aDNA Studies Research Articles

Genotyping human ancient mtDNA control and coding region polymorphisms with a multiplexed Single-Base-Extension assay: the singular maternal history of the Tyrolean Iceman.

BackgroundProgress in the field of human ancient DNA studies has been severely restricted due to the myriad sources of potential contamination, and because of the pronounced difficulty in identifying authentic results. Improving the robustness of human aDNA results is a necessary pre-requisite to vigorously testing hypotheses about human evolution in Europe, including possible admixture with Neanderthals. This study approaches the problem of distinguishing between authentic and contaminating sequences from common European mtDNA haplogroups by applying a multiplexed Single-Base-Extension assay, containing both control and coding region sites, to DNA extracted from the Tyrolean Iceman.ResultsThe multiplex assay developed for this study was able to confirm that the Iceman's mtDNA belongs to a new European mtDNA clade with a very limited distribution amongst modern data sets. Controlled contamination experiments show that the correct results are returned by the multiplex assay even in the presence of substantial amounts of exogenous DNA. The overall level of discrimination achieved by targeting both control and coding region polymorphisms in a single reaction provides a methodology capable of dealing with most cases of homoplasy prevalent in European haplogroups.ConclusionThe new genotyping results for the Iceman confirm the extreme fallibility of human aDNA studies in general, even when authenticated by independent replication. The sensitivity and accuracy of the multiplex Single-Base-Extension methodology forms part of an emerging suite of alternative techniques for the accurate retrieval of ancient DNA sequences from both anatomically modern humans and Neanderthals. The contamination of laboratories remains a pressing concern in aDNA studies, both in the pre and post-PCR environments, and the adoption of a forensic style assessment of a priori risks would significantly improve the credibility of results.

Improving the sensitivity of negative controls in ancient DNA extractions

Much attention has been paid on ancient DNA (aDNA) studies, and negative control was used as one of the stringent quality assurance criteria in order to detect potential contamination. However, the results of some aDNA studies showed the evidence of contamination despite their negative controls failed to do so. Using lambda DNA to mock extraneous contaminating DNA, our study showed that aDNA had a property of improving the efficiency of extraction including contaminating DNA, while negative controls had low sensitivity to detect contamination. To circumvent this problem, carrier DNA such as poly(dA) is suggested to be introduced into aDNA extraction.

Non-Destructive Sampling of Ancient Insect DNA

BackgroundA major challenge for ancient DNA (aDNA) studies on insect remains is that sampling procedures involve at least partial destruction of the specimens. A recent extraction protocol reveals the possibility of obtaining DNA from past insect remains without causing visual morphological damage. We test the applicability of this protocol on historic museum beetle specimens dating back to AD 1820 and on ancient beetle chitin remains from permafrost (permanently frozen soil) dating back more than 47,000 years. Finally, we test the possibility of obtaining ancient insect DNA directly from non-frozen sediments deposited 3280-1800 years ago - an alternative approach that also does not involve destruction of valuable material.Methodology/Principal FindingsThe success of the methodological approaches are tested by PCR and sequencing of COI and 16S mitochondrial DNA (mtDNA) fragments of 77–204 base pairs (-bp) in size using species-specific and general insect primers.Conclusion/SignificanceThe applied non-destructive DNA extraction method shows promising potential on insect museum specimens of historical age as far back as AD 1820, but less so on the ancient permafrost-preserved insect fossil remains tested, where DNA was obtained from samples up to ca. 26,000 years old. The non-frozen sediment DNA approach appears to have great potential for recording the former presence of insect taxa not normally preserved as macrofossils and opens new frontiers in research on ancient biodiversity.

A preliminary neutron crystallographic study of an A-DNA crystal.

The LADI-III diffractometer at the Institut Laue-Langevin has been used to carry out a preliminary neutron crystallographic study of the self-complementary DNA oligonucleotide d(AGGGGCCCCT)(2) in the A conformation. The results demonstrate the viability of a full neutron crystallographic analysis with the aim of providing enhanced information on the ion-water networks that are known to be important in stabilizing A-DNA. This is the first account of a single-crystal neutron diffraction study of A-DNA. The study was carried out with the smallest crystal used to date for a neutron crystallographic study of a biological macromolecule.

