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Isr. J. Earth Sci.; 56: 217–230
© 2008 Science From Israel/ LPPLtd. 0021-2164/07 $4.00
*Author to whom correspondence should be addressed.
E-mail: greenbl@cc.huji.ac.il
Molecular archaeology: People, animals, and plants of the Holy Land
Marina Faerman,
a
Gila Kahila Bar-Gal,
b
Israel Hershkovitz,
c
Mark Spigelman,
d,e
and Charles L. Greenblatt
e,
*
a
Laboratory of Bio-anthropology and Ancient DNA, Faculty of Dental Medicine, The Hebrew University of Jerusalem,
Jerusalem 91120, Israel
b
Koret School of Veterinary Medicine, Faculty of Agriculture, Food and Environment Quality Sciences,
The Hebrew University of Jerusalem, Rehovot, 76100, Israel
c
Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
d
Centre for Infectious Diseases and International Health, Department of Infection, Windeyer Institute of Medical Sciences,
University College London, London, UK
e
Kuvin Centre for the Study of Infectious and Tropical Disease, Faculty of Medicine, The Hebrew University of Jerusalem,
Jerusalem 91120, Israel
(Received 2 March 2008; accepted in revised form 24 June 2008)
ABSTRACT
Faerman, M., Kahila Bar-Gal, G., Hershkovitz, I., Spigelman, M., and Greenb-
latt, C.L. 2008. Molecular archaeology: People, animals, and plants of the Holy
Land. Isr. J. Earth Sci 56: 217–230.
Scientists, by employing various innovative techniques, have succeeded to put the
“esh back on the bones” of people, animals, and plants of prehistoric and historic
Israel. Classic morphometrics and modern molecular genetics, epidemiology and
botany, biblical texts and archaeological contexts—every single piece of information
becomes crucial when individual and/or population life histories are considered. Anal-
ysis of DNA recovered from fossils has added a new dimension to our understanding
of human evolution and population movements, disease patterns and host–pathogen
relationships, and plant and animal domestication.
INTRODUCTION
Genetic data on present-day populations are being
increasingly applied to reconstruct the origins, migra-
tions, and relationships of past human and non-human
populations (e.g., Cavalli-Sforza and Feldman, 2003).
An independent but complementary approach to such
studies will be to obtain direct evidence from the past
by analyzing DNA preserved in archaeological remains.
Bones and teeth can give us clues of the life history of
people in various ways. They are the human materials
found in archaeological excavations, but there are other
organic remains that provide an interface to human
activities of the past. These are the plant and animal
source materials as well as their products such as leath-
er goods, seeds, and wood. The retrieval and further
evaluation of ancient DNA (aDNA) sequences from
fossils, archaeological nds, and museum specimens is
a major goal of the ancient DNA eld.
218 Israel Journal of Earth Sciences Vol. 56, 2007
aDNA is severely degraded into fragments of less
than 200 “letters” of the genetic code (base pairs),
and the Polymerase Chain Reaction (PCR) helps us
to restore these minute traces of DNA fragments into
essentially unlimited numbers of copies. Each round
of amplication doubles the number of copies of the
template DNA, thus ending with amounts that can be
further characterized with the help of standard molecu-
lar biology techniques.
Working with aDNA is not an easy, but rather a
challenging and time-consuming task. This is mainly
because of the postmortem DNA degradation and the
high risk of contamination with modern human DNA
that may compromise aDNA ndings in archaeo-
logical specimens, in particular, of human origin. Re-
cently, Salamon et al. (2005) have described a certain
bone niche—crystal aggregates—where relatively
well-preserved ancient DNA is present and its amount
is sufcient for further genetic analysis, thus offering
a novel approach to obtain reliable genetic information
from fossil specimens including those of humans.
Contamination may be introduced at almost every
step of the analysis: it may result from inappropriate
handling of the specimens by people (eld workers,
archaeologists, anthropologists, geneticists, and labo-
ratory technicians) or may originate from the equip-
ment, reagents, and disposables used. Since PCR is
a very sensitive tool and modern DNA contaminants
might over-compete with their badly degraded ancient
counterparts leading to false-positive results, it is ex-
tremely important to follow stringent precautions from
the very beginning. Thus, the initial bone sampling
for further DNA analysis should be performed at the
archaeological site under sterile conditions, preferably
by a trained investigator. To insure the authenticity of
the aDNA ndings, a set of stringent criteria has been
developed (Cooper and Poinar, 2000). They include
blank extraction controls and negative PCR controls;
repeated DNA extractions and PCR amplications;
quantitation of the number of ampliable DNA mol-
ecules; inverse correlation between amplication
efciency and length of PCR products; sequencing
and cloning of PCR products; estimation of macromo-
lecular preservation; independent reproduction of the
results by a second laboratory; and DNA analysis of
accompanying faunal remains (when analyzing human
material).
