* Institute of Anthropology and Human Genetics, Division of Molecular Genetics, University of Tübingen, Tübingen, Germany
Department of Zoology, Natural History Museums and Botanical Garden, University of Oslo, Oslo, Norway
Correspondence: E-mail: bachmann{at}nhm.uio.no.
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Abstract |
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Key Words: ancient DNA extracts mitochondrial DNA mutation PCR errors PCR inhibition
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Introduction |
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Contamination with modern DNA has plagued ancient DNA research, and this is a matter of particular concern when working with hominid samples. It might be impossible to prove authenticity of the obtained data simply because of the expected very high level of sequence similarity between authentic ancient DNA from a hominid fossil and contaminating contemporary DNA. Even minute amounts of contaminating DNA might question the results obtained by amplification of ancient DNA using the extremely sensitive polymerase chain reaction (PCR). However, it must be stressed that contamination is a general problem in ancient DNA research and affects the analysis of samples from any taxon (Pusch et al. 2000). Usually, PCR protocols are optimized using DNA from closely related taxa and carryover contaminations might occur.
PCR artifacts such as PCR jumping, allelic dropouts, regular polymerase errors, and assumed postmortem damage of authentic DNA molecules are also great obstacles in the retrieval of authentic sequence data from ancient DNA (Pääbo 1989; Willerslev et al. 1999; Hansen et al. 2001; Gilbert et al. 2003a). Strand breaks decrease the average molecular weight of nucleic acids (Pääbo 1989). Oxidative and hydrolytic damage may lead to incorporation of incorrect nucleotides or block strand elongation during PCR (Willerslev et al. 1999). The conversion of adenine to hypoxanthine and cytosine to uracil, respectively, are considered common forms of DNA damage (Lindahl 1996; Gilbert et al. 2003a). Region- and position-specific damage rates add to the problem (Gilbert et al. 2003a). Unfortunately, DNA survival and postmortem damage of DNA of a particular sample are unpredictable and difficult to assess. The indirect determination of ancient nucleotide sequences is accompanied by very high standards that must be safeguarded to "guarantee" authenticity of the results (summarized by Cooper and Poinar 2000).
Here, we show that one important aspect is neglected in the discussion on the authenticity of PCR-based results, i.e., the mutagenic effect of ancient DNA extracts themselves. We have noticed such mutagenic effects of ancient DNA extracts in another study (Pusch et al., in preparation). Here, we present evidence that artificial (i.e., nonauthentic) HVRI sequences can be obtained from modern human DNA templates when spiked with ancient DNA extracts. The results indicate that the authenticity of PCR-generated ancient DNA sequences must be reconsidered and illustrate the need for developing standards for an assessment of the mutagenic effect of ancient DNA extracts prior to analysis.
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Material and Methods |
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For some initial control experiments, the "voltage-induced release method" (Bachmann et al. 2000) and the "mix-and-clean method" (Scholz and Pusch 1997) were used. In short, the voltage-induced release method is based on an electrophoretic separation using 2% w/v SeparideTM (Gibco BRL Life Technologies, Carlsbad, Calif.) gels in 1 X Tris-borate-EDTA (TBE) buffer. A maximum of 2530 mg ground sample is loaded into a slot along with 25 µl of 1.5 X loading buffer (15% glycerol, 3% SDS, 150 mM dithiothreitol, and 50 mM TrisHCl, pH 7.5). After gentle stirring, electrophoresis is carried out at 7 V/cm until the xylenecyanol/bromophenol blue dye loaded into empty lanes moved into the gel. The DNA is subsequently isolated from the gel following Pusch's method (1997). For the mix-and-clean method up to 0.2 g, the ground sample is vigorously vortexed for 1 min at 60°C in 500 µl 8% sucrose, 5% Triton-X-100, 10 mM EDTA, and 5 mM TrisHCl, pH 8.0 buffer. After adding 500 µl phenol, the mixture is incubated for 5 h at room temperature on a shaker. Following an extraction of the aqueous phase with 1 vol chloroform the DNA is precipitated with 0.7 vol propan-2-ol and 20 µg glycogen. The air-dried DNA pellet is resuspended in 8%, 0.1% Triton-X-100, 5 mM EDTA, and 1.2 M NaCl, pH 8.0. The precipitation and resuspension of DNA is repeated twice before the DNA is finally dissolved in TE buffer.
PCR Amplifications for Subsequent Sequencing
Human mitochondrial HVRI (1614716294) was amplified for 30 cycles. Each cycle consisted of 30-s denaturation at 94°C, 30-s annealing between 55°C and 63°C (5 cycles at 63°C, 5 cycles at 59°C, and 20 cycles at 55°C), and 30-s extension at 72°C. A final extension step of 10 min at 72°C terminated the program. The PCR mix (50 µl) consisted of 0.2 mM of each dNTP, 0.2 µM of each primer, 1 U Ampli-Taq polymerase (Applied Biosystems, Foster City, Calif.), and 50 ng contemporary human DNA in 30 mM MgCl2, 500 mM KCl, and 100 mM Tris, pH 8.9. To test the effect of various ancient DNA extracts on PCR fidelity, 1 µl water was replaced by 1 µl ancient DNA extract. The primers used for amplification were: L16170 5'-CCACCTGTAGTACATAAAAACCCA-3' and H16271 5'-GTGGGTAGGTTTGTTGGTATCCTA-3' for the full-size products, L16170 and H16245 5'-TGAGGGGTGGCTTTGGAGTTG-3' for the short left side (sls) products, and L16182 5'-TACATAAAAACCCAATCCACATCAAA-3' and H16271 for the short right side (srs) products.