Novel methods of molecular sex identification from skeletal tissue using the amelogenin gene

Sex identification from skeletal material is of vital importance in order to reconstruct the demographic variables of an individual in forensic genetics and ancient DNA (aDNA) analysis. When the use of conventional methods of sex identification are impossible, molecular analysis of the X and Y chromosomes provides an expedient solution. Two novel systems of molecular sex identification suitable for skeletal material using the amelogenin gene are described, beginning in intron 2–3, spanning exon 3 and ending in intron 3–4. This area was optimal for sexing, as it includes 14 sex-specific polymorphic regions in addition to an indel (insertion or deletion of nucleotides). Once optimised and working with 100% efficiency on the controls, these procedures were applied to a collection of miscellaneous archaeological skeletons ( ex situ) sourced from the Raymond Dart Collection of Human Skeletons (Dart Collection). This collection was used to optimise these techniques for skeletal remains derived from an archaeological context. These methods produced 46.66% sex results for the ex situ sample, which is within the normal range for aDNA studies. These new techniques are optimal for sex identification, with both the inherent control of isolating many sex-specific features and combined with the use of sensitive micro-fluidic electrophoresis.

Kinship between burials from Grave Circle B at Mycenae revealed by ancient DNA typing

The richness of the burials in Grave Circle B at Mycenae, Greece indicates that the 35 people interred there held elite status during their lifetimes 3500 years ago. It has been speculated that the groups of burials represent different dynasties or branches of the same family. To test this hypothesis, we carried out an exhaustive ancient DNA (aDNA) study of 22 of the skeletons. We were unable to identify nuclear aDNA in any specimen, but we obtained authentic mitochondrial aDNA sequences for four individuals. The results were compared with facial reconstructions and interpreted within the archaeological context represented by the organisation of the graves and the positions of the burials within the graves. We conclude that the contemporaneous male Γ55 and female Γ58 skeletons, which both possess the UK mitochondrial haplogroup, were brother and sister. The implication is that Γ58 was buried in Grave Circle B not because of a marital connection but because she held a position of authority by right of birth. The results illustrate the difficulty in using aDNA to study kinship relationships between archaeological specimens, but also show that aDNA can advance understanding of kinship when used to test hypotheses constructed from other evidence.

Environment and excavation: Pre-lab impacts on ancient DNA analyses

Ancient DNA (aDNA) analyses enjoy an increasing role in palaeontological, archaeological and archaeozoological research. The limiting factor for aDNA studies is the degree of DNA preservation. Our study on 291 prehistoric cattle remains from Europe, the Near East and North Africa revealed that DNA preservation is mainly influenced by geographic and climatic conditions. Especially in hot climates, the preservation of sample material is generally low. We observed that these specimens are prone to further degradation and contamination during and after excavation. We give a description of the main caveats and a short guideline for adequate sample handling in order to facilitate the cooperation between archaeologists and geneticists and to improve the outcome of future research.

HIV-1 protecting CCR5-Δ32 allele in medieval Poland

CCR5-Δ32 is the mutation in the chemokine receptor CCR5 that gives its homozygous carriers nearly complete protections from HIV-1 infection. Restricted almost exclusively to Europe, the mutation is thought to have originated in the continent and risen in frequency to the present-day value of approximately 10% due to a selective advantage it gave its carriers. The mutation bearing allele was initially calculated to be ∼1000 years old and pandemic diseases, such as Bubonic Plague or smallpox were postulated to have selected it. However, new reports appear, that question these hypotheses. Data from ancient DNA (aDNA) studies prove the mutation to be much older, as suggested by calculations based on newer genetic maps. In order to investigate if the plagues of the last millennium selected the allele, and add to the discussion on CCR5-Δ32 origin and age, we searched for the mutation in aDNA isolated from individuals whose skeletal remains were collected at archaeological sites in Poland, dated back to 11–14th centuries. The calculated mean frequency of the allele in medieval Poland (5.06% as compared to contemporary 10.26%), implies its longer than previously believed presence in European populations, and suggests that historic pandemics had little effect on its present-day frequency.