If its message is properly deciphered, aDNA can
provide information from the past that is unavailable
by any other approach. Many elds—archaeology,
anthropology, history, evolutionary biology, genetics,
and forensic medicine—have beneted from aDNA
research. Questions related to human evolution and
population history, species phylogenies, genetic
and infectious diseases, diet and behavior, plant and
animal domestication, host–pathogen relationship, and
many more specic queries have been viewed through
the aDNA perspective (reviewed in Hofreiter et al.,
2001; Pääbo et al., 2004; Drancourt and Raoult, 2005;
Willerslev and Cooper, 2005).
Studies on the Neanderthal genetics are probably
the best example to illustrate the development of the
aDNA eld as a discipline. Ten years ago, the rst mi-
tochondrial hypervariable region I sequence (HVS-I)
from the most famous Neanderthal specimen, Feld-
hofer 1 from the Neander Valley, Germany, was re-
trieved (Krings et al., 1997). Analysis of this sequence
suggested that there was no archaic Neanderthal
mtDNA in the current European mitochondrial DNA
(mtDNA) pool and that the most recent common an-
cestor (MRCA) of modern humans and Neanderthals
dated to some 300,000–700,000 years ago. Since then,
mtDNA sequences have been successfully retrieved
from many more Neanderthal bones found all over
Europe, strengthening the original ndings. Unfortu-
nately, these do not include the famous Neanderthals
and anatomically modern humans found in caves in
Mt. Carmel, Israel.
Most recently, these conclusions have been re-
visited by analyzing nuclear (autosomes and sex
chromosomes) DNA retrieved from a 38,000-year-old
Neanderthal from Croatia (Vindija 80) (Green et al.,
2006). Direct high-throughput sequencing of a DNA
extract from this fossil has yielded over one million
base pairs of the Neanderthal nuclear DNA sequences.
In addition, for the rst time DNA-based sex identi-
cation was successfully achieved in a Neanderthal by
showing the individual was a male.
In a simultaneous study of the same Neanderthal
specimen—based on the development of a Neander-
thal
metagenomic library, which was followed by mas-
sively parallel
pyrosequencing—Noonan et al. (2006)
showed that the 65,250 base pairs
of hominid sequence
identied so far were of
Neanderthal origin. According
to both studies, the time of the MRCA of Neanderthals
and modern humans was very similar to the mtDNA
estimates by Krings et al. (1997, 2000). Altogether, the
application of high-throughput sequencing technolo-
gies
and the recent advances in metagenomic analysis
of complex DNA mixtures
have allowed a new strat-
egy to analyze DNA sequences from ancient
samples,
thus opening a new eld of palaeogenomics.
M. Faerman et al. Molecular archaeology of the Holy Land 219
* * *
In the early 1990s when ancient DNA studies were just
at the beginning, Patricia Smith, Ariella Oppenheim,
and Charles Greenblatt from The Hebrew University
of Jerusalem founded the rst ancient DNA laboratory
in Israel. The opening of this eld to the archaeologists
and museum curators helped them to start thinking
about the possibilities of using DNA in order to under-
stand their sites in greater depth.
Since 1995, Israeli researchers have actively par-
ticipated in international and local meetings, reporting
on their ndings. Moreover, in 1997, a rst sympo-
sium “Digging for Pathogens” focusing on ancient
emerging diseases, their evolutionary, anthropologi-
cal, and archaeological aspects, was held in Jerusalem
(Greenblatt, 1998). In 2000, the “Ancient DNA VI”
meeting held in Israel allowed Israeli scientists and
students to benet from fascinating discussions with
the top-level experts in the aDNA eld. Along with
the variety of research activities, a course in aDNA
analysis for graduate students has been designed and
held since 1996 at the Hadassah Faculty of Medicine,
The Hebrew University of Jerusalem.
We would like to present here our joint attempt to
summarize some major achievements and to outline
future perspectives of such studies in Israel.
1. ANIMAL AND PLANT DOMESTICATION
The location of the southern Levant as an important
corridor between three continents enabled faunal
and human migrations throughout the Pleistocene
(1.8 million to 11,550 years before present). Their
ngerprints are still evident in the many cave sites in
Israel. Towards the end of the Natuan period, human
economical strategy suddenly shifted; the two million
years of hunting-gathering way of life was abandoned
in favor of a farming and food-producing economy
(e.g., Smith and Horwitz, 1998). The point of no return
was crossed in the Pre-Pottery Neolithic (PPN) period
when the rst large permanent human settlements
were established and people had begun to manipulate
their environment, starting with the process of animal
and plant domestication—the “Agricultural Revolu-
tion”. Thousands of years later, the local inhabitants of
the region overcame technological and genetic barriers
to start the “Secondary Product Revolution”, utilizing
milk products extensively. Goats and sheep became a
crucial element in the human diet and hence a focus of
our research.
