Ancient DNA: Recovery and Analysis of Genetic Material from Paleontological, Archaeological, Museum, Medical, and Forensic Specimens

274 Pages·1994·15.501 MB·English

by  Bernd Herrmann, Susanne Hummel (auth.), Bernd Herrmann, Susanne Hummel (eds.)

Ancient DNA
Bernd Herrmann Susanne Hummel
Editors
Ancient DNA
Recovery and Analysis of Genetic Material
from Paleontological, Archaeological, Museum,
Medical, and Forensic Specimens
With 50 Illustrations
Springer-Verlag
New York Berlin Heidelberg London Paris
Tokyo Hong Kong Barcelona Budapest
Bernd Herrmann Susanne Hummel
InslitUi rur Anlhropologie Inslitul rur Anlhropologie
Univcrsitiil COllingen Universitiil COllingen
37073 COllingen, Cermany 37073 COllingen, Cennany
Cover an plUl'ided by Prof. Dr. Bernd Herrmann.
Library of Congress Cataloging-in-Publication Data
Ancienl DNA : recovery and analysis of geroetic material from
paleontological, arcllaeological, museum. medical. and forensic
specimens' editors. Bernd Herrmann, Susanroe Hummel.
p. em.
Includes bibliograpllical refereoces and illdell.
ISBN-13: 978-0-381-94308-4 e-ISBN-13: 978-1-4612-4318-2
DOl: 10.10071978-1-4612-4318-2
I. DNA. Fossil. I. Herrmann. Bernd. II. Hummel. Susanne.
[QP620.AB 1994b]
574.87'3282- dc20 94-11352
Printed on acid-free paper.
© 1994 Springer-Verlag New York Inc.
Softcover reprint orlhe harcover 1s l edition 1994
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Preface
When we began our attempts to clone DNA from archaeological specimens
of bones in 1986 we were not successful, either with DNA or with funding.
We assume that other scholars had similar experiences. Since that time, the
field of ancient DNA recovery and analysis has developed into one of the
most exciting approaches to studying the past. Application of polymerase
chain reaction (peR) technology to ancient DNA has revolutionized the
field within the past few years. Interest in recovering DNA from unconventional
material, particularly old specimens, has ranged from the purely scientific to
very practical applications, such as law enforcement and medicine.
We are pleased that many of the "first generation" scholars involved in
ancient DNA research have contributed to this book. It is our intention to
present a general overview of the field before the diversity of disciplines and
scientific questions separates workers too much from central issues and themes.
We express our thanks to the contributors and also to the organizations
that provided funds to support this research in the days before the remarkable
successes that are described in this book were demonstrated. Their faith in
"high risk" enterprises is vital to the health of scholarly endeavor.
Bernd Herrmann
Susanne Hummel
Gottingen, Germany
31 May 1992
v
Contents
Preface V
Contributors IX
Introduction
BERND HERRMANN and SUSANNE HUMMEL
Access to Kinship and Evolution
DN A Fingerprinting
2 Simple Repeat Loci as Tools for Genetic Identification 13
JORG T. EpPLEN
Evolutionary Analysis
3 Spatial and Temporal Aspects of Populations Revealed by
Mitochondrial DNA . . . . . . . . . . . . . . . . . . . . 31
FRANCIS X. VILLABLANCA
Sample Preparation and Analysis
4 General Aspects of Sample Preparation 59
SUSANNE HUMMEL and BERND HERRMANN
Fixed and Embedded Samples
5 Screening for Pathogenic DNA Sequences in Clinically Collected
Human Tissues . . . . . . . . . 69
WAYNE W. GRODY
6 DNA from Amber Inclusions .................... 92
GEORGE O. POINAR, JR., HENDRIK N. POINAR, and RAUL J. CANO
Wet Samples
7 DNA Analysis of the Windover Population 104
WILLIAM W. HAUSWIRTH, CYNTHIA D. DICKEL, and
DA VID A. LAWLOR
VII
Vlll Contents
Frozen Samples
8 DNA from Arctic Human Burials 122
HENRIK NIELSEN, JAN ENGBERG, and INGOLF THUESEN
Dried Samples: Body Fluids
9 DNA Typing of Biological Evidence Material 141
GEORGE F. SENSABAUGH
Dried Samples: Sofi Tissues
10 DNA from Museum Specimens 149
ALAN COOPER
11 DNA from Herbarium Specimens. . . . . . . . . . . . . . . 166
JOHN W. TAYLOR and ERIC C. SWANN
12 High-Fidelity Amplification of Ribosomal Gene Sequences
from South American Mummies . . . . . . . . . . . . 182
PETER K. ROGAN and JOSEPH J. SALVO
Dried Samples: Hard Tissues
13 Mitochondrial DNA from Ancient Bones 195
ERIKA HAGELBERG
14 Y-Chromosomal DNA from Ancient Bones 205
SUSANNE HUMMEL and BERND HERRMANN
15 Genomic DNA from Museum Bird Feathers 211
HANS ELLEGREN
16 DNA and RNA from Ancient Plant Seeds .. 218
FRANCO ROLLO, FRANCO MARIA VENANZI, and AUGUSTO AMICI
Fossil Samples
17 DNA from Plant Compression Fossils 237
EDWARD M. GOLENBERG
Index 257
Contributors
AUGUSTO AMICI
Dipartimento di Biologia, Universita degli Studi di Camerino, 1-62032
Camerino, Italy
RAUL 1. CANO
Biological Sciences Department, California Polytechnic State University, San
Luis Obispo CA 93407, USA
ALAN COOPER
Molecular Genetics Laboratory, National Zoological Park, Washington, DC
20008, USA
CYNTHIA D. DICKEL
Departments of Immunology and Medical Microbiology, University of
Florida, Gainesville, FL 32610, USA
HANS ELLEGREN