Burial Practices at Titriş Höyük, Turkey: An Interpretation

Next article No AccessBurial Practices at Titriş Höyük, Turkey: An Interpretation*Nicola LaneriNicola LaneriIstituto Italiano per l’Africa e l’Oriente, Rome Search for more articles by this author Istituto Italiano per l’Africa e l’Oriente, RomePDFPDF PLUS Add to favoritesDownload CitationTrack CitationsPermissionsReprints Share onFacebookTwitterLinkedInRedditEmail SectionsMoreDetailsFiguresReferencesCited by Journal of Near Eastern Studies Volume 66, Number 4October 2007 Article DOIhttps://doi.org/10.1086/524179 Views: 120Total views on this site Citations: 16Citations are reported from Crossref © 2007 by The University of Chicago. All rights reserved.PDF download Crossref reports the following articles citing this article:Meliha Melis Koruyucu, Yılmaz Selim Erdal Reconstruction of dietary habits in the Early Bronze Age of Anatolia through the analysis of dental caries and wear, International Journal of Osteoarchaeology 31, no.55 (Jun 2021): 902–915.https://doi.org/10.1002/oa.3007Eirini Skourtanioti, Yilmaz S. Erdal, Marcella Frangipane, Francesca Balossi Restelli, K. Aslıhan Yener, Frances Pinnock, Paolo Matthiae, Rana Özbal, Ulf-Dietrich Schoop, Farhad Guliyev, Tufan Akhundov, Bertille Lyonnet, Emily L. Hammer, Selin E. Nugent, Marta Burri, Gunnar U. Neumann, Sandra Penske, Tara Ingman, Murat Akar, Rula Shafiq, Giulio Palumbi, Stefanie Eisenmann, Marta D’Andrea, Adam B. Rohrlach, Christina Warinner, Choongwon Jeong, Philipp W. Stockhammer, Wolfgang Haak, Johannes Krause Genomic History of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus, Cell 181, no.55 (May 2020): 1158–1175.e28.https://doi.org/10.1016/j.cell.2020.04.044Benjamin Irvine, Yılmaz Selim Erdal, Michael P. Richards Dietary habits in the Early Bronze Age (3rd millennium BC) of Anatolia: A multi-isotopic approach, Journal of Archaeological Science: Reports 24 (Apr 2019): 253–263.https://doi.org/10.1016/j.jasrep.2019.01.015Nicola Laneri The Impact of Wine Production in the Social Transformation of Northern Mesopotamian Societies during the Third and Second Millennia BCE, Die Welt des Orients 48, no.22 (Dec 2018): 225–236.https://doi.org/10.13109/wdor.2018.48.2.225 Timothy Matney Infant Burial Practices as Domestic Funerary Ritual at Early Bronze Age Titriş Höyük, Near Eastern Archaeology 81, no.33 (Nov 2018): 174–181.https://doi.org/10.5615/neareastarch.81.3.0174Elif Ünlü The Handle Wagging the Cup. Formal Aspects of Alcohol Consumption in the Transfer of Ideology: Anatolia and the Aegean Towards the End of the Third Millennium BC, Oxford Journal of Archaeology 35, no.44 (Oct 2016): 345–358.https://doi.org/10.1111/ojoa.12093Alexis Mantha Houses, Residential Burials, and Identity in the Rapayán Valley and the Upper Marañón Drainage, Peru, During Late Andean Prehistory, Latin American Antiquity 26, no.44 (Jan 2017): 433–451.https://doi.org/10.7183/1045-6635.26.4.433Karina Croucher Life and Death in Late Prehistoric to Early Historic Mesopotamia, (Oct 2015): 223–236.https://doi.org/10.1017/CBO9781316014509.015Nicola Laneri, Mark Schwartz, Jason Ur, Anacleto d’ Agostino, Remi Berthon, Mette Marie Hald, and Anke Marsh Ritual and Identity in Rural Mesopotamia: Hirbemerdon Tepe and the Upper Tigris River Valley in the Middle Bronze Age, American Journal of Archaeology 119, no.44 (Dec 2021): 533–564.https://doi.org/10.3764/aja.119.4.0533Yoko Nishimura A Systematic Comparison of Material Culture Between Household Floors and Residential Burials in Late Third-Millennium B.C.E. Mesopotamia, American Journal of Archaeology 119, no.44 (Dec 2021): 419–440.https://doi.org/10.3764/aja.119.4.0419Andrew T. Creekmore The Social Production of Space in Third-Millennium Cities of Upper Mesopotamia, (Apr 2014): 32–73.https://doi.org/10.1017/CBO9781107110274.003Yoko Nishimura North Mesopotamian Urban Neighborhoods at Titriş Höyük in the Third Millennium BC, (Apr 2014): 74–110.https://doi.org/10.1017/CBO9781107110274.004Diane Bolger, Rita P. Wright Gender in Southwest Asian Prehistory, (Jan 2014): 372–394.https://doi.org/10.1002/9781118294291.ch18T. Matney, G. Algaze, M. C. Dulik, Ö. D. Erdal, Y. S. Erdal, O. Gokcumen, J. Lorenz, H. Mergen Understanding Early Bronze Age social structure through mortuary remains: A pilot aDNA study from Titriş Höyük, southeastern Turkey, International Journal of Osteoarchaeology 22, no.33 (Oct 2010): 338–351.https://doi.org/10.1002/oa.1213Ö.D. Erdal A possible massacre at Early Bronze Age Titriş Höyük, Anatolia, International Journal of Osteoarchaeology 22, no.11 (Jun 2010): 1–21.https://doi.org/10.1002/oa.1177Nicola Laneri 8 A Family Affair: The Use of Intramural Funerary Chambers in Mesopotamia during the Late Third and Early Second Millennia B.C.E., Archeological Papers of the American Anthropological Association 20, no.11 (May 2011): 121–135.https://doi.org/10.1111/j.1551-8248.2011.01031.x