1.1. Goats
In the southern Levant two species of Caprinae are
commonly found in archaeological sites dated from
the Middle Paleolithic to the Pre-Pottery Neolithic B
(PPNB) period, namely: the wild goat (bezoar, Capra
aegagrus aegagrus) and the Nubian ibex (Capra ibex
nubiana). Goats (Capra species) were among the
rst pastoral animals to be successfully domesticated
during the Neolithic revolution (Bar-Yosef and Belfer-
Cohen, 1989; Bar-Yosef and Meadow, 1995). A vari-
ety of reasons enabled their domestication including
their relatively undemanding food requirements; ease
of handling; versatility of products (meat, milk, and
wool) and their important role as sacricial animals in
many religions.
The domestication process was based on conscious
and unconscious selection for goat types suitable for
human requirements. As agriculture spread and devel-
oped, numerous breeds were developed partly due to
selection by man (selected for phenotypic character-
istics) and due to the adaptation to different climates
and nutrient supplies. Once the goat was domesticated,
its appearance in the zooarchaeological assemblages
starts to increase, whereas the presence of the Nubian
ibex remains unchanged over 10,000 years.
Our studies on goat domestication emphasized re-
search on the mitochondrial genes (cytochrome b and
d-loop) of Capra species dated to different periods
before, during, and after domestication. Analysis of
these ancient sequences has allowed us to quantify
the rate of genetic changes and the amount of genetic
variability within and between selected species of
wild and domesticated forms (Kahila Bar-Gal et al.,
2002a). Altogether, the results indicate that during the
PPNB, both wild and domestic goats are present in the
zooarchaeological assemblages (Kahila Bar-Gal et al.,
2002b). From the Pottery Neolithic (PN) period on-
ward, the animal bone assemblages are dominated by
the Baladi goat, a local breed of C. hircus. This nding
is consistent with the scenario of rapid genetic changes
in the Capra species from the PPNB to PN period.
However, no genetic changes have been observed in
the Nubian ibex during the last 2,000 years (Kahila
Bar-Gal, 2000).
At Hirbet Qumran, a site on the northwestern coast
of the Dead Sea, nearly 850 scrolls were found includ-
ing books of the Hebrew Bible, sectarian writings of
the local Qumran community, and other manuscripts
(Fig. 1). Since their discovery, the Dead Sea Scrolls
have been a subject of controversial discussions
220 Israel Journal of Earth Sciences Vol. 56, 2007
(Broshi, 1999). Most of the scrolls were written on
parchments made of animal skins. Based on morpho-
logical analysis (structure of the hair follicles), it was
determined that the parchments were made of sheep
skin or were from an unknown species.
Based on the analysis of mtDNA sequences (cy-
tochrome b and d-loop regions), retrieved from the
sampled parchments, including the Temple Scroll,
the researchers concluded that most of them were
made of domestic goat skin (Woodward et al., 1996;
Kahila Bar-Gal, 2000). Other parchments were made
of Nubian ibex skin, which is not surprising since it is
one of the most common large mammals in the Judean
Desert.
Worth noting, is that when the Nature Reserves Au-
thority wanted to reintroduce the Cretan goat into the
nature reserves of Israel as a progenitor species of the
domestic goat, using the genetic data bank of modern
goats, we indicated that this was not the correct candi-
date animal, i.e., underneath the long horns there was
simply a feral domesticated goat.
1.2. Grapes and olives
About 10,500 years ago, farming had originated in the
Eastern Mediterranean region with a group of seven
grain crops, namely einkorn wheat, emmer wheat,
barley, pea, lentil, chickpea, and ax, the so-called
“founder crops package” (Zohary and Hopf, 2000).
The main criteria for selecting these plants by the
rst farmers from a wealth of surrounding species
were their nutritional values, storage stability (dura-
tion), taste, and cultivating facilities. In recent years,
studies have shifted from genetic changes related to
seed morphology, dispersal, and dormancy associated
with cultivation efciency (Zohary, 1996; Abbo et al.,
2003) to the nutritional values of the domesticants
(Kerem et al., 2007). Whatever the mechanism or
reasons for domestications were, their outcome has
Fig. 1. Qumran, a view from the Qumran plateau showing entrances to caves that contained Dead Sea Scrolls. Lower right: a
Scroll fragment.
M. Faerman et al. Molecular archaeology of the Holy Land 221
had a tremendous impact on almost every aspect of the
human life—division of labor, social organization and
stratication, establishment of political and religious
institutions, changes in family structure, level of inter-
and intra-personal violence (Hershkovitz and Gopher,
1990; Cauvin, 2000; Eshed et al., 2004).
Much of what we know of the utilization and culti-
vation of grapes (among the rst plants to be domesti-
cated) is found in biblical references. Wine is central to
Jewish ritual, and to that of many other religions. What
can we learn from molecular studies of the indigenous
grapes? A wonderful collection of vines has been gath-
ered at the Indigenous Fruit Tree Rescue Gardens at
Sataf, located about 13 kilometers west of Jerusalem.