PCR Amplifications for Length-Inhibition Analysis
To study the inhibitory effect of ancient DNA extracts on strand elongation during PCR the human mitochondrial region encompassing the ATPase 6, cytochrome oxidase subunit 3, tRNA-Gly, and NADH dehydrogenase subunit 3 (Anderson et al. 1981) was targeted. One reverse primer (H strand) was used in combination with seven forward primers (L strand) in order to amplify fragments of increasing length. The PCR mixture was as the one described earlier. The PCR protocol for cycling consisted of 30 cycles with 30 s denaturation at 94°C, 30 s annealing between 55°C and 60°C (5 cycles at 60°C, 5 cycles at 58°C, and 20 cycles at 55°C), and 30-s extension at 72°C. A final 10-min extension at 72°C terminated the program. The following primers were used for amplification: H10152 5'-CTATGTAGCCGTTGAGTTGTG-3', L9952 5'-GACTATTTCTGTATGTCTCCATC-3' (201 bp), L9747 5'-ACTTCGAGTCTCCCTTCACCA-3' (406 bp), L9501 5'-TGAGCCTTTTACCACTCCAGC-3' (652 bp), L9301 5'-CCATGTGATTTCACTTCCACTC-3' (852 bp), L9081 5'-CCTTCCCTCTACACTTATCATC-3' (1072 bp), L8901 5'-AGCCCACTTCTTACCACAAGG-3' (1252 bp), and L8650 5'-CTAATCACCACCCAACAATGAC-3' (1503 bp).
Plasmid Cloning and DNA Sequencing
The obtained PCR products were cleaned by means of the Concert Gel Extraction System (Invitrogen) and subsequently cloned using a TA cloning kit (Invitrogen). Plasmid DNA from positive colonies was prepared by means of the Plasmid Mini Kit (Qiagen) and subsequently sequenced using BigDye chemistry (Applied Biosystems).
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Results |
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To test if the observed sequence alterations were caused by the DNA molecules in the ancient DNA extracts, six ancient DNA extracts (i.e., Falco spp, rodent coprolite, Sequoia spp, and Homo erectus listed in table 1, and Araucaria spp (wood) from Madagascar (190230 Myr), and Carcharocles angustidens (tooth) from the USA (2328 Myr)) were pretreated with DNaseI prior to the spiking experiments. A total of 67 sequences were deduced and the majority of them (71.6%) were altered. Many mutations were identical to those observed previously and were grouped into 14 different interim consensus sequences (fig. 3).
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Discussion |
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Our experiments show that failure of amplification of large fragments does not necessarily indicate absence of high molecular weight template DNA in the PCR mixture (in our inhibition studies by spiking experiments all PCR mixtures contained high molecular weight human template DNA). This argument is frequently applied in the literature (e.g., Caramelli et al. 2003, Poinar et al. 2003) in order to support lack of contamination in ancient DNA extracts according to the "appropriate molecular behavior" criterion of Cooper and Poinar (2000), i.e., large 5001,000 base pair products are unusual.
We also present experimental evidence that ancient DNA extracts may induce mutations under PCR amplifications. The strength of the "spiking contemporary human DNA templates with ancient DNA extracts approach" is that properties of ancient DNA extracts can be studied in a modern DNA experimental setup. Doing so, the shortcomings of ancient DNA experiments can be avoided. The nucleotide sequence of the modern PCR template used in our experiments can be determined unambiguously, i.e., it is identical to the human mtDNA determined by Anderson et al. (1981) when amplified without spiking. The approach allows us to conclude that the frequently observed sequence alterations in sequences from spiked amplifications must have occurred under PCR.
Analysis of 547 sequences from cloned amplicons of a 148-bp stretch (1614716294) of the mitochondrial HVRI indicates that extract-induced mutations do not occur at random. In total, 34 positions of a 103-bp alignment (PCR primers excluded) are affected, the majority of those repeatedly in independent PCR amplifications. However, this does not mean that extract-induced mutations can predictably be reproduced. It is more that particular positions of the target sequence have a high likelihood of being altered.