Bayesian Estimation of Sequence Damage in Ancient DNA

DNA extracted from archaeological and paleontological remains is usually damaged by biochemical processes postmortem. Some of these processes lead to changes in the structure of the DNA molecule, which can result in the incorporation of incorrect nucleotides during polymerase chain reaction. These base misincorporations, or miscoding lesions, can lead to the inclusion of spurious additional mutations in ancient DNA (aDNA) data sets. This has the potential to affect the outcome of phylogenetic and population genetic analyses, including estimates of mutation rates and genetic diversity. We present a novel model, termed the delta model, which estimates the amount of damage in DNA data and accounts for its effects in a Bayesian phylogenetic framework. The ability of the delta model to estimate damage is first investigated using a simulation study. The model is then applied to 13 aDNA data sets. The amount of damage in these data sets is shown to be significant but low (about 1 damaged base per 750 nt), suggesting that precautions for limiting the influence of damaged sites, such as cloning and enzymatic treatment, are worthwhile. The results also suggest that relatively high rates of mutation previously estimated from aDNA data are not entirely an artifact of sequence damage and are likely to be due to other factors such as the persistence of transient polymorphisms. The delta model appears to be particularly useful for placing upper credibility limits on the amount of sequence damage in an alignment, and this capacity might be beneficial for future aDNA studies or for the estimation of sequencing errors in modern DNA.