Twenty-four cultivars were analyzed to determine their
genotype identity and their genetic relatedness. Six
microsatellite regions were amplied and the amplicon
sizes were measured by genotyping (Klein et al., 2008).
Marked genetic similarity was observed between the
local cultivars, with three cultivars having identical
allele sizes for all six microsatellites. Two of these
cultivars are probably genetically identical, but one,
although closely related, showed phenotypic difference
in the color of the berries. The allelic frequencies, when
compared to available databases of European and Med-
iterranean cultivars, were found to be closest to Greek
vines (Ben-Yair et al., 2006). This relationship ts the
accepted version that the Philistines as the sea-people
of the Aegean brought the culture of the grape and
wine-making with them. Historical and archaeological
information indicates that the Sataf collection may only
represent part of the diversity of local vines. It has been
suggested that many vines still occur as feral plants.
We are currently shifting our study from the use of
living grape cultivars to examining the survival and
retrieval of DNA from grape seeds found at archaeo-
logical sites. Seeds from an archaeological site located
only a few kilometers from the Sataf nature reserve
were provided to us by Shimon Gibson. Preliminary
tests have shown these seeds to contain fragmented
DNA, but which is still suitable for micro-satellite
analyses. Moreover, Zohar Kerem has found unique
grape bio-markers for use in tracing residues of these
plants on ceramics (Kerem and Rosen, 2006). These
will allow the tracking of wine through the processes
of production and commerce.
Our colleagues, Rivka Elbaum and Steve Weiner,
from the Weizmann Institute of Science, have car-
ried out studies to determine the possibility of work-
ing with ancient olive pits (Elbaum et al., 2006). By
analyzing proportions of lignin (L-ratio) in fossil and
modern olives using infrared spectroscopy, they were
able to identify well-preserved fossil pits in terms of
DNA template quality, such as olive-specic template
length amplied by regular PCR, and DNA template
quantity determined by real-time PCR. They have
found that DNA preservation was better in those olive
pits for which L-ratios were the same as that in modern
ones. aDNA sequences obtained from Qumran olive
pits dated to 600 years ce were most similar, although
not identical, to modern Olea europae ssp. laperrinei
and Olea europae ssp. cerasiformis.
2. DISEASES
History of disease is an integral part of human history.
Information on diseases, their spectrum and incidence
in past populations, can be obtained from ancient med-
ical manuscripts, literature, and art, and directly from
archaeological remains, both of humans and animals.
Biological anthropologists have developed numerous
techniques for diagnosing diseases in human remains
and their possible causes, from visual observations and
histological examination, X-rays, and CT-scans to the
search of bacterial DNA, described rst by Spigelman
and Lemma (1993).
Recently, aDNA methodologies have been applied
to identify the genetic mechanisms and pathogens as-
sociated with specic skeletal lesions in prehistoric
specimens and to name the agents that were respon-
sible for numerous reported epidemics in human his-
tory. It has allowed the researchers to evaluate existing
hypotheses on an early onset of these conditions in
human evolution. A completely different view may be
drawn now that permits a better understanding of the
interaction between human populations and the envi-
ronment (Greenblatt and Spigelman, 2003).
2.1. Infections
Diversity of human diseases has changed as a
result of human behavior, which has altered in the
last 10–20,000 years (Diamond, 1997; Stearns 1999;
Cleaveland et al., 2001). As hunter-gatherers, humans
resembled other primates in their diseases (Martin,
2003). The shift to animal husbandry and plant do-
mestication brought about changes in the environment,
society, population size and density, as well as diet,
and had radical effects on the nature and burden of
our diseases (Cohen and Armelagos, 1984; Smith and
Horwitz, 1998; Cohen, 1989). With sedentism, the
accumulation of human waste led to contamination of
water sources, and opened the door to transmission of
222 Israel Journal of Earth Sciences Vol. 56, 2007
a vast number of pathogens, ranging from viruses to
worms. However, it was the close contact of newly
domesticated pets and livestock to humans that was
probably the greatest source of infection. The appear-
ance of agriculture and domestication of animals some
10,000 years ago, and the Industrial Revolution some
200 years ago, introduced new dietary and disease
pressures for which little adaptation has been possible
in such a short time span. As a result it is possible to
study this evolutionary process in terms of genetic
changes.
Animal–human disease transmission was assured
with the sharing of living space and the intimacy of
animal husbandry. This may have introduced inu-
enza from pigs, brucellosis from goats, and pertussis
from dogs into the realm of humans during this early
time. Low-level diseases could then spread as “crowd
diseases” (Diamond, 1997), when success depends
directly on the size of the population. Environmental
perturbation opened breeding sites for vector-borne
diseases such as malaria (Livingstone, 1958), yellow
fever, and leishmaniasis (Beran and Steele, 1994).
