Journal of

Archaeological
SCIENCE
Journal of Archaeological Science 30 (2003) 629–635
http://www.elsevier.com/locate/jas

Short survey

Ancient DNA in pre-Columbian archaeology: a review

Martin Jones
Department of Archaeology, University of Cambridge, Downing Street, Cambridge CB2 3DZ, UK
Received 13 September 2001; revised 30 July 2002; accepted 20 August 2002

Abstract

Ancient DNA research from its inception in the 1980s is reviewed in the context of pre-Columbian archaeology. Changing
approaches to the recovery of DNA from human remains are followed, and the accumulated records considered in the light of
hypotheses about the post-Columbian depletion and augmentation of the New World gene pool.
 2003 Elsevier Science Ltd. All rights reserved.

Keywords: Ancient DNA; Molecular archaeology; New World

1. Introduction still debate and disagreement about what constitutes a

The detection of ancient DNA has been recorded
in publications spanning the last two decades (cf.
Refs. [27,77]). From the late 1980s the potential of the
polymerase chain reaction (PCR) brought wide recog-
nition to the potential of ancient DNA science [52]. The
past two decades have seen a wide range of publications
reporting ancient DNA from New World specimens,
particularly from pre-Columbian human remains.
Ancient DNA from the New World has also been
identified and studied from other species, including such
domesticates as the dog [38], various camelids [67] and
maize [15], various megafauna including mastodon [80],
ground sloth [29,60], bears [4,39] and such bacteria as
the source of trypanosomiasis [19] and tuberculosis
[2,64], and the benign gut bacterium Clostridium [73].
It is not only ancient DNA science that has been
experiencing rapid growth. That growth has been in the
context of equally rapid changes in the interface between
archaeology and modern genetics [61], and in genetics
itself, fast transforming the kind of questions that might
be addressed by ancient DNA, and indeed the niche of
ancient DNA within a wider archaeogenetic endeavour.
It is also the case that ancient laboratory protocol and
awareness of the problems of contamination have
changed significantly over the period (cf. Refs.
[11,33,55]). All these issues, and in particular the final
issue, might constrain the possibilities of reviewing
the accumulated body of ancient DNA data. There is
0305-4403/03/$ - see front matter  2003 Elsevier Science Ltd. All rights reserved.
doi:10.1016/S0305-4403(02)00239-X
rigorous protocol for the secure identification of an
ancient sequence. A number of the earliest claims for
ancient DNA, including those published in established
journals, have subsequently been queried. A number of
reports of ancient DNA have yet to be replicated or fully
published in refereed journals. For these reasons, the
review attempted here is presented within a historical
framework, following the different episodes and the fast
changing context of molecular archaeology, with an
awareness of the caveats surrounding the various
records of ancient DNA.
2. Pioneer studies
In retrospect, we can see that the first aDNA analyses
were working under two misconceptions. The first of
these was that if DNA survived, it would be confined to
specimens in which the preservation, particularly of soft
tissue, was remarkable. The second was that, where such
remarkable preservation was encountered, the DNA
might survive indefinitely.
The first misconception steered attention to speci-
mens from extremes of wet and dry contexts, where
decay was visibly constrained, and to some rather par-
ticular specimens such as those embedded in amber [7,8].
In terms of human remains, these extremes of wet and
dry steered research towards two key groups. The key
‘wet’ group was a series of geological sinkholes in
630 M. Jones / Journal of Archaeological Science 30 (2003) 629–635
Florida in which archaic bodies had been placed
[25,26,36,58,66]. The most prominent of these was the
Windover Pond, yielding over 170 bodies, of which
preservation was so extreme that in over 50% of cases,
intact brains were recovered. The key ‘dry’ group was
the series of South American mummies, such as those
of the Chinchorro group, preserved by the intensely
desiccating conditions of the Atacama desert along the
Chilean coast [1,2,28,63]. Another series of arid speci-
mens that formed part of early studies were the ancient
cobs of central and South America studied by
Goloubonoff et al. [15]. One notable feature of this
maize study was the attempt to test the reliability of a
molecular clock. This avenue of ancient DNA research
has received little attention, the majority of subsequent
analyses being aimed instead at recovering evidence of
lost genetic diversity.
Each of these data-sets appeared to contribute some