More on Contamination: The Use of Asymmetric Molecular Behavior to Identify Authentic Ancient Human DNA

Authentication of ancient human DNA results is an exceedingly difficult challenge due to the presence of modern contaminant DNA sequences. Nevertheless, the field of ancient human genetics generates huge scientific and public interest, and thus researchers are rarely discouraged by problems concerning the authenticity of such data. Although several methods have been developed to the purpose of authenticating ancient DNA (aDNA) results, while they are useful in faunal research, most of the methods have proven complicated to apply to ancient human DNA. Here, we investigate in detail the reliability of one of the proposed criteria, that of appropriate molecular behavior. Using real-time polymerase chain reaction (PCR) and pyrosequencing, we have quantified the relative levels of authentic aDNA and contaminant human DNA sequences recovered from archaeological dog and cattle remains. In doing so, we also produce data that describes the efficiency of bleach incubation of bone powder and its relative detrimental effects on contaminant and authentic ancient DNA. We note that bleach treatment is significantly more detrimental to contaminant than to authentic aDNA in the bleached bone powder. Furthermore, we find that there is a substantial increase in the relative proportions of authentic DNA to contaminant DNA as the PCR target fragment size is decreased. We therefore conclude that the degradation pattern in aDNA provides a quantifiable difference between authentic aDNA and modern contamination. This asymmetrical behavior of authentic and contaminant DNA can be used to identify authentic haplotypes in human aDNA studies.

Quids and Aprons: Ancient DNA from Artifacts from the American Southwest

The success of ancient DNA (aDNA) studies rests on the preservation of DNA through time, and can be limited by the availability of skeletal samples from particular times and locations. To help overcome this limitation, we sought to extract, amplify, and type human mitochondrial DNA (mtDNA) preserved within 1000- to 2000+-year-old artifacts from the American Southwest. In this study, we successfully typed mtDNA from 21 quids and aprons from Basketmaker II and Mimbres contexts. Recovery and analysis of human DNA from such artifacts will be helpful in confirming and extending genetic characterization of ancient populations for which human remains are scarce or unavailable. To illustrate the potential of these techniques, we tested them as a preliminary and independent line of evidence, relevant to the hypothesis that Western Basketmaker populations in the U S. Southwest were descendants of migrant farmers from central Mexico.

Challenges of phylogenetic analyses of aDNA sequences

One of the crucial steps of authentication of aDNA sequences is phylogenetic consistency. Amplified sequences should fit into the phylogenetic framework of their supposed origin. An inherent property of aDNA sequences however, is their short sequence length. Additionally, genes for aDNA studies are often chosen by their preservation potential rather than by phylogenetically informative content. This poses potential challenges regarding their analyses, and might result in an inaccurate reflection of the supposed phylogenetic history of the sequence or organism under study. In this paper some fundamental problems of phylogenetic analysis and interpretation of aDNA datasets are discussed. Suggestions for character sampling and treatment of missing data are made. The publication is the result of a talk from the 1st PAMINSA Meeting in Rio de Janeiro, July 2005.

Tracking down Human Contamination in Ancient Human Teeth

DNA contamination arising from the manipulation of ancient calcified tissue samples is a poorly understood, yet fundamental, problem that affects the reliability of ancient DNA (aDNA) studies. We have typed the mitochondrial DNA hypervariable region I of the only 6 people involved in the excavation, washing, and subsequent anthropological and genetic study of 23 Neolithic remains excavated from Granollers (Barcelona, Spain) and searched for their presence among the 572 clones generated during the aDNA analyses of teeth from these samples. Of the cloned sequences, 17.13% could be unambiguously identified as contaminants, with those derived from the people involved in the retrieval and washing of the remains present in higher frequencies than those of the anthropologist and genetic researchers. This finding confirms, for the first time, previous hypotheses that teeth samples are most susceptible to contamination at their initial excavation. More worrying, the cloned contaminant sequences exhibit substitutions that can be attributed to DNA damage after the contamination event, and we demonstrate that the level of such damage increases with time: contaminants that are >10 years old have approximately 5 times more damage than those that are recent. Furthermore, we demonstrate that in this data set, the damage rate of the old contaminant sequences is indistinguishable from that of the endogenous DNA sequences. As such, the commonly used argument that miscoding lesions observed among cloned aDNA sequences can be used to support data authenticity is misleading in scenarios where the presence of old contaminant sequences is possible. We argue therefore that the typing of those involved in the manipulation of the ancient human specimens is critical in order to ensure that generated results are accurate.