Infectious pathogens that originate in wild animals
have become increasingly important throughout the
world in recent decades, as they have had substantial
impact on human health, agricultural production,
wildlife-based economies, and wildlife conservation
(Bengis et al., 2004). Increased diversity of infectious
diseases clearly acted as a major evolutionary force
on human populations. They became the main source
of natural selection for human populations (Haldane,
1949), and continue today as a central challenge to
our survival and tness. The evolutionary game with
the human host has enabled new diseases to emerge.
These diseases have shaped our societies, human de-
mography, and our genetic makeup. The 1918 u epi-
demic killed some 40 million people, but made many
millions more immune. In its wake it inuenced the
outcome of war, research into vaccination, and genetic
change in the virus itself (Crosby, 1989). Presently,
global medicine is mobilized to confront a pandemic
of avian u, and the strategic planning for this war has
been inuenced by studies of the past.
In today’s world, infectious disease specialists are
attempting to deal with so called “emerging diseases”.
To a large extent these are often zoonotic diseases.
That is, they are transmitted from animals to humans,
with the latter often described as an accidental host. In
the Southern Levant, three diseases that are transmit-
ted to humans may offer insights into the history, evo-
lution, and nature of transmission today. Among the
rst diseases that were transmitted were tuberculosis,
leishmaniasis, and brucellosis, which are associated
with three of the rst wild animals to be domesticated,
i.e., the cow, the dog, and the goat.
2.1.1. Tuberculosis
In the Southern Levant, domesticated cattle are
found in archaeological sites at least since the Pottery
Neolithic (Davis, 1982, 1991) and were among the
central animals in the pastoral economy of this region,
providing meat and milk (Tchernov and Horwitz,
1990; Grigson, 1995). Moreover, since the “Neolithic
Revolution” human settlement has increased in num-
ber and density. Given the presence of both a suitable
animal host and human conditions for tuberculosis
(TB) in humans, the question is posed as to whether
aDNA can conrm the commonly held view that this
disease was a form of Mycobacterium bovis in early
ruminant herds that “jumped” to human populations
during domestication?
Six samples of human bones from Israel (from
Karkur, Vered-Jericho, and Qasr el-Yehud) have been
tested for the presence of M. tuberculosis complex
DNA. Of these, ve were conrmed positive and two
were able to shed light on the broader issues of zoono-
ses and co-infection (Lev-Manor, 2002; Donoghue et
al., 2004). Spoligotyping, a method that distinguishes
bovine mycobacterium from human forms, was suc-
cessfully applied to a single sample of calcied pleura,
and in fact it was not of bovine origin, but clearly seen
to be M. tuberculosis, the human pathogen. Although
it is a singular sample, extensive studies of Egyptian
mummies (more than 40) have failed to reveal any
M. bovis (Zink and Nerlich, 2004). A most spectacular
sample from North America from an extinct bison also
turned out to be M. tuberculosis (Rothschild et al.,
2001). The absence of ruminant-to-human transmis-
sion has as yet not been studied in ancient samples. A
result from such research would support or reject the
nding of Baker et al. (2004), which indicates that M.
tuberculosis and M. bovis separated from a common
ancestor, and reinforces the evidence that M. tuber-
culosis could not have arisen from M. bovis, as previ-
ously thought (Brosch, 2002; Donoghue et al., 2004).
In the early nineties, Hershkovitz et al. (1991)
described a Pre-Pottery Neolithic C site at Atlit-Yam,
dated to 8,180–7,300 years BP. The rich, well-pre-
served nds of Atlit-Yam include botanical, faunal,
and human remains (Fig. 2). This is one of the earliest
sites where man and cows lived together. Since then,
a total number of 63 individuals were uncovered, with
M. Faerman et al. Molecular archaeology of the Holy Land 223
three of them showing bony lesions suggestive of tu-
berculosis. DNA of the tubercle bacillus was found in
all three individuals, with two of them being a mother
and child, as suggested by the mtDNA ndings. The
preliminary results of spoligotyping, which, as noted,
distinguishes between the human and the bovine tuber-
culosis organisms, suggested that it was of the human
type. So the transfer of TB from animal to human was
not observed, and in general this supports the concept
that TB evolved separately in man and beast (Roth-
schild et al., 2001).
In 1996 during the excavation of a Byzantine basil-
ica in the Negev Desert at Karkur, a fragment of what
appeared to be calcied tissue, possibly lung pleura,
was found in the chest cavity of the body of a male
aged 35–45 years, buried together with three other
skeletons (Fig. 3). No other lesions relating to TB were
noted on the remainder of the skeletal remains in this
grave. Indeed, none of the other 52 skeletons exca-
vated from this site manifested osseous lesions specic
to tuberculosis. DNA of the M. tuberculosis complex
was identied in this sample. Mycolic acids—lipid
products found in the cell walls of mycobacteria—
were also present in this sample and were found to be
specic to M. tuberculosis. It is believed this is the rst
example of M. tuberculosis DNA being detected in
non-mummied archeological tissue other than bone
with both the DNA and species-specic mycolic acid
being found (Donoghue et al., 1998).
