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Ancient genomics
rstb.royalsocietypublishing.org
Review
Cite this article: Der Sarkissian C et al. 2015
Ancient genomics. Phil. Trans. R. Soc. B 370:
20130387.
http://dx.doi.org/10.1098/rstb.2013.0387
One contribution of 19 to a discussion meeting
issue ‘Ancient DNA: the first three decades’.
Subject Areas:
evolution, genomics
Keywords:
ancient DNA, genomics, next
generation sequencing
Author for correspondence:
Ludovic Orlando
e-mail: lorlando@snm.ku.dk
Clio Der Sarkissian, Morten E. Allentoft, Marı́a C. Ávila-Arcos, Ross Barnett,
Paula F. Campos, Enrico Cappellini, Luca Ermini, Ruth Fernández,
Rute da Fonseca, Aurélien Ginolhac, Anders J. Hansen, Hákon Jónsson,
Thorfinn Korneliussen, Ashot Margaryan, Michael D. Martin, J. Vı́ctor MorenoMayar, Maanasa Raghavan, Morten Rasmussen, Marcela Sandoval Velasco,
Hannes Schroeder, Mikkel Schubert, Andaine Seguin-Orlando, Nathan Wales,
M. Thomas P. Gilbert, Eske Willerslev and Ludovic Orlando
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
The past decade has witnessed a revolution in ancient DNA (aDNA) research.
Although the field’s focus was previously limited to mitochondrial DNA and a
few nuclear markers, whole genome sequences from the deep past can now be
retrieved. This breakthrough is tightly connected to the massive sequence
throughput of next generation sequencing platforms and the ability to target
short and degraded DNA molecules. Many ancient specimens previously
unsuitable for DNA analyses because of extensive degradation can now
successfully be used as source materials. Additionally, the analytical power
obtained by increasing the number of sequence reads to billions effectively
means that contamination issues that have haunted aDNA research for
decades, particularly in human studies, can now be efficiently and confidently
quantified. At present, whole genomes have been sequenced from ancient
anatomically modern humans, archaic hominins, ancient pathogens and
megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and
admixture patterns. As such, the field of aDNA has entered the new era of
genomics and has provided valuable information when testing specific
hypotheses related to the past.
1. The impossible genome
Ancient DNA (aDNA) research is full of surprises. Less than a decade ago, most
experienced aDNA researchers believed that full genome sequencing of extinct
species such as the woolly mammoth and Neandertals was impossible. The
best available technology at the time was incredibly demanding in terms of
fossil material, experimental work load and cost. First, each piece of target genomic DNA had to be amplified several times by PCR, then ideally PCR amplicons
had to be propagated using bacterial vectors, and a number of clones had to be
sequenced before a consensus sequence devoid of sequencing errors could be generated [1]. Furthermore, this whole procedure often needed to be replicated in
another laboratory, before DNA sequences could be considered authentic [2].
The size of PCR amplifiable fragments was most often limited to approximately 100–150 base pairs (bp) at best, which represented little sequence
information. With exceptionally well-preserved samples, the characterization of
the whole approximately 16.5 kilobases (kb) of mitochondrial genomes [3–5]
could be achieved using overlapping amplicons [6], but nuclear markers [7,8]
were more difficult to amplify owing to their lower copy number per cell. Considering usual aDNA concentrations, each microlitre of DNA extract yielded one PCR
amplicon at best. Therefore, it was generally necessary to destructively sample
large amounts of fossil material to sequence complete mitochondrial genomes.
The sequencing of the cave bear mitochondrial genome required for instance
& 2014 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution
License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original
author and source are credited.
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An alternative approach consisted of shotgun sequencing following aDNA ligation into bacterial plasmids [13,14]. This
could be done at large sequencing centres, though with two
major limitations. First, most of the sequences generated in
fact do not originate from the organism of interest, but
from environmental microbes that colonize the tissue after
deposition. Therefore, no more than 26.9 kb of the cave
bear genome could be reconstructed with this approach
from a total of 14 027 sequences [13]. The second limitation
was the heavy experimental load required for bacterial cloning.
The invention of ‘emulsion PCR’, whereby each DNA library
template is amplified in a water–oil emulsion droplet, and
the development of the 454 platform provided a time-effective
alternative to bacterial cloning by processing hundreds of
thousands of sequencing reactions in parallel [15]. Applied to
DNA extracts from an approximately 28 000 years (28 kyr)
old mammoth bone sample, this technology provided, in a
6 h long run, 28 megabases (Mb) of metagenomic data, of
which approximately 13 Mb belonged to the mammoth
genome [16]. This demonstrated for the first time that
sequencing of complete mammalian genomes was probably
achievable from realistic amounts of bone material.
The field improved further, with the realization that
hair constitutes a remarkable source of high-quality aDNA
[17,18] that could be subjected to efficient decontamination
procedures [19] inapplicable to bones. Deep sequencing of
DNA from ancient mammoth hair yielded approximately
80% of sequences identified as being of mammoth origin
[20], thus providing a first draft covering approximately
70% of the mammoth genome, with an overall sequencing
error rate estimated at 0.345%. These data revealed that
99.4% of the sequenced mammoth genome was identical to
the African elephant genome and identified 29 mammoth
genes with specific non-synonymous mutations of potential
functional importance. Testing this list of gene candidates
following the methodology that revealed the association
between an allelic variant at the MC1R gene and blond
coat-colour [9] could illuminate our understanding of the
genetic make-up of mammoths.