archaeologically non-trivial information. However, they
may not have been drawn from the most appropriate
materials for study. In soft issue, the wide range of
complex organic molecules that persist may actually
inhibit DNA amplification. This is illustrated, for
example, by the lack of success in amplifying DNA from
South American camelids, which in physical terms are
among the best preserved specimens in the archaeologi-
cal record (cf. Ref. [67]). It is also illustrated by the fact
that neither the South American mummies, nor the
bodies from the Windover Pond, have generated any-
where near the amount of sequence data as the more
conventional skeletal remains at Norris Farm (see
Table 1 for details). Furthermore, none of the context
discussed above is ideal in terms of temperature con-
ditions. This is because the main problems of DNA
preservation are chemical rather than biological, a point
elaborated in papers by Tomas Lindahl [40,41,42]. Small
increases in temperature significantly affect the rates of
relevant chemical breakdown reactions (cf. Ref. [10]).
Following Lindahl’s papers on the chemical kinetics of
DNA, the time frame for DNA analysis shifted to the
last 100,000 years in cold environments, shorter in
warmer regions. If DNA persisted at all within this
shortened time period, it could survive in such common-
place bio-archaeological materials as bone, teeth and
seeds [5,20,46]. Furthermore, the series of positive am-
plifications from geological specimens, now seen to be
spurious, have heightened the need for controls against
contamination in younger specimens, controls that have
proved to be only variously in place [11].
3. The progress of routine analyses
With the realisation that DNA could survive in
microsites within ordinary bio-archaeological materials,
amplifications have come to be reported from over
400 pre-Columbian human skeletons, contributing to a
palaeogenetic data-set that now spans from the far north
to the far south (Table 1). A further 300 pre-Columbian
samples from three human burial sites in North, Central
and South America, respectively, have been analysed by
Merriwether and colleagues, but have yet to proceed to
full publication. Preliminary reports would suggest a
haplotype distribution consistent with the patterns
reported here [44,48] (Fig. 1). These research pro-
grammes proceeded in an environment of optimism
about what could be achieved, and research goals
ranged between global issues, such as the colonisation of
America, to more local issues such as the spread of
ethnic groups, and the kinship structure of particular
communities. While this research in ancient DNA was
progressing, so were two other intimately related fields;
the genetic make-up of living indigenous Americans, and
the genetic make-up of the human species as a whole.
4. The colonisation of America
In the same year that Pääbo [57] first published a
DNA sequence from an ancient human specimen,
Wallace et al. [76] published his findings that living
indigenous Americans constituted a very restricted
portion of the mitochondrial evolutionary tree, itself fast
emerging after the publication of the full mitochondrial
sequence 4 years earlier. Wallace recorded just four
particular mitochondrial haplotypes, labelled A,B,C and
D, that seemed to account for all the diversity of
recorded indigenous populations. An early goal of
ancient DNA research was to establish whether this
four-haplotype pattern reflected an ancient pattern, or
whether it was a modern phenomenon, reflecting post-
contact genocide rather than initial colonisation. It soon
became apparent that the pre-Colombian populations
were not throwing up a series of ‘extinct’ haplotypes for
the mitochondrial regions studied. Indeed, at first less
haplotypes were turning up, as the ancient specimens
seemed to be restricted to A, C and D [28,45,58,63].
The apparently missing haplotype B was also
enigmatic in modern populations. It was the one major
haplotype absent along the presumed ancient route into
America, across the dry land that once linked Siberia
and Alaska (cf. Ref. [47]). Haplotype B occurred on
both sides of the Pacific Ocean, but at fairly southerly
latitudes, prompting the possibility of a later colonis-
ation by sea, the B group coming across from the Pacific
islands. In fact, this was a fairly short-lived hypothesis.
It was eventually amplified from individual from South
American mummies [49,51]. Most decisively, Stone
and Stoneking [69] amplified the B sequence from
an 8000-year-old hunter–gatherer from the Rocky
Mountains, which is generally considered too early for
the relevant boat technology for a Pacific crossing. The
current position is that, not only are the principal
mitochondrial haplotypes found in living indigenous
Table 1