2.1.2. Brucellosis
Brucella melitensis is the most important zoonotic
agent, followed by Brucella abortus and Brucella suis.
Worldwide, the control of bovine brucellosis (B. abor-
tus) has been achieved to a greater extent than the con-
trol of sheep and goat brucellosis (B. melitensis), the
latter two species being the most important domestic
animals in many developing countries (Godfroid et al.,
2005). This situation is probably similar to that which
human populations in the Southern Levant were facing
in the past. The decline in cattle and pigs in many of
the sites during the Early Bronze Age (Tchernov and
Horwitz, 1990) emphasizes the increased role of sheep
and goats as the main source for transmission of Bru-
cella at this time. In the Roman-Byzantine period the
pig population in the archaeological record increases
(Hesse, 1990; Grigson, 1995), and in many sites both
domestic pig and wild boar are represented together.
Brucellosis has several presentations: sub-clinical,
acute and sub-acute, relapsing, or chronic. The incuba-
Fig. 2. Atlit-Yam, a human burial at the sea oor. Note the fetal position of the skeleton and the excellent preservation of the
bones.
224 Israel Journal of Earth Sciences Vol. 56, 2007
tion period may be weeks to months. It may be mild or
an explosive, toxic illness. Symptoms are non-specic
and few localizing physical signs develop.
As we began to study ancient brucellosis, we
gained the impression that it is the most underrated and
unreported plague in the Middle East and the Mediter-
ranean. We have suggested that just as leprosy opens
the immunological “door” to tuberculosis; so may bru-
cellosis (Greenblatt et al., 2003). Morphologically the
bony changes are difcult to distinguish from tubercu-
losis. Ancient texts do not cover it to any degree. Not
a killer, like tuberculosis, and failing to be transmitted
by human contact, it has been ignored. One apparent
description of the disease is in Acts 28:7 to 10 (~70 ce)
where Luke, a physician, wrote about the healing of
the Chief Ofcial, Plubius, in Malta. Known vari-
ously as Maltese, Mediterranean, or relapsing fever,
the disease tends to chronicity and generally does not
kill (Greenblatt et al., 2003). Brucellosis can be con-
sidered as one of the rst zoonotic diseases starting in
the Neolithic period. The disease affected the health of
the community and probably had a profound impact on
diet due to the loss of meat and milk. Although it has
been present for the last 10,000 to 8,000 years, there is
no human vaccine for brucellosis and the occurrence
of brucellosis is directly linked to the status of animal
brucellosis in a region (Godfroid et al., 2005).
2.1.3. Leprosy
Of all the Biblical diseases described, none is so
widely known or misunderstood as the dermatological
conditions that are listed in Leviticus: 13–14 under the
term “tsara’ath”. The confusion surrounding the exact
meaning of the Hebrew term and its Greek translation
lepra from a historical, religious, and medical perspec-
tive has generated over the millennia a vast literature.
In 1992, Hershkovitz et al. reported a skeleton
from Bet Guvrin, Israel, dating from the Byzantine
period (300–600 years ce) with pathological changes
in the lower extremities, which presented signicant
diagnostic problems. Their original diagnosis was of
Madura foot, based on the absence of typical medul-
lary changes associated with osteomyelitis, and on the
presence of severely ankylosed and deformed bilat-
eral foot bones. However, in reply, Manchester (1993)
noted that Madura foot is usually a predominantly uni-
lateral condition, and that many of the surface changes
were consistent with secondary pyogenic infections
following plantar ulceration associated with leprous
peripheral neuropathy. There was evidence that at least
one joint was a typical Charcot’s joint suggestive of
the presence of some form of neuropathy. Manchester
(1993) noted that this skeleton was from the same
period as one reported by Zias (1985), which was the
rst ancient skeleton from which M. leprae DNA was
extracted and amplied (Ra et al., 1994). In a further
rejoinder, Hershkovitz et al. (1993) admitted that the
pathological features could t both Madura foot and
leprosy, but still considered Madura foot more likely.
Here the controversy rested. A few years later the
skeleton was examined for the species-specic DNA
Fig. 3. Karkur, a 35–45-year-old male burial. In the insert is
a fragment of calcied tissue, possibly lung pleura.
M. Faerman et al. Molecular archaeology of the Holy Land 225
of M. leprae (Donoghue et al., 2001). The authors con-
cluded that while there was no doubt that this patient
suffered from Hansen’s disease, at the same time they
could not exclude Madura foot on the basis of DNA
analysis since the causative agent could well have
been a common soil fungus and thus even by nding
DNA they could not conrm if this was a contaminant
or a causative organism.