2
By the time the first draft of the mammoth genome was
characterized, new sequencing technologies with higher
throughput were available [21]. The Illumina Genome Analyzer II platforms could generate 180 million sequence reads
per run. This massive sequencing throughput, combined
with the high endogenous DNA content of hair, and preservation in a cold environment made the sequencing of the first
ancient human genome possible. The individual sequenced
was a palaeo-Eskimo belonging to the Saqqaq culture, who
lived along the southwestern coast of Greenland 4 kyr ago
[22]. The sequence information gathered represented an average depth of 20-fold across 79% of the genome and led to the
identification of a large catalogue of high-confidence single
nucleotide polymorphisms (SNPs), some of which not only
confirmed his hair colour but also showed that he was of
the Aþ blood type and most likely had brown eyes, dry
earwax, as well as a metabolism and body mass index
adapted to cold climate. ADMIXTURE [23] and principal component analysis [24] of the SNP information indicated no
affinity with modern-day Europeans, thus ruling out possible
contamination, a problem that had plagued ancient human
DNA studies for decades [25], as well as attempts at sequencing the Neandertal genome a few years earlier [26,27].
Analyses also revealed a much closer genetic affinity with contemporary Chukchis and Koryak populations of northeast
Siberia, than with present-day Greenlandic Inuit. Divergence
times with the Chukchi population closely matched the radiocarbon date for the ancient individual, suggesting that the
Saqqaq ancestors entered Greenland soon after they separated
from their Old World relatives and were later replaced by the
ancestors of modern-day Inuits. This study demonstrated
the immense potential of palaeogenomics towards reconstructing the population history of humans in much greater detail
than what can be achieved from patterns of modern genomic
variation alone.
A recent re-analysis of the Saqqaq sequences also revealed
epigenomic signatures indicative of gene expression. Sequence
depth variation showed a strong approximately 200 bp periodicity, which is characteristic of the length of one nucleosome and
spacer block [28]. Within a shorter range, a 10 bp periodicity corresponding to the size of a DNA helix turn was also detected,
reflecting preferential cleavage of the DNA backbone that
faces away from nucleosome protection. Importantly, patterns
of sequence depth variation at known nucleosome arrays
showed strong correlations with nucleosome occupancy. It
therefore seemed that in addition to the DNA sequence, the
compaction state of the chromatin could survive in fossils, and
that variation in read depth, corrected for base compositional
bias, could be used as a footprint of nucleosome protection to
reconstruct genome-wide nucleosome maps. Regional methylation levels could also be tracked in the Saqqaq genome
sequence owing to the fact that it had been obtained by amplifying DNA libraries using a polymerase that amplifies cytosines
deaminated due to post-mortem damage only when methylated [29–31]. Focusing on read starts, where deamination
rates are highest, estimated methylation levels were found
to recapitulate known genomic patterns at different classes of
CpG promoters, splice sites and CTCF transcriptional repressor
sites. Strikingly, the Saqqaq methylome also appeared closer to
that of modern hair than to other somatic tissues. As nucleosome occupancy and cytosine methylation influence gene
Phil. Trans. R. Soc. B 370: 20130387
2. Shotgun sequencing of the first ancient
mammalian genome
3. The first ancient human genome
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1 g of bone material and not less than 570 PCR amplicons [5].
Assuming approximately 3 gigabases as the size of the nuclear
genome and similar PCR success rates for mitochondrial and
nuclear templates, this technology would have required
approximately 180 kg of material and more than 103 million
amplicons to generate a first draft of the cave bear genome.
Given standard PCR and sequencing times, even on platforms
with the highest throughput at the time (384 reactions per run),
this would have required approximately 48 000 years of experimental work, excluding the time required for cloning! The
characterization of even the best-preserved woolly mammoth
specimens would have required similar efforts [4]. Tworound multiplex reactions [9], whereby a set of PCR targets
are co-amplified from the same microlitre of DNA extract,
could help reduce material and time requirements by one or
two orders of magnitude [10,11], but operational costs would
still amount to billions of US dollars. In summary, this technology limited palaeogenomics to the shorter ancient microbial
genomes [12].
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Recent mixed ancestries among modern human groups can
limit our ability to infer their true past population history.
Following the sequencing of the Saqqaq genome [22], a variety
of ancient human genomic studies have shed light on major
events in the human population history [34–41]. Of key importance, post-mortem DNA damage patterns and heterozygosity
levels observed in the mitochondrial genome [42], or on the
X-chromosome of male individuals, have provided robust
approaches to rule out modern contamination.
Using 600 mg of hair collected in the 1920s from an Aboriginal Australian male, Rasmussen et al. [34] were able to
reconstruct his genome at 6.4-fold coverage and found no evidence for recent European admixture or contamination.
