of DNA from an extinct zebra-like animal, the Quagga (9) (Fig. 2), and quickly advanced to cloning DNA from human mummies (14). In the first case, the specimen was over 100 years old; in the latter, the DNA was thousands of years old.
Although there was continued interest in isolating ancient DNA, there were
technical problems that made the study of these molecules difficult. Chief among
these were the findings that the ancient DNA is often damaged (14) (with the
majority of the damage occurring immediately after death), and the statistical
problems associated with analyzing clones, each having arisen from individual
molecules. The development of the Polymerase Chain Reaction (PCR) (17) solved
these problems to different degrees and has made possible many interesting and
informative studies of ancient materials.
Although PCR and direct sequencing of PCR products has overcome some of the
technical problems associated with studying ancient or archival DNA, there
remains serious resistance (3, 15) to accepting the results that have been
proffered on evolutionary time scales. Some of these arguments are based on the
theoretical stability of the DNA molecule under laboratory conditions, while others
are based on the likelihood of introducing contemporary contaminants into the
reactions. Scrupulous adherence to good laboratory practice can reduce the
chance of introducing modern DNA, but only the weight of numerous successful
studies will overcome the resistance based on the idea that DNA cannot survive
millions of years. This is based upon the premise that DNA naturally degrades
chemically at a predictable rate. This has been investigated (8) and it is clear
that the rate of DNA degradation in solution is different from that seen under
the conditions that allow DNA to survive millions of years. Recent work with
mitochondrial DNA from Neanderthal remains (13), used to investigate the
relationship among primate lineages, demonstrates the extent to which the studies
with ancient DNA are being accepted in the scientific community.
Focus of the Symposium
The symposium held at the APS/ESA meeting looked at how phytopathologists and entomologists are applying the techniques developed to investigate ancient DNA to questions relevant to these disciplines. Among these, population genetics and epidemiology are the main goals of studies looking at genetic changes taking place over tens or hundreds of years. These studies do not have many of the problems facing studies looking at mummies or bacteria in amber and they are relatively straightforward to undertake. A number of such studies have been carried out in various fields. Among those topics not discussed at the 'Jurassic Park' symposium include the identification of tobamoviruses from Australia in 1899, Borrelia in British ticks from 1896, extinct and extant New Zealand wrens, and extinct wolves. Recent work has looked at short tandem repeats from ancient human skeletal material, the phylogenetic position of the extinct moa from Hawaii and Oak chloroplast DNA from ancient and modern specimens. Even though directed work of this type has been widely undertaken, other studies, such as that by Hummel et al. (10) defend the validity of using DNA from ancient sources.
The symposium did include talks describing isolation of DNA from bees in
amber, from bacteria in bees in amber and isolation of bacteria from amber. We
will hear about reproductive strategies in Phytophthora and Puccinia,
about the use and value of museum specimens in mammalian and insect systems, and
finally about using museum-curated flies for systematic studies.
Among the scientists making the largest impact on the analysis
of ancient DNA and
even ancient organisms, Dr. R. Cano of the California Polytechnic State
University has been a pioneer, unearthing DNA and even a living bacterial strain
from bees in 20-45 million-year-old amber from the Dominican Republic (5, 6)
(Figs. 3 and 4).
There has been a significant amount of controversy surrounding the isolation and
reviving of the ancient Bacillus (3, 15), but Dr. Cano's group has overcome most
criticism and the validity of this discovery is well accepted. Although this
work does not come close to the popular image of recovering life from ancient
amber, it suggests that the accepted limits to the survival of DNA and even of
organisms may need to be re-thought.
Every plant pathologist knows of the terrible disease, late blight of potato,
caused by Phytophthora infestans. Recent changes in the global distribution of
this pathogen make it increasingly important to understand the biology of this
organism. One way to do that is to look at specimens that were collected before
the mass movement of plant materials common in the practice of modern
agriculture. Dr. Jean Beagle Ristaino of the Department of Plant Pathology at
North Carolina State University, Raleigh has done just that. Her talk, and a
recent review in Phytopathology (16), described the possibility of studying the
genetics of this important pathogen using materials from archives and herbaria.
Important questions addressed by this and related studies include whether sexual
reproduction was occuring in Europe when the pathogen was first detected there
and when both mating types were introduced into Europe (16).
If you could go back in time and sample a stem rust population before the barberry eradication programs, what would you find? This type of study may be possible using herbarium materials. A similar project aimed at understanding the population genetics of Puccinia grindeliae (11, 12) (Fig. 5), a potential biological control agent, was carried out by Dr. Craig Liddell, now at Paradigm Genetics, and his colleagues at New Mexico State University.
Te1iospores from naturally infected plant material were used to amplify the
Intervening Transcribed Spacer of the ribosomal RNA genes. Although their
herbarium samples yielded different success rates, the overall findings of this
study support the observation that this fungus reproduces primarily by sexual
reproduction and has done so prior to the introduction of intensive agriculture
into the region.
Do It Yourself
While the value of museum specimens for public appreciation and even for
systematic study has been long acknowledged, the use of museum specimens for
paleogenetic studies is relatively new and as such the approaches to using these
specimens and for analyzing the data generated with these studies is still in
its development. Dr. Rob DeSalle of the American Museum of Natural History and
author of the book, "The Science of Jurassic Park and The Lost World"
(1997, Basic books), spoke about several studies using different organisms. His
talk described how the use of museum specimens can help shed light on different
evolutionary and population genetic questions relevant to the interaction of
human activity and the environment. In addition to being an author of popular
books, Dr. DeSalle is an entomologist and has investigated the phylogenetic
impact of DNA from amber-preserved specimens (7).
Fly in the Ointment
Finally, Dr. J. William Ballard of the Field Museum of Natural History described how the method of preparing specimens for museums affected the ability to later extract DNA suitable for genetic studies. Dr. Ballard's research aims to unite the studies of the pattern and the process of evolution and as such curated materials play an important role. His research has delved into questions of whether the mitochondrial genome (1) is a useful molecular marker for phylogenetic research. Additional work has looked at more worldly traits including features of traps for catching blackflies, determining the gender of blackflies (Fig. 6), and horsefly feeding strategies.
Overall, the techniques developed to analyze ancient DNA are finding their
way into wider applicability. The careful preservation of materials in herbaria
and other biological collections provides an opportunity to delve into the
otherwise impenetrable past.
DeSalle, R. and Lindley, D. The Science in Jurassic Park. Basic Books, New York: 1997
Paabo, S. Ancient DNA. Scientific American. November 1993: 86-92
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