It is certainly difficult to identify the cause of the observed sequence heterogeneity. Intuitively, one might suspect human DNA in the ancient DNA extracts used for spiking (note: in this context it is irrelevant whether such human DNA is authentic for a particular find or results from contamination). Such DNA might serve as a proper template and differ in sequence from targeted human DNA of a known sequence. Alternatively, such DNA might be degenerated and, therefore, not serve as proper template but cause sequence variation in the obtained amplicons through the process of PCR jumping (Pääbo 1989). We believe that this line of argument has to be rejected for the following reasons. First, the majority of DNA extracts used for spiking had to be diluted prior to PCR amplification (table 1). Only 1 µl diluted extract was then added to 50 ng modern human template DNA; i.e., the number of modern human template DNA molecules in the PCR mixture therefore exceeded by far putative human DNA molecules from the spiking extracts by several orders of magnitudes. Second, human DNA from other sources than the targeted modern human DNA can hardly explain why 11 mutations were found in more than 30% of the analyzed clones (table 3). Third, human DNA from other sources than the targeted modern human DNA can hardly explain that a combination of, e.g., 16 mutations (interim consensus sequence XXVI in table 2) occurs in 86 clones, i.e., 15.7% of all sequences, generated in seven different spiking experiments. Fourth, human DNA from other sources than the targeted modern human DNA can hardly explain why many interim consensus sequences occur that do not match any HVRI sequences deposited in sequence databases. Finally, spiking experiments using six ancient DNA extracts pretreated with DNaseI (67 sequences) also yielded mutated sequences with similar nucleotide alterations. Accordingly, DNA could be excluded as the mutagenic agent.
We speculate that coextracted chemicals other than DNA might induce the observed sequence alterations. Such coextracted mutagenic substances may accumulate in the samples during diagenesis. Although diagenetic processes are barely understood, we know that specimens accumulate postmortem multivalent metal ions. For example, concentrations of manganese, barium, strontium, iron, and uranium can be enriched up to 5,000 times compared with contemporary samples (Bischoff 1981, Velasco-Vazquez et al. 1997, Kohn et al. 1999). In particular, manganese is known for its mutagenic effect, and molecular biologists use this effect when using mutagenesis kits. In preliminary studies, we noticed substantially elevated manganese concentrations for the samples used here (data not shown). In contrast, manganese was not detected in 87 modern controls. If coextracted manganese is the reason for the observed mutations, one would, at least at first glance, expect to see a predictive relationship between manganese concentration and reliability of sequences. However, there is no such relationship, and, even worse, there is no reason to expect such a simple correlation. This is because the chemistry of manganese is very complex. The element occurs with a variety of valence stages that differ in their biological activity. However, manganese measurements refer to the total amount of manganese and cannot differentiate valence stages. In addition, the mutagenic effect of manganese also depends on the concentration of other ions. Svetlov and Cooper (1998) and Kunichika et al. (2002), for example, noticed that the mutagenic effect of manganese changed with changing concentration of magnesium. Other reasons may be added (see, e.g., Fletcher et al. 1994, Pelletier et al. 1996). Nevertheless, Pusch et al. (in preparation) showed in other experiments that a GA transition occurs frequently at cDNA position 1,138 of the human FGFR3 gene in PCR amplifications under the presence of 0.25 mM MnCl2. The same diagnostic mutation also occurs when contemporary human template DNA is spiked with an ancient DNA extract from a Pleistocene Ursus spelaeus bone. Future research will have to address this topic.
If coextracted chemicals such as multivalent metal ions were the reason for the observed sequence alterations, they might be removable by extraction methods, which are based on different extraction principles than the default silica-based protocol. In preliminary experiments, we also tested two other extraction methods, i.e., the "voltage-induced release method" (Bachmann et al. 2000) and the "mix-and-clean method" (Scholz and Pusch 1997). However, DNA extracted according to these alternative methods also yielded altered sequences in spiking experiments (data not shown). Future studies will have to address why hypothetical coextracted mutagenic substances cannot be removed by currently applied methods.
The data presented here have implications for ancient DNA research and may challenge the authenticity of a number of PCR-generated sequences from ancient samples. For some reasons it is, however, impossible to assess how frequently sequence alterations induced by ancient DNA extracts may have affected published sequences. Many papers report only the deduced consensus sequences and neither the sequences of the individual clones nor information on the observed sequence variation. Furthermore, as can be seen from table 1, different ancient DNA extracts induce sequence alterations to a different extent. For some extracts, the majority of sequences were identical to CRS and the obtained mutations occurred at very low frequencies. In those cases, extract-induced sequence alterations would not make it into a consensus sequence when applying the majority rule (hypothetical consensus sequence A in tables 1 and 4). In other instances, the majority of sequences were altered and the deduced consensus sequences wrong (hypothetical consensus sequences BJ in tables 1 and 4). It might also be a matter of chance which mutations are considered to be authentic, because usually the clones used for analysis are selected at random.
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Our data imply that an unknown number of published ancient DNA sequences have to be considered with caution. There is an urgent need to identify the causes for the observed mutations in the spiking experiments and to develop standards for an assessment of the mutagenic effect of ancient DNA extracts as a mandatory criterion for authenticity. Although to a different extent in different studies, it is likely that extract-induced mutations are an intrinsic and a general problem of PCR amplifications of ancient templates.
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Acknowledgements |
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Footnotes |
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