Genomic affinity was revealed with present-day Aboriginal
Australians, as well as Bougainville and New Guinea Highland
Papuans. More importantly, being the first Aboriginal Australian genome sequenced, this dataset allowed for the testing of
two alternate models of modern human dispersal into eastern
Asia. A statistics based on quartet genome alignments (D4P)
showed an excess of genomic sites in support of a population
tree where Aboriginal Australians and Africans cluster together,
separate from Europeans and Asians. Population split times
suggested that Aboriginal Australians separated from the
ancestral Eurasian population around 62–75 kyr ago, which in
turn radiated into the European and Asian branches some
25–38 kyr ago. These results favour the hypothesis of the ‘multiple dispersal’ model [43], which was also supported by the
excess of shared derived alleles observed between Asians and
Aboriginal Australians, reflecting population migration from
the mainland. By contrast, the Australian Aboriginal genome
lent little support to the alternative ‘single dispersal’ model proposing that humans expanded out of Africa into Eurasia 50 kyr
ago [44] through a series of founder events, which ultimately
gave rise to the colonization of Australia and the diversification
of Aboriginal Australian populations.
Ancient human genomic data has also shed light on
another fiercely debated topic in anthropology, namely the
peopling of the Americas. Genomic signatures of an Upper
Palaeolithic (approx. 24 kyr ago) male juvenile excavated at
the Mal’ta site, south central Siberia, Russia revealed no
strong connection with present-day eastern Asians [39]. Treebased analyses of population splits and admixture events
(TREEMIX [45]) instead placed the Mal’ta specimen basal to western Eurasians and identified gene flow from Mal’ta to Native
Americans. Shotgun sequencing of another individual from
the same region and dating to post-last glacial maximum
(LGM; 17 kyr ago) showed a strong affinity with the Mal’ta
specimen, suggesting that the population’s gene pool was
rather stable during the LGM, and consequently, that the
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Phil. Trans. R. Soc. B 370: 20130387
4. Ancient anatomically modern humans
populations from the region changed within the last 17 kyr.
The western Eurasian component of the Mal’ta specimen
suggests that Upper Palaeolithic populations ancestral to present-day western Eurasians had a distribution range that
extended further northeast. This is consistent with the discovery of a number of anthropomorphic Venus figurines at
the Mal’ta site, reminiscent of Upper Palaeolithic sites in
western Eurasia. Interestingly, no particular genetic affinity
was detected between present-day western Eurasians and a
40 kyr old individual excavated at the Tianyuan cave in north
east China [38], confirming that the results were not affected
by recent events in the population history of modern eastern
Asians. The contribution of the Mal’ta lineage to the Native
American gene pool gives further support to the hypothesis
of a Siberian origin for present-day Native Americans, and
the gene flow between Mal’ta and the ancestors of 52 Native
American populations from Greenland to southern Chile was
estimated to be responsible for 14–38% of the current Native
American ancestry. This gene flow occurred before 12.6 kyr,
which is the age of a child excavated at the Anzick site, Montana, USA, whose genome also revealed a ‘Mal’ta-like’
component [40]. The Anzick child belonged to the Clovis culture, the oldest archaeological complex in North America,
and was part of a meta-population directly ancestral to all contemporary Native Americans outside of Canada and the
Arctic. Overall, it appears that the ancestors of present-day
Native Americans were the descendants of at least two population backgrounds, one related to the Mal’ta individual,
showing a western Eurasian affinity, and another related to present-day eastern Asians, as suggested by the strong eastern
Asian genetic component found among Native Americans
[46]. This new model for the origin of Native Americans potentially solves the mystery surrounding the presence of non-east
Asian morphological features in the skulls of the first
Americans.
Ancient genomics has also provided invaluable clues to
understand the complex genetic make-up of Europeans.
The genome of a 5.3 kyr old Copper Age ‘Tyrolean Iceman’
revealed genetic discontinuity with current inhabitants of
the Alps, with the Iceman showing a greater genetic affinity
with southern European populations, and in particular with
Sardinians [35]. This finding suggests that the current Sardinian population represents a remnant of an ancient and
previously more widespread component of the European
gene pool. Similarly, genome-wide data indicated that an
approximately 5 kyr old early farmer from Sweden was
more closely related to southern Europeans than to presentday northern Europeans and three contemporary hunter –
gatherers of Sweden [36]. Those three hunter –gatherers as
well as two 7 kyr old hunter –gatherers from the Spanish
cave called La Braña [37,41] fell outside the present-day
European genomic diversity but exhibited a closer genetic
affinity with present-day populations of northern Europeans.
One La Braña individual [41] was found to share ancestry with
the Siberian Mal’ta individual, thus providing further evidence
for the genetic and cultural links between the West Eurasian
Mesolithic and the Siberian Upper Palaeolithic. All together,
these results suggest a shared genomic background of
hunter–gatherers across North Eurasia, as well as a migrationdriven transition associated with the advent of the agricultural
lifestyle in Europe.
Genomic data from ancient humans in Europe revealed
information about their likely phenotypes and health status.
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expression, those could be used to predict gene expression levels
in the Saqqaq hair cells. As expected, key structural components
of hair, such as keratins and trichohyalin, were predicted as
highly expressed, demonstrating that ancient gene expression
levels can be gathered directly from ancient sequence data,
even in the absence of RNA. This approach can therefore complement functional SNP genotyping [32] and proteomics [33]
to gather functional information from ancient individuals
and investigate the dynamics and evolutionary significance of
epigenomic changes.
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The Neandertal genome project represents a milestone
in ancient genomics, as it led to major technical improvements, both for generating and analysing aDNA data [47].