In 2000, archaeologist Shimon Gibson discovered
a body in a rock cut cave dating to the Second Temple
period in the Hinom Valley directly opposite the Temple
Mount, Jerusalem. The burial was exceptional in two
ways: (1) it did not follow the traditional manner of
Jewish burial of the time, which entailed re-burial in os-
suaries, as attested to by all 32 other bodies found in the
same cave; (2) there was a preserved shroud intermixed
with the skeletal remains. This led to extensive scientic
research of the skeleton and the other remains found in
ossuaries in this family tomb. When the ‘Shroud Cave’
skeletons were rst recovered a fundamental question
was asked: Why, in an obviously important and pos-
sibly highly religious family, were the normal rituals
and burial practices not carried out on one particular
deceased, namely the one with the shroud.
Taking this in consideration, the bony material from
the Shroud Cave was initially tested for the presence
of M. tuberculosis and only subsequently for M. lep-
rae. The skeletal material exhibited lesions diagnostic
of infection. Thus, if any bacterial DNA was present
there had to have been septicemia at the time of death
in order for it to spread. Initial testing performed at the
Kuvin Centre of The Hebrew University—Hadassah
Medical School proved positive for TB, and this was
later conrmed in an independent laboratory by Helen
Donoghue at the Department of Medical Microbiology,
The Royal Free and UCL Medical Schools, UK. The
methods differed at the two laboratories, however the
results left little doubt that there was miliary TB pres-
ent in this skeleton at the time of death. The individual
from the Shroud Cave died of TB, but it was his leprosy
that probably prevented his reburial. As a result of this
nding, all previously positive cases of leprosy from
various area and periods were analyzed for the presence
of co-infection. The results showed that up to 30% of
patients with Hansen’s disease died of TB (Donoghue
et al., 2005), which has led to a new hypothesis for the
disappearance of leprosy in Europe. This suggests that
such double infections, in which tuberculosis kills the
leper whose immune system is suppressed, can explain
the demise of leprosy and leprosaria from Europe
(Donoghue et al., 2005). Other than the Shroud Cave,
all conrmed cases of leprosy in Israel are dated no
earlier than the Byzantine period.
2.2. Porotic hyperostosis and hemoglobinopathies
In archaeological skeletal remains, differential diag-
nosis of anemias using traditional anthropological
methods presents a certain problem since similar
bone lesions may have different etiologies. Thus, the
spectrum and actual prevalence of diseases in past
populations might be misinterpreted. Porous lesions
of the skull might be a result of genetic (b-thalasse-
mia, sickle-cell anemia) or acquired anemias due to
nutritional conditions (iron-deciency anemia, rickets,
scurvy) or even chronic infections (Ortner and Put-
schar, 1981). When a genetic cause is implied, most
severe changes are observed in the skull resulting
from increased spatial demands for the hyperplastic
erythropoetic marrow. Angel (1966) was the rst to
propose that osteoporosis and extreme thickening of
the diploe observed in skeletal remains of children
from the Bronze Age in Greece and Cyprus were the
result of thalassemia. Analysis of b-globin sequences
recovered from bone specimens with pathological le-
sions suggestive of anemia might provide direct proof
of the genetic mechanism causing the disease.
This approach was successfully applied to identify
a ß-thalassemia mutation in an archaeological speci-
men showing severe porotic hyperostosis from Akhziv
(Filon et al., 1995). Tel Akhziv, located 15 km north
of Acre, has been inhabited with only slight interrup-
tions for at least 4000 years. The region was infested
by malaria until the beginning of the 20th century.
Excavations of the Northern Phoenician cemetery
at Akhziv also revealed a number of unmarked later
intrusions and among them a skull of a child aged 7–8
years. The skull showed severe porotic hyperostosis
with extensive pitting of the cranial bones and cribra
orbitalia in the orbital roof. Moreover, X-ray and CT
ndings showed the cranial bones to be almost two and
a half times thicker (especially in the parietal region)
than that of other individuals of the same age. The re-
searchers suspected thalassemia major to have caused
such pathology and consequently the child’s death.
Indeed, the analysis of DNA retrieved from the bones
conrmed this suggestion by revealing a severe muta-
tion (FS8) in the β-globin gene of the child. Thus for
the rst time, Angel's hypothesis on the relationship
of porotic hyperostosis and thalassemia in skeletal re-
mains found in the Mediterranean region has received
a direct proof from the past.
226 Israel Journal of Earth Sciences Vol. 56, 2007
3. GENDER AND BURIAL CUSTOMS
Archaeological studies of gender differences, espe-
cially in regard to children, have been traditionally
explored through identication of grave goods con-
sidered indicative of female or male roles. Physical
anthropology expands the study of mortuary practices
through direct identication of sex, even when grave
goods are absent. The reliability of such analyses var-
ies with the condition of the bones. Using classical
morphometric analyses, it approximates 90–95% for
a complete adult skeleton. However, if the bones are
poorly preserved or those of infants or children, the re-
liability of sex identication from these methods falls
as low as 60% (Mays and Cox, 2000).