Ancient DNA from ice age insects: proceed with caution

The paucity of ancient DNA (aDNA) studies in insects can be traced to the dismissal of the 1990s reports of DNA isolation from amber-entombed insects. In retrospect, amber was an obvious place to start, but it has since been demonstrated that DNA preservation is not necessarily correlated with physical preservation. The discipline of aDNA is rapidly progressing as issues regarding contamination with modern sequences and detection of DNA damage are addressed. Two major concerns in ancient DNA studies are the co-purification of DNA polymerase inhibitors and the presence of DNA lesions. Preliminary data demonstrate DNA extraction is possible from beetle remains isolated from packrat middens. Although specimens from permafrost sediments and ancient rodent middens are potential sources of aDNA, collection and curation procedures require modification to minimize contamination and optimize DNA yield. Since aDNA isolation in insects requires the complete destruction of fossil material, another consideration is the taxonomic groups that are adequately represented to justify the sacrifice of geological specimens. Although most recommended aDNA authentication procedures are easily followed, some are impossible for insect samples due to their small size, making the establishment of authentication procedures of aDNA from small samples a final consideration.

Ancient DNA forces reconsideration of evolutionary history of Mediterranean pygmy elephantids

During the Pleistocene pygmy elephantids, some only a quarter of their ancestors' size, were present on Mediterranean islands until about 10,000 years ago (y.a.). Using a new methodology for ancient DNA (aDNA) studies, the whole genomic multiple displacement amplification method, we were able to retrieve cytochrome b (cytb) DNA fragments from 4200 to 800,000 y.a. specimens from island and mainland samples, including pygmy and normal-sized forms. The short DNA sequence (43 bp) retrieved from the 800,000 y.a. sample is one of the oldest DNA fragment ever retrieved. Duplication of the experiments in two laboratories, the occurrence of three diagnostic sites and the results of the phylogenetic analyses strongly support its authenticity. Our results challenge the prevailing view that pygmy elephantids of the eastern Mediterranean originated exclusively from Elephas, suggesting independent histories of dwarfism and the presence of both pygmy mammoths and elephant-like taxa on these islands. Based on our molecular data, the origin of the Tilos and Cyprus elephantids from a lineage within the genus Elephas is confirmed, while the DNA sequence from the Cretan sample falls clearly within the mammoth clade. Thus, the name Mammuthus creticus rather than Elephas creticus, seems to be justified for this form. Our findings also suggest a need to re-evaluate the evolutionary history of the Sicilian/Maltese species, traditionally included in the genus Elephas.

Anthropological Applications of Ancient DNA: Problems and Prospects

The analysis of DNA extracted from archaeological specimens to address anthropological questions is becoming increasingly common. Despite widespread interest in ancient DNA (aDNA), the difficulties inherent in aDNA analysis are not generally appreciated by researchers outside of the field. The majority of samples subjected to aDNA analysis often fail to produce results, and successful analysis is typically limited to specimens that exhibit excellent preservation. Contamination of samples with exogenous DNA is an ongoing problem and requires careful design of research strategies to limit and identify all DNA contaminants. Overall, aDNA analysis is a highly specialized and technical field that requires extensive training and can be quite expensive. Thus, each aDNA study should be carefully planned with significant input from archaeologists, physical anthropologists, linguists, and related researchers and should focus on well-preserved samples that are likely to produce a clear answer to a question that is not amenable to nongenetic analysis. In this manuscript, I explain the problems and prospects of various anthropological applications of aDNA technology. I present a series of previously published studies, which are of general anthropological interest, to illustrate the strengths and weaknesses of aDNA methods in each case. I also provide a checklist of questions to evaluate the utility of archaeological remains for aDNA analysis and to provide guidelines when designing an aDNA study.