Most of the final sequences used for the first genome draft
assembly required no more than 400 mg of bone material
sampled from three female specimens excavated at the
Vindija cave, Croatia and dated to 38–44 kyr ago [47]. More
recently, Prüfer et al. [48] generated a high-quality genome
from a female Altai Neandertal from the Denisova cave,
Russia, and a low-coverage draft genome from an approximately 60– 70 kyr old Neandertal infant. The high-quality
genome could be obtained owing to a combination of exceptionally high fraction of reads aligning to the human genome
and minimal contamination levels. This vast genomic dataset
makes the Neandertals the best-characterized extinct species
today. The high-quality Altai genome revealed high inbreeding coefficients compatible with half-sibling mating, and
temporal variations in the Neandertal population size,
which was estimated to have been about a tenth of that of
present-day humans, despite a broad Eurasian geographical
range extending from the Iberian Peninsula to the Altai
mountains.
Earlier genetic screening of a finger bone excavated at the
Denisova cave had revealed the presence of an archaic hominin belonging to a mitochondrial lineage very distinct from
modern humans and Neandertals [49]. Enzymatic treatment
prior to DNA library preparation eliminated the vast majority
of nucleotide misincorporations resulting from post-mortem
damage, and further, employing paired-end sequencing
and collapsing mate reads that showed sufficient overlap
delivered a first draft of the nuclear genome with limited
error rates [50]. The nuclear sequence data supported a different population scenario than the mitochondrial data. The
archaic hominin appeared indeed to belong to a group distinct from both modern humans and Neandertals, but more
closely related to Neandertals than to modern humans. This
group was named Denisovans after the cave where it was
first discovered. A molar tooth excavated at the Denisova
cave contained enough endogenous DNA to reconstruct
another full mitochondrial sequence using target enrichment.
The latter appeared closely related to the sequence from the
finger bone. The development of a new DNA library preparation method targeting single-stranded molecules enabled
the reconstruction of an ancient genome showing a quality
comparable to that of modern genomes sequenced at similar
depth [51].
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5. The genomics of archaic hominins
The temporal limits of archaic human genomics were
recently pushed back with the sequencing of the complete
mitochondrial genome of a 400 kyr old hominin from
the Sima de los Huesos cave in northern Spain [52]. The
sequenced individual is morphologically characterized as
Homo heidelbergensis, a lineage commonly considered as preNeandertal. Yet, the mitochondrial genome appeared closer
to Denisovans than Neandertals. Further genetic information,
at the nuclear level, is required before this mitochondrial
affinity can be confirmed or this result can alternatively
be demonstrated as a consequence of a complex population
history involving incomplete lineage sorting and/or gene
flow [53].
The Neandertal and Denisovan genomes have revealed
important information regarding admixture among archaic
hominins and anatomically modern humans. D-statistics [54]
indicate that Neandertals shared an excess of derived alleles
with non-African modern populations [47–48,50–51]. This
suggests that anatomically modern humans and Neandertals
admixed in Eurasia. According to the latest estimates [48],
this gene flow introduced 1.5–2.1% of Neandertal ancestry
(most closely related to the individual from the Caucasus
than the Altai) into the genome of non-African individuals.
However, it is still debated whether the genomic patterns
observed result from admixture between anatomically
modern humans and Neandertals [55,56] or reflect ancestral
population structure in Africa [57,58]. In contrast to Neandertals, Denisovans showed no evidence of gene flow into most
present-day Eurasian populations, but did contribute to the
gene pool of modern Melanesians [51,59] and, to a lower
extent, of mainland Asian populations [48,60]. The admixture
signature in present-day Papuans is greater on the autosomes
than on the X-chromosome, possibly indicating the presence
of hybrid incompatibility alleles on the X-chromosome, or
that the gene flow preferentially involved Denisovan males
and human females. Archaic hominin populations also
appear to have mixed with each other. The level of Neandertal
gene-flow into Denisovans is currently estimated at more
than 0.5% [48] and an additional gene-flow into Denisovans
originating from an unidentified hominin population (representing an outgroup to modern humans, Denisovans and
Neandertals) has been proposed.
The archaic hominin genomes have importantly helped
narrow down the genetic changes that make us humans
[47 –48,50 –51]. Our understanding of how those relate to
phenotype is, however, still in its infancy. In Denisovans,
one difference was found in EVC2, a gene whose mutated
alleles cause wider dental pulp cavities and fusion of tooth
roots, both of which are common in the teeth of archaic hominins [51]. In Neandertals, some genetic variants in the
RUNX2 gene have been linked to cleidocranial dysplasia,
which is associated with bell-shaped rib cages and changes
in dental morphology, all of which represent major phenotypic differences between Neandertal and modern humans
[47]. Functional assays also showed that the microRNA
mir-1304 might be one factor involved in the difference in
tooth morphology between modern humans and Neandertals [61]. The availability of the genome sequence allows
anyone interested in a particular locus to investigate the variants present in archaic hominins, and potentially discover
advantageous alleles that some modern human populations
acquired from archaic hominins. Many such examples are
now described and concern genes that are almost exclusively
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For instance, the Tyrolean Iceman probably had brown eyes,
belonged to the Oþ blood group and was lactose intolerant.