M. Jones / Journal of Archaeological Science 30 (2003) 629–635

DNA sequence data from pre-Columbian human DNA

Site Reference: (brief interim reports and review articles in italics) Age (kya) Successful amplifications claimed Haplotypes
Aleutian islands Hayes, 1998 [21]; Hayes et al., 2002 [23]; O’Rourke et al., 2000 [56] <4 16 A,D
Hudson Bay Hayes, 1999 [22]; Hayes et al., 2002 [24] <2 42 A,D
Great Basin Kaestle, 1997 [30]; Kaestle and Smith, 2001 [32]; O’Rourke et al., 2000 [56] 1–9 40 A,B,C,D
Fremont, Utah Parr et al., 1996 [59]; O’Rourke et al., 2000 [56] 1–2 32 B,C,D
Anasasi, South-West Carlyle et al., 2000 [9] 1–2 27 A,B,C
Norris Farm, Illinois Stone and Stoneking, 1993, 1996, 1998 [68–70] 0.7 108 A,B,C,D,X
Windover Pond, Florida Hauswirth et al., 1994 [25,26]; Smith et al., 2002 [66] 7–8 20 A,B,C,D,X
Xcaret, Yucatán González-Oliver et al., 2001 [16] 0.5–1.4 25 A,B,C
La Caleta, Dominican Rep. Lalueza-Fox et al., 2001 [35] 0.5–1.3 24 C,D
Copán, Honduras Merriwether et al., 1997 [48] 1 9 C,D
Boyaca and Santander, Colombia Monsalve et al., 1994, 1996 [50,51]; Monsalve, 1997 [49] 0.15–1.5 8 A,B,C
Para, Brazil Ribeiro-dos-Santos et al., 1996 [62] 4 26 A,B,C,D,X
Chilean Andes Horai et al., 1993 [28]; Rogan and Salvo, 1990 [63] 0.5–4 12 A,C,D
Tierra del Fuego Lalueza-Fox, 1996 [34] <5 60 C,D
Sites are listed in broad geographical terms, from the Bering Straits to the southern tip. The Haplotype designations follow Torroni et al. [72] for A, B, C and D, and Brown et al. [6] for
X. In the source publications, Hauswirth et al. [25,26] follow the I–IV classification of Ward et al. [78] and Ribeiro-dos-Santos et al. [62] follow the I–V classification of Horai et al. [28]. For a
discussion of the correspondence between the three systems, see Bailliet et al. [3]. For simplicity, here and in Fig. 1, all are expressed within the A–D, X notation. Note also that elsewhere, the
notation ‘X’ has been attributed in various ways, but here and in Fig. 1 specifically follows that of Brown et al. [6].