Extensive Human DNA Contamination in Extracts from Ancient Dog Bones and Teeth

Ancient DNA (aDNA) sequences, especially those of human origin, are notoriously difficult to analyze due to molecular damage and exogenous DNA contamination. Relatively few systematic studies have focused on this problem. Here we investigate the extent and origin of human DNA contamination in the most frequently used sources for aDNA studies, that is, bones and teeth from museum collections. To distinguish contaminant DNA from authentic DNA we extracted DNA from dog (Canis familiaris) specimens. We monitored the presence of a 148-bp human-specific and a 152-bp dog-specific mitochondrial DNA (mtDNA) fragment in DNA extracts as well as in negative controls. The total number of human and dog template molecules were quantified using real-time polymerase chain reaction (PCR), and the sequences were characterized by amplicon cloning and sequencing. Although standard precautions to avoid contamination were taken, we found that all samples from the 29 dog specimens contained human DNA, often at levels exceeding the amount of authentic ancient dog DNA. The level of contaminating human DNA was also significantly higher in the dog extracts than in the negative controls, and an experimental setup indicated that this was not caused by the carrier effect. This suggests that the contaminating human DNA mainly originated from the dog bones rather than from laboratory procedures. When cloned, fragments within a contaminated PCR product generally displayed several different sequences, although one haplotype was often found in majority. This leads us to believe that recognized criteria for authenticating aDNA cannot separate contamination from ancient human DNA the way they are presently used.

Morphological and genetic studies of waterlogged Prunus species from the Roman vicus Tasgetium (Eschenz, Switzerland)

Morphological and genetic studies were performed on waterlogged Prunus fruit stones from the Roman vicus Tasgetium (Eschenz, Switzerland). Some fruit stones could be identified to species level based on morphological and metric criteria. Other fruit stones found were not identifiable to species level. Of the latter, the morphological group Prunus insititia/ spinosa represents either native sloe, cultivated primitive plum (damson) or a hybrid of both. In one out of 10 individual fruit stones of this group Prunus specific chloroplast trnL- trnF and nuclear ITS1 markers were verifiably amplified. Sequences of trnL- trnF led to the identification of Prunus spinosa. The presence of authentic DNA was confirmed by phylogenetically meaningful sequences from the archaeobotanical group Prunus avium/ cerasus of the same sample using chloroplast rbcL and nuclear ITS1 DNA markers. The results demonstrate the utility of waterlogged plant remains for genetic analysis: as seeds of fruit trees are often preserved waterlogged in the archaeological record. Ancient DNA (aDNA) studies are a promising tool to answer archaeobotanical issues concerning early horticulture, which probably started in the Northern alpine region with the onset of Romanisation.

Post-mortem DNA damage hotspots in Bison ( Bison bison) provide evidence for both damage and mutational hotspots in human mitochondrial DNA

Post-mortem damage-driven mutations are a phenomena associated with ancient DNA (aDNA) studies. A previous study has demonstrated that the distribution of such mutations in human mitochondrial DNA is not random, but is concentrated in ‘hotspots’ that correlate with sites of elevated mutation rate in vivo. However, as the previous study was undertaken on human samples, it is possible for a critic to argue that the results might be biased through the presence of modern contaminant DNA sequences among the ancient DNA extracts. In this study we confirm the phenomena of DNA damage hotspots using a data set that is unlikely to be affected by contamination – cloned mitochondrial control region sequences extracted from 81 ancient bison ( Bison bison). Furthermore, using published data from modern bovid specimens, we confirm that the damage hotspots correlate with sites of in vivo hypermutation. In conclusion, the aDNA sequences from archaeological specimens provide evidence that structural elements of mitochondrial DNA confer a degree of in vivo and post-mortem protection from sequence modification. This in turn provides useful insights into the debate as to whether mutational hotspots or mitochondrial recombination might best explain homoplasies observed on phylogenetic trees of human mitochondrial sequences.