He was also homozygous for alleles associated with major
risks for coronary heart disease and atherosclerosis, and
infected with Borrelia burgorferi, the pathogen responsible
for Lyme disease [35]. La Braña hunter–gatherers probably
had difficulties digesting milk and starch, were dark haired
and dark skinned and had non-brown eyes. The derived variants of immunity genes found in the La Braña genome
suggested that hunter– gatherers were adapted to resist
multiple types of infection that were commonly believed to
have emerged much later with the advent of the agricultural
lifestyle [41].
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involved in the innate immune system (STAT2 [62]; OAS1
[63]; HLA [64]).
Phil. Trans. R. Soc. B 370: 20130387
With high-quality genomes from the Holocene and the Late
Pleistocene in hand, the question soon became how far
back in time palaeogenomics could be pushed. In 2012,
deep sequencing of DNA extracts from a 110 –130 kyr old
bone delivered genome-wide information from a polar bear
[65]. This suggested that, at least in cold environmental conditions, such as those found in the Arctic Ocean Svalbard
archipelago where the polar bear material was discovered,
palaeogenomics could break the Middle Pleistocene time
barrier (125–781 kyr ago). At that time, the genetic evidence
that DNA could survive over several hundreds of thousand
years was rather scarce and limited to the pyrosequencing
of no more than 16 bp of mitochondrial bases from approximately 400 kyr old cave bear specimens [66], PCR amplicon
sequencing of minibarcodes from 450 –700 kyr old ice cores
[67] and 400 –600 kyr old sediment cores [68]. Yet, successfully sequencing Middle Pleistocene genomes would
provide much needed perspectives across a broad range of
evolutionary biology questions. Not less than five archaic
hominins were living during the Middle Pleistocene [69],
including the most recent common ancestor of anatomically
modern humans, Neandertals and Denisovans. The Middle
Pleistocene also experienced numerous radiations and extinctions of fascinating megafauna lineages [70,71], as well as
major climatic changes, involving the succession of many
glacial and interglacial episodes, in contrast to only one for
the Late Pleistocene. Clearly, pushing the limits of palaeogenomics to the Middle Pleistocene would represent a major
step forward.
The empirical demonstration that such a step is possible
came from a fragment of horse metapodial bone excavated in
2003 at Thistle Creek (TC), Yukon, Canada [72]. The specimen
was found within a stratigraphic layer associated with the Gold
Run tephra and dated to 735 + 88 kyr BP, in agreement with
palaeobotanical and micromammal fossil analyses, which
also indicated an Early–Middle Pleistocene age [73–75]. The
line of evidence suggesting that biomolecules, including
DNA, could survive for such a long time included: (i) the detection of amino acids within the bone matrix by time of flight
secondary ion mass spectrometry, (ii) the identification of the
three most abundant amino acids in the primary sequence of
collagen (glycine, proline and alanine) in the bone matrix,
(iii) the direct sequencing of a variety of peptides representing
72 proteins from the bone matrix and the circulating blood,
(iv) the presence of significantly greater levels of protein degradation by glutamine deamidation in the TC horse than in a
younger Late Pleistocene Siberian mammoth, and (v) the estimation of considerably higher levels of DNA damage in the
TC horse than in younger Late Pleistocene horses also preserved in the Arctic permafrost. Additionally, phylogenetic
inference based on complete mitochondrial genomes revealed
that the TC horse fell outside the range of genetic variation of
modern and Late Pleistocene horses. This was confirmed
using the full set of protein-coding nuclear genes and a total
of eight other genomes sequenced for comparison, including
a 43 kyr old horse [72]. In addition, the retrieval of genomic
5
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6. Towards Middle Pleistocene genomes and
proteomes
information from Middle Pleistocene specimens is compatible
with the long-term survival of DNA predicted by the empirical
model of DNA degradation through time proposed in [76].
The TC horse genome was sequenced at approximately
1.1-fold coverage using a combination of second-generation
(Illumina) and third-generation (Helicos) sequencing. The
latter, based on true single DNA molecule sequencing
(tSMS), appeared to be advantageous when targeting short
and damaged molecules for several reasons. First, this technology is PCR-free and, thus, devoid of PCR-related bias. Second,
it does not require extensive enzymatic manipulation or
repeated DNA purification steps, thereby maximizing DNA
recovery and reducing the risks of enzyme incompatibility with chemically modified ancient templates. Third, this
technology operates with single DNA strands and from any
available 30 -hydroxyl group available. Consequently, with
higher densities of single-strand breaks compared with
modern DNA, aDNA templates present a higher chance
of being sequenced on this platform. Methodological improvements of the sequencing protocol [77,78] and the development
of dedicated bioinformatics strategies to improve the sensitivity and accuracy of read alignment against the horse
reference genome [79] were necessary to optimize the analysis
of aDNA molecules using tSMS. Altogether, this resulted in the
identification of 4.21% of Helicos reads as endogenous horse
DNA versus only 0.47% for Illumina reads.
The TC horse genome sequence was used first to date the
time of the most recent common ancestor of horses, donkeys,
zebras and asses at approximately 4.0–4.5 million years
(Myr), which corresponds to twice the age of the first widely
accepted Equus fossil from the palaeontological record. This
new calibration point provided a genome-wide mutation rate
that was used for scaling the palaeodemographic profile reconstructed from high-quality modern diploid genomes following
pairwise sequentially Markovian coalescent inference. The profile revealed three major periods of demographic expansions
and contractions for horses within the last 2 Myr, the last of
which was consistent with ecological niche modelling and
palaeoenvironmental data showing grassland expansion prior
to the LGM followed by a massive post-LGM range contraction
[80]. Interestingly, Bayesian skyline reconstructions based on
the ancient mitochondrial genomes sequenced in this study,
as well as tip-calibration, showed similar demographic changes,
providing an independent validation of the novel calibration
point proposed for Equus.