Department of Animal Breeding and Genetics, Swedish University of
Agricultural Sciences, S-75007 Uppsala, Sweden
JAN ENGBERG
The Royal Danish School of Pharmacy, Department of Biological Sciences,
DK-2100 Copenhagen, Denmark
JORG T. EpPLEN
Molekulare Humangenetik, Gebaude MA, 5.0G Nord, Ruhr-Universitat
Bochum, D-4630 Bochum, Germany
EDWARD M. GOLEN BERG
Department of Biological Sciences, Wayne State University, Detroit, MI
48202, USA
IX
x Contributors
WAYNE W. GRODY
Division of Medical Genetics and Molecular Pathology, and Diagnostic
Molecular Pathology Laboratory, Department of Pathology and Laboratory
Medicine, UCLA School of Medicine, Los Angeles, California 90024-1732,
USA
ERIKA HAGELBERG
MRC Molecular Haemotology Unit, Institute of Molecular Medicine,
University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
WILLIAM W. HAUSWIRTH
Departments of Immunology and Medical Microbiology, University of
Florida, Gainesville, FL 32610, USA
BERND HERRMANN
Institut fUr Anthropologie, Universitat G6ttingen, 37073 G6ttingen,
Germany
SUSANNE HUMMEL
Institut fUr Anthropologie, Universitat G6ttingen, 37073 G6ttingen,
Germany
DA VID A. LAWLOR
Department of Immunology, University of Texas, M.D. Anderson Cancer
Center, Houston, TX 77030, USA
HENRIK NIELSEN
Department of Biochemistry B, The Panum Institute, University of
Copenhagen, DK-2200 Copenhagen N, Denmark
GEORGE O. POINAR JR.
Department of Entomological Science, University of California - Berkeley,
Berkeley, CA 94720, USA
HENDRIK N. POINAR
Biological Sciences Department, California Polytechnic State University, San
Luis Obispo, CA 93407, USA
PETER K. ROGAN
The Milton S. Hershey Medical Center, Department of Pediatrics,
Pennsylvania State University, Hershey, 17033, USA
FRANCO ROLLO
Dipartimento di Biologia Molecolare, Cellulare Animale, University of
Camerino, 1-62032 Camerino, Italy
Contributors xi
JOSEPH J. SALVO
Environmental Research Center, General Electric Co., Research &
Development Center, Schenectady, NY 12301-0008, USA
GEORGE F. SENSABAUGH
Forensic Science Group, Department of Biomedical and Environmental
Health Sciences, School of Public Health, University of California - Berkeley,
Berkeley, CA 94720, USA
ERIC C. SWANN
Department of Plant Biology, University of California - Berkeley, Berkeley,
CA 94720, USA
JOHN W. TAYLOR
Department of Plant Biology, University of California - Berkeley, Berkeley,
CA 94720, USA
INGOLF THUESEN
The Carsten Niebuhr Institute, University of Copenhagen, DK-2300
Copenhagen, Denmark
FRANCO VENANZI
Dipartimento di Biologia, Universita degli Studi di Camerino, 1-62032
Camerino, Italy
FRANCIS X. VILLABLANCA
Department of Integrative Biology and Museum of Vertebrate Zoology,
University of California, Berkeley, CA 94720, USA
1 Introduction
BERND HERRMANN and SUSANNE HUMMEL
The detection of high molecular organic compounds in ancient remains has
turned out to open a new research area with many implications, the most
important being the extraction of ancient DNA (aDNA) (to be characterized
below) from fossils, subfossil remains, artifacts, traces from biological sources,
and museum specimens. Since this technique provides access to the basic
molecules of organismic evolution, it opens up the possibility of studying
evolution at the molecular level over a principally unlimited time scale.
It should not be forgotten that knowledge on the preservation of nucleic
structures and nucleic acids has been available for a surprisingly long time.
As early as the beginning of our century, scholars of plant biology tried to
sprout seeds from excavations after they had succeeded in demonstrating
nucleic materials by staining old plant tissues. Although not purposely,
similar evidence of nucleic materials was obtained in microscopic (histo
chemical) inspections by the pioneers of human paleopathology investigating
ancient mummified remains.
Successful extraction of aDNA and aRNA was carried out, presumably
for the first time, by a Chinese team from rib cartilage of the Old Lady of
Mawangtui, a corpse preserved for almost 2,000 years (Hunan Medical
College 1980). The introduction of molecular cloning techniques initiated a
breakthrough in the search for aDNA. The first successful amplification of
aDNA from animal tissues, reported by Higuchi et al. (1984), was soon
followed by molecular cloning of aDNA from Egyptian mummies (Paabo
1985). Unfortunately, this technique required so much aDNA to be extracted
from the source that it was (and is) restricted to extraordinarily well-preserved
samples.
However, the invention of the Polymerase Chain Reaction (PCR) in the
mid-1980s (Saiki et al. 1985; Mullis and Fallona 1987) led to a boom in the
search for aDNA and aRNA, since it required only traces of target nucleic
acid. Thus it became the method of choice for all researchers interested in
molecular approaches to the past. In fact, the past in this context includes
all eras of biological evolution up to the present, since it turns out that the
basic problems in handling DNA traces from recent biological material are