Technological innovations in molecular biology
have provided reliable methods for sex identication
in skeletal remains based on amplication of DNA
sequences specic to the X and Y chromosomes (Faer-
man et al., 1995; Brown, 1998). Population structure,
male and female status in past societies, and sex dif-
ferences in burial practices can now be attempted even
based on fragmentary skeletal remains as well as those
of infants and children. This approach gains even
greater importance in Israel where bone preservation is
poor and secondary burial with mixing of bones from a
number of different individuals is common. The stud-
ies summarized below exemplify how the attitude of
society towards infants and children and the extent to
which it was inuenced by the sex of the child can be
approached using aDNA analyses.
To clarify a possible cause of infanticide in nearly
100 infants found in a sewer of a small bathhouse built
over earlier Roman villas at Ashkelon, Faerman et al.
(1997, 1998) analyzed DNA of 43 of them. Earlier,
Patricia Smith and Gila Kahila (1992)—based on the
casual mode of disposure, absence of disease signs or
skeletal malformation, and the large number of indi-
viduals aged close to birth—suggested that the remains
might have been those of the victims of infanticide.
Both in ancient and modern societies more daughters
than sons were selected for infanticide; therefore, the
researchers expected that the Ashkelon bones would
have been of females, but the results showed that infants
of both sexes were present: 14 males and 5 females (the
rest of the bones did not contain ampliable DNA).
This unusually high ratio of males to females—almost
3 to 1—raised the intriguing possibility that the infants
in the sewer were the unwanted offspring of courtesans
working in the bathhouse, with some female infants
kept and raised as future replacements in the profes-
sion. This hypothesis was also supported by the linkage
of baths with prostitution previously emphasized by the
classic authors and by the entire archaeological context
including a room full of oil lamps decorated with erotic
images and a signpost “Enter, enjoy, and …” placed by
the owner at the entrance (Stager, 1991).
At Tel-Teo in the Huleh Valley, unlike in Ash-
kelon, ten infants aged from birth to 3 months were
found carefully buried in jars or under potsherds
beneath house oors. Five of these when subjected to
DNA-based sex identication provided consistent re-
sults—all being male (Smith et al., 1999). This nding
suggests that special treatment might have been given
to male infants.
During the 1995 season at Tel Beit Shean, a Middle
Bronze Age skeleton termed “Marcia” by the team,
was located close to the southern boundary. It belonged
to an 8-year-old child. Two pairs of gold earrings were
found associated with the skull, thus allowing the ar-
chaeologists to refer to the child as “she”. A gold ring
containing an amethyst scarab was also found together
with two alabaster jars, all showing strong Egyptian
inuence. A second skeleton, of a similarly aged child,
was found in close proximity.
DNA recovered from the teeth was analyzed for
the human nuclear and mtDNA sequences and for
the presence of M. tuberculosis in order to identify
the sex, ethnic origin, and possible cause of death of
the children (Mazar et al., 2002). The genetic ndings
showed that despite the earrings, the “Marcia she” ap-
peared to be male. According to the authors’ hypoth-
esis, the burial might belong to a prince who would
naturally have been given a richer burial than would
a princess. The second child was also male. mtDNA
sequences indicated that these two children were most
likely maternally unrelated. Moreover, the presence of
a certain African variant in the boys’ DNA allowed the
researchers to suggest an African and not Levantine
origin of both individuals.
4. SUMMARIZING REMARKS
We have so far only scratched the surface, both liter-
ally and guratively, of the molecular archaeology of
the Holy Land. The work is only beginning. So far,
technological innovations have been minimal since the
polymerase chain reaction was invented. Yet we are
now encouraged by the knowledge that new technolo-
gies, such as metagenomic sequencing, will enable us
to retrieve DNA sequences at a level we never thought
was possible.
M. Faerman et al. Molecular archaeology of the Holy Land 227
We are now able to ask serious questions and arrive
at denitive answers. We should be able to construct ge-
netic databases of ancient populations similar to those of
modern ones. Only now has one begun to tap the genet-
ics of domestication of plants and animals, and we are
certain that new ndings regarding these critical events
will help us to understand what was indigenous, what
was imported, and what was exported. Understanding
the trade and commerce will put a human imprint on the
material culture that cries out to be understood.
Analysis of ancient pathogens may shed light on
population decline and re-emergence. Here we have
only seen rare cases of tuberculosis and leprosy. The
co-infection of these two diseases led us to new in-
sights regarding their interaction at much later periods
of history. Yet malaria, leishmaniasis, and brucellosis
endemic presently or in the recent past must have left
their footprints in bones found in ancient Israel. Plague
should also have made its presence felt in the armies of
Napoleon, as well as in those of other invaders. Many
more insights into the present are still waiting for their
discovery in the past.
ACKNOWLEDGMENTS
We gratefully acknowledge the generosity of the
Horowitz Foundation. In the very beginning of these
studies they had the foresight to support a very risky
venture both at the research level and also in promot-
ing the eld through workshops and conferences. Now
that substantial results are in hand, they have helped us
create ESHMOR, an all-Israel program to develop the
conservation sciences through training and research.
We are also indebted to Maria Ines Zylber for her help
in editing this article.
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