More fundamentally, the sequence data provided a unique
snapshot of aDNA molecules from the Middle Pleistocene,
revealing for the first time the presence of 30 overhangs [77]
and fragmentation levels compatible with the survival of
ultra-short fragments (25 mers) over 1 Myr. As the latter provide sufficient information for mapping, environmental
conditions close to those in place at TC should therefore
enable the characterization of 1 Myr old genome [81]. Outside
the Arctic, temperate caves that represent an environment with
virtually no variation in temperature are also likely to offer
preservation conditions compatible with the reconstruction of
Middle Pleistocene genomes, as shown recently by the analysis
of bone material from Sima de los Huesos at Atapuerca [52,82].
In these studies, the experimental procedure, which combined
a newly developed extraction method tailored to the retrieval
of ultra-short DNA fragments, single-strand Illumina DNA
libraries [51,83] and target-enrichment capture, recovered
enough high-quality DNA reads to reconstruct a near complete
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mitochondrial genome of a Middle Pleistocene cave bear and
H. heidelbergensis [52].
8. Ancient genomes: a user’s manual
(a) DNA damage patterns as authenticity indicators
With the introduction of genomics, new authentication criteria for DNA have emerged, with one of the most essential
being the detection of typical signatures of post-mortem
damage. Using blunt-end ligation of double-stranded templates, cytosine deamination at 50 -overhangs results in
greater C ! T misincorporation rates towards sequence
starts [98]. At read ends, this signature is converted into a
complementary increase in G ! A misincorporation rates.
This typical post-mortem damage signature is modified
depending on the molecular tools used during library building and amplification. AT-overhang ligation, for instance,
was shown to introduce significant biases in the sequence
composition of library inserts, which discriminates against
templates starting with thymine residues [99] and, consequently, deaminated cytosines (molecular analogues of
thymines). This not only reduces the molecular complexity
(b) Limiting the impact of post-mortem DNA damage
Fitting a DNA damage model to the data can also be used to
limit the impact of C ! T and G ! A misincorporations in
downstream analyses. In particular, the confidence placed on
any nucleotidic base along a sequence can be downscaled
post-mapping according to the probability of the base being
affected by post-mortem damage [104]. This approach was
shown to reduce the false positive rate of SNP calls on the
Saqqaq data [104]. Ideally, the damage model should be
applied during the mapping step itself, in order to improve
read alignment accuracy and sensitivity, as currently
implemented in the programs MIA [105], ANFO [47] and
sesam [22], but usage of these softwares has been limited
mostly owing to long-running times (MIA) and the inability
to handle indels (sesam).
For now, the most common strategy for limiting the
impact of misincorporations in downstream analyses has
consisted in a first authentication of the data based on a
Phil. Trans. R. Soc. B 370: 20130387
Despite major advances in genomic technologies, assembling
complete plant genomes is a major challenge even for modern
samples owing to their large, highly repetitive and heterozygous genomes, confounded by varying ploidy-levels, even
within genera. Thus small-scale plant aDNA studies have
been undertaken on maize [84], barley [85], cotton [86], wheat
[87] and bottle-gourd [88], revealing patterns of crop adaptation
and migration (reviewed in [89]). Larger and more in-depth
studies using ancient plant genomes are expected in the
coming years given the economic importance of major crops
and the possibility of reintroducing alleles involved at various
stages of the domestication process. Herbarium collections
hold great potential as resources for future investigations of historical genomics as the specimens are generally well preserved
and often meticulously annotated. High endogenous DNA content has allowed the genomic characterization of ‘ancient’
genomes of the plant pathogen Phytophthora infestans, the
oomycete responsible for the Irish potato famine [90–92]. Herbarium collections also hold potential for population genomics.
Future studies on ancient plant pathogens should reveal more
details about their coevolution with food crops and the history
of their human-mediated migrations, potentially leading to
insights for crop breeding and management. Furthermore, the
study of aDNA from non-domesticates such as forest trees
will probably shed light on changes in biodiversity during
past climatic events [93].
It has also recently been shown that RNA is preserved in
some ancient seeds, even better than aDNA in maize kernels
[94], presenting an opportunity to directly test evolutionary
changes in gene expression at a key developmental stage [94].
Comparative genomic approaches and selection scans will
also probably narrow a series of candidate loci that were adaptive in a range of environmental conditions. It should also be
stressed that new aDNA reservoirs, such as egg shells [95]
and dental calculus [96,97], are constantly being discovered,
and should greatly benefit from deep-sequencing approaches.
6
rstb.royalsocietypublishing.org
7. Non-mammalian palaeogenomics
of DNA libraries, but also transforms the expected nucleotide
misincorporation pattern, which peaks at the second position
from sequencing termini. Likewise, DNA polymerases of the
Pfu family, such as Phusion, cannot bypass uracil residues
[22]. As a result, no increase in C ! T misincorporation
rates are detected at sequence starts [31], except at methylated
CpGs [29].