631
632 M. Jones / Journal of Archaeological Science 30 (2003) 629–635
Fig. 1. Distribution of ancient DNA haplotypes across America. See
Table 1 for data sources.
populations the same as the four haplotypes recorded in
pre-Columbian specimens, their biogeography is also
broadly similar (cf. Ref. [56]).
Closest to the northern land-bridge, along the
Aleutian Island chain Hayes [21] recorded haplotypes A
and D in the same proportions (1:3) in ancient skeletons
as in modern skeletons, and in Hudson Bay, Canada, a
slightly more complex patterning of A and D in ancient
and modern specimens was also reported [22,24]. At
the other geographical extreme, ancient DNA amplifi-
cations from the southern tip of America in Tierra del
Fuego, fell almost exclusively into haplogroups C and D
[34]. In more central latitudes, all four haplotypes
may be found together. The pronounced north–south
patterning of haplotypes has been recorded from
modern and ancient specimens alike.
Following Wallace’s work and the series of pro-
grammes it stimulated, there has been growing interest in
rarer haplotypes, beyond the original four, found in some
living populations. Some have argued for 10 or more
founder haplotypes [12,47]. One such rare haplotype that
raised once again the possibility of a later ancient episode
of immigration was labelled haplotype ‘X’ [6].
5. The ‘European’ haplotype X
Only 75% of living members of the Ojibwa, who live
around the Great Lakes region of North America, are of
the principal four haplotypes [6]. The remainder belongs
to a distinctive haplotype X that, like haplotype B, is
now absent from the original route into America [13].
Furthermore, it seemed until recently to be absent from
the entire Asian continent, and found only in America
and Europe. Around the time of its recognition, interest
in a possible ancient immigration from Europe was
further stimulated by the recovery of ‘Kennewick Man’,
a pre-Columbian skull displaying some supposedly
‘European’ features. No DNA has yet been securely
detected from the Kennewick specimen, and further
scientific analysis is a matter of some political contention
[31,43,65]. However, amplifications of Haplotype X
started coming to light from the ancient record, most
clearly form an Oneota cemetery at Norris Farm,
Illinois, a few hundred kilometers to the south of where
the Ojibwa live today [68,70,71]. The Norris Farm site is
dated to AD1300, and this in itself does not preclude an
earlier influx from the direction of Europe. Sequences
attributable to haplotype X have also been amplified
from 4000-year-old burials from Pará in Brazil [62], and
8000-year-old bodies from the Windover Bog in Florida
[25,26,66], making its presence as part of the original
influx more plausible.
Current models of American haplotype geography
emphasise the influence of global climatic patterns
rather than the series of distinct ‘journeys’ that charac-
terised earlier arguments (cf. Refs. [17,18,75]). For
example, Forster et al. [13] argue for climatic oscillation
and ecological depletion on both sides of the Pacific,
leading to the current zonations and restricted distri-
butions of haplotypes B and X. While the journey-based
arguments brought to mind small intrepid groups com-
pleting a hazardous passage, Forster’s model is consist-
ent with the idea of a more stable, long-standing human
population in the ancient Holarctic region which is
emerging from other sorts of evidence (cf. Ref. [79]),
including DNA from non-human species.
6. Local studies: kinship and local movement
The studies considered earlier usually addressed
broad issues of New World colonisation by references to
the presence or absence of particular haplotypes. A
smaller number of more intensive studies have opened
up the possibility of elucidating human demography at a
more local scale. Most notable are the analyses by Stone
and Stoneking [68,70,71] of the Oneota cemetery from
Norris Farm, Illinois. As mentioned previously, these
analyses provide the clearest pre-Columbian evidence
for all four Wallace haplotypes and Brown’s ‘X’. They
further reveal mitochondrial diversity in greater detail,
allowing the authors to examine in depth phylogenetic
relationships between American and Asian populations.
Examination of variation within the mitochondrial con-
trol region indicated that, although the overall pattern
 M. Jones / Journal of Archaeological Science 30 (2003) 629–635
of Wallace haplotypes has remained intact, there does
appear to have been discernible reduction in genetic
diversity since AD1300.
The authors also explore kinship patterns and the
spatial organisation of the cemetery. As is typical of
studies in the mid-1990s the work targets the mito-
chondrial sequence, with a consequent emphasis on the
maternal line. The high mitochondrial diversity within
the group would be consistent with a patrilocal com-
munity, and one might anticipate a lower diversity
within the male lines. The most promising kinship
studies from ancient DNA now combine these with Y
microsatellite studies (cf. Refs. [37,74]), providing the
equivalent information about the paternal line (cf. Ref.
[14]).
A further series of ancient DNA studies have been
aimed at relating the geography of a local pattern of
material culture traditions with demographic history.
One such study involves two major cultural groups of
the Western United States, the Anasasi of the Colorado
Plateau and the Rio Grande, and the Fremont of the
Eastern Great Basin directly to the north. Around 30
amplifications each were achieved, respectively, for the
Anasasi [9] and the Fremont [59]. From comparisons
between the two the inference was drawn that the two
cultures shared a relatively recent common ancestry, but
had become sufficiently genetically isolated to accumu-
late distinctive haplotype signatures. In a connected
project, Kaestle and Smith [32] extended the northern
survey to explore the Numic expansion hypothesis.
Drawn from historical linguistics, this hypothesis argues
that the Great Basin experienced a significant popu-
lation replacement within the last thousand years.
Essentially, the ancient DNA samples were compared
with those of living indigenous Americans from that
region, with the conclusion that living and recent
Great Basin Americans did indeed contrast with earlier
inhabitants of the area.
A comparable project has been conducted in Arctic
Canada, exploring the relationship between the whaling
Thule Culture that expanded eastward across the region
between the 9th and 12th centuries AD, and fishing/
sealing Dorset Culture of the Eastern Arctic that corre-
spondingly shrunk [22,24]. All three Dorset Culture
individuals amplified were of haplotype D, whereas all
20 Thule Culture individuals amplified were of haplo-
type A. The more recent, protohistoric Sadlermiut
Culture, thought by some to have its roots in the Dorset
Culture, displayed a mix of A and D. Hayes et al. [24]
infer that the Sadlermiut may indeed derive from the
Dorset, with significant introgression from the Thule.
While outside the immediate scope of this review, studies
of ancient DNA from Siberian skeletal remains have
similarly indicated population replacements in later pre-
history, with a significant impact on haplotype patterns
[53,54].
633
7. Summary
Reports of ancient human DNA from New World
specimens have spanned almost the entire history of
ancient DNA science. As such, they have passed through
a series of episodes reflecting the history of that science.
They have moved from an early focus upon rather
particular specimens such as the Florida brains and
Chinchorro mummies to a series of more commonplace
teeth and bones. There is still some difficulty in establish-
ing which records should still be considered scientifically
robust, particularly in the case of the earlier publications
that preceded currently accepted ancient DNA protocols.
Nonetheless, the accumulated data from pre-Columbian
humans are genetically and geographically plausible and,
taken as a whole are informative, even if it transpires they
may contain a few rogue amplifications in their midst.
What they collectively indicate is an ancient population
broadly mirroring the haplotype geography of surviving
Amerindian populations, and not requiring a combination
of later prehistoric sea journeys to explain the geographi-
cally restricted haplotypes. The more recent studies are
revealing a potential to situate, within this broader picture,
local patterns of demographic change, from regional popu-
lation movement through to the kinship and residence
patterns at the heart of human demographic process.
Acknowledgements
I am most grateful for the assistance and information
on ongoing research provided to me by Peter Forster,
Bill Hauswirth, Geoff Hayes, Rika Kaestle, Andy
Merriwether, Dennis O’Rourke and Anne Stone, and
for the invaluable comments of anonymous reviewers
of the original draft. Responsibility for any errors of
synthesis and interpretation rest with me.
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