Procedures based on single-stranded templates also show a
different nucleotide misincorporation profile. With Helicos
tSMS, a sequence reverse complementary to the original template strand is generated by extension from the blocking site
(figure 1a). Cytosine deamination at 30 -overhangs of the template strand will, therefore, increase G ! A instead of C ! T
misincorporation rates [77,78]. With single-strand Illumina
DNA libraries [51,83], whenever inserts are paired-end
sequenced or sequenced over their full length, the expected misincorporation pattern corresponds to an increase of C ! T rates
at both sequence starts and sequence ends (figure 1b).
One type of DNA damage pattern, where the genomic position located upstream of sequence starts is enriched in purines
[98], appears to be common to all library building protocols.
This probably reflects a mostly depurination-driven postmortem DNA fragmentation process. Preferential loss of adenine over guanine residues has been observed for aDNA
extracts younger than a century [100], but guanine residues
are preferentially lost for much older material, suggesting
two temporally independent depurination dynamics at adenine and guanine residues. The resonance structure present
within guanine residues and reducing the activation energy
required to break the bond with the deoxyribose might influence these dynamics [101].
Restricting analyses to the population of sequences exhibiting typical damage patterns has been shown to enable
genuine data recovery, even in the presence of significant
levels of contamination [39,52,102]. Nucleotide misincorporation and DNA fragmentation patterns can be detected using
ad hoc programs such as the MAPDAMAGE software [103,104],
and post-mortem degradation parameters can be quantified
from read alignments against reference genomes [103,104].
In light of the versatility of the signatures described above,
we recommend that the same molecular methods should be
used when comparing DNA damage parameters across a
range of samples.
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(a)
Helicos tSMS template preparation
3¢
3¢ 5¢
5¢
single-stranded library preparation
3¢
5¢
5¢
3¢
3¢
3¢ 5¢
5¢
5¢
3¢ 5¢
3¢
5¢
3¢
3¢
5¢
3¢
5¢
3¢
3¢
5¢
amplification
5¢
5¢
5¢
sequencing
Figure 1. Accessing single-strand information from aDNA templates. Comparison of template preparation for (a) Helicos tSMS [77] and (b) single-stranded library
building [51], in the case of a double-stranded DNA molecule showing a single-strand break ‘j’ and two cytosines deaminated to uracils (U). Both methods lead to
three sequence reads, each represented by a different colour ( pink, blue and green), thus providing strand information. Conversely, double-stranded molecules
with a single-strand break built into double-stranded libraries lead to the sequencing of one read. Cytosine deamination in overhangs leads to an artefactual
increase in G ! A transitions in Helicos tSMS sequence reads and C ! T transitions in sequence reads obtained from single-stranded libraries. (a) ‘B’, dCTP,
dGTP or dATP virtual terminator. (b) ‘X’, ‘Y’ and ‘Z’ adapter/primer sequence.
small subset of sequences followed by a second production
phase using nucleotide misincorporation-free libraries
[47,106–108]. This is done by treating the aDNA extract with
a cocktail of two enzymes, where the uracil-DNA glycosylase
targets deaminated cytosines and generates abasic sites,
which represent the targets for the EndoVIII endonuclease
[29]. As a result, shorter DNA templates cleaved at damaged
sites are ligated to adapters and incorporated into libraries.
This strategy, in addition to high depth-of-coverage and
paired-end sequencing where almost every single base position
of the insert is read twice, has been essential for generating the
high-quality Denisovan genome sequence [51].
(c) Increasing the relative amount of target DNA I:
ancient DNA extraction
While standard silica-based extraction procedures [108]
are biased towards molecules longer than approximately
40 bp, a recent extraction method has been developed to
target the ultra-short fraction of DNA extracts [82]. Assuming
that DNA fragmentation follows a one-order kinetics, the
amount of aDNA available decreases exponentially with fragment size [76,109]. By targeting short DNA fragments, the new
extraction method should thus drastically increase the amount
of aDNA material in extracts, thereby increasing the molecular
complexity of DNA libraries. This method is an important
advance towards the sequencing of significantly older DNA
templates, as well as DNA from environments offering poor
preservation conditions. Methods have been devised for the
preferential extraction of DNA from molecular preservation
niches that can be found within fossils. Such niches have
been proposed to correspond to crystal aggregates present in
the most interior parts of bones where endogenous DNA is
protected from hydrolysis and microbial invasion [110]. One
promising method has shown great success with permafrost
preserved bone material, such as mammoth [111] and horses
[77,78,112]. This method involves a first partial digestion of
the bone powder, before undigested bone pellets are recovered
and digested a second time in a fresh buffer. Pairwise tests have
shown higher endogenous contents in the extract prepared
from the second digest, as well as lower levels of cytosine deamination [77,78,112] and fragmentation [78]. If confirmed by
additional tests on a range of ancient samples, targeting such
molecular preservation niches could significantly reduce the
costs related to ancient genome sequencing.
(d) Increasing the relative amount of target DNA II:
ancient DNA library construction and amplification
Apart from library construction methods [99], the type of DNA
polymerase used also significantly impacts the complexity of
amplified DNA libraries [113]. Standard polymerases for
aDNA research, such as Taq Gold, significantly skew the size
distribution and base composition of the pool of molecules
amplified towards short and GC-rich templates, which limits
the ability to sequence the entire molecular diversity originally
present in the DNA library. DNA polymerases can also be
blocked during library amplification owing to the presence of
atypical bases in aDNA templates [114], which can in turn provide an advantage to non-modified modern contaminants. The
exact amount of such blocking DNA lesions is still largely
unknown but would represent 10–40% of library templates
according to a recent estimate using a limited number of
fossil specimens from permafrost and temperate caves [114].
Devising methods for repairing such templates and/or capturing preferentially damaged templates [53] could further
improve accessibility to aDNA molecules. DNA polymerases
capable of bypassing damage lesions in DNA molecules have
Phil. Trans. R. Soc. B 370: 20130387
sequencing
3¢
5¢
3¢
5¢
3¢
5¢
3¢
5¢
7
rstb.royalsocietypublishing.org
3¢ 5¢
5¢
(b)
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8
0.5%
70%
70%
1–5%
90
17%
%
90%
21%
48%
78%
84%
61%
Aboriginal Australian34
100 yBP
Greenlandic Palaeo−Eskimo22
4000 yBP
Tyrolean Iceman35
5300 yBP
European hunter−gatherer41
7000 yBP
Montana Clovis boy40
12 600 yBP
Siberian mammoth20
19 000 yBP
Siberian Mal’ta boy39
24 000 yBP
Croatian Neandertals47
40 000 yBP
Altai Neandertal48
50 000 yBP
Altai Denisovan50,51
74 000–82 000 yBP
present
Svalbard polar bear65
120 000 yBP
Yukon horse72
700 000 yBP
past
Figure 2. Endogenous content of ancient genomic extracts. Datasets are ordered from the most ancient sample to the most recent. ‘yBP’, years before present.
been engineered and shown to significantly increase amplification success from Pleistocene specimens, but their efficiency
has not been investigated yet with next generation sequencing
approaches [115].
(e) Increasing the relative amount of target DNA III:
ancient DNA enrichment
The fact that most aDNA extracts show a minority of
endogenous templates (figure 2) has led to the development
of enrichment approaches aimed at reducing sequencing
costs and improving the sequence quality of the targeted
loci. Primer extension capture was the first of such methods
and succeeded in recovering full mitochondrial sequence
information from five Neandertal specimens [116] and from
an approximately 30 kyr old modern human [117]. It was
later superseded by other in-solution enrichment methods
relying on biotinylated baits, either designed from known
sequences and manufactured commercially [118], or prepared
from modern DNA extracts [119]. These baits are subsequently used to target complementary library inserts.
Both methods have shown great success in various aDNA
contexts, often delivering complete mitochondrial genome
sequences with high depth of coverage [42,72,117,119– 123]
and even pre-selected regions from the Mycobacterium
tuberculosis genome [124]. The method has also been found
to be relatively robust to the evolutionary distance separating
probes and targets, yielding to significant enrichment despite
10– 13% of sequence divergence [125]. Microarray-based
hybridization capture has also performed well in enriching
Neandertal DNA libraries [32] containing very low endogenous DNA content, and delivering the full bacterial genome
of the causative agent of the mediaeval Black Death epidemic [106,126] as well as of historical leprosy strains [127].
One drawback of such approaches is that microarrays are
designed from modern reference genomes. As a consequence,
untargeted plasmids and/or loci potentially present in the
historical strains and/or chromosomal rearrangements
specific to the historical strain could remain undetected.
This problem can be solved by using de novo genome assembly in cases where samples with exceptionally high pathogen
DNA contents are available, such as for one of the three
ancient leprosy samples that were genome sequenced [127].
Other types of enrichment approaches have been developed
to target full human chromosomes [38], and even complete genomes [128,129], which performed well on poorly preserved
DNA material. One such approach converts custom-designed
microarray probes into an immortalized and amplifiable biotinylated library of baits that can be used for pulling-down
orthologue inserts from aDNA libraries. This strategy enabled
Fu et al. [38] to reconstruct all non-repetitive sequences of
chromosome 21 in a 40 kyr old anatomically modern human
from Tianyuan cave, China, from a set of immortalized baits
recovered from nine microarrays and corresponding to 8.7
million probes across 30 Mb of the chromosome. A second
approach achieves full genome enrichment in solution with
Phil. Trans. R. Soc. B 370: 20130387
0.5–4%
rstb.royalsocietypublishing.org
non-endogenous
endogenous - hair
endogenous - bone/tooth
Downloaded from http://rstb.royalsocietypublishing.org/ on December 8, 2014
Looking back 5 years, no one could have predicted the current
state of ancient genomics. New sequencing technologies
requiring no heavy infrastructure are being developed with
the promise of delivering gigabases of sequence information
at small cost. We can anticipate that ancient genomics will
move on to the scale of population studies, with probable
research areas in the reconstruction of human dispersal
routes and demographic processes, such as the ones associated
Acknowledgements. We thank all members of the Centre for GeoGenetics
for fruitful discussions.
Funding statement. This work was supported by the Danish National
Research Foundation (DNRF94), two Marie-Curie Intra-European
Fellowships IEF (299176 and 302617), the Marie-Curie Career Integration grant no. CIG-293845 and a Danish National Research
Foundation FNU grant attributed to L.O.
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