Ancient DNA (ancient + dna)

Distribution by Scientific Domains

Selected Abstracts

Paleogenetical study of pre-Columbian samples from Pampa Grande (Salta, Argentina)

Fransisco R. Carnese
Abstract Ancient DNA recovered from 21 individuals excavated from burial sites in the Pampa Grande (PG) region (Salta province) of North-Western Argentina (NWA) was analyzed using various genetic markers (mitochondrial DNA, autosomal STRs, and Y chromosomal STRs). The results were compared to ancient and modern DNA from various populations in the Andean and North Argentinean regions, with the aim of establishing their relationships with PG. The mitochondrial haplogroup frequencies described (11% A, 47% B, and 42% D) presented values comparable to those found for the ancient Andean populations from Peru and San Pedro de Atacama. On the other hand, mitochondrial and Y chromosomal haplotypes were specific to PG, as they did not match any other of the South American populations studied. The described genetic diversity indicates homogeneity in the genetic structure of the ancient Andean populations, which was probably facilitated by the intense exchange network in the Andean zone, in particular among Tiwanaku, San Pedro de Atacama, and NWA. The discovery of haplotypes unique to PG could be due to a loss of genetic diversity caused by recent events affecting the autochthonous populations (establishment of the Inca Empire in the region, colonization by the Europeans). Am J Phys Anthropol 2010. © 2009 Wiley-Liss, Inc. [source]

Mitochondrial DNA analysis of Jomon skeletons from the Funadomari site, Hokkaido, and its implication for the origins of Native American

Noboru Adachi
Abstract Ancient DNA recovered from 16 Jomon skeletons excavated from Funadomari site, Hokkaido, Japan was analyzed to elucidate the genealogy of the early settlers of the Japanese archipelago. Both the control and coding regions of their mitochondrial DNA were analyzed in detail, and we could securely assign 14 mtDNAs to relevant haplogroups. Haplogroups D1a, M7a, and N9b were observed in these individuals, and N9b was by far the most predominant. The fact that haplogroups N9b and M7a were observed in Hokkaido Jomons bore out the hypothesis that these haplogroups are the (pre-) Jomon contribution to the modern Japanese mtDNA pool. Moreover, the fact that Hokkaido Jomons shared haplogroup D1 with Native Americans validates the hypothesized genetic affinity of the Jomon people to Native Americans, providing direct evidence for the genetic relationships between these populations. However, probably due to the small sample size or close consanguinity among the members of the site, the frequencies of the haplogroups in Funadomari skeletons were quite different from any modern populations, including Hokkaido Ainu, who have been regarded as the direct descendant of the Hokkaido Jomon people. It appears that the genetic study of ancient populations in northern part of Japan brings important information to the understanding of human migration in northeast Asia and America. Am J Phys Anthropol, 2009. © 2008 Wiley-Liss, Inc. [source]

Ancient DNA and Family Relationships in a Pompeian House

Giovanni Di Bernardo
Summary Archaeological, anthropological and pathological data suggest that thirteen skeletons found in a house at the Pompeii archaeological site, dated to 79 A.D., belong to one family. To verify this and to identify the relationships between these individuals, we analyzed DNA extracted from bone specimens. Specifically, hypervariable segment 1 (HVS1) of the human mitochondrial DNA (mtDNA) control region was amplified in two overlapping polymerase chain reactions and the sequences were compared to the revised Cambridge Reference Sequence. As independent controls, other polymorphic sites in HVS1, HVS2 and in the coding region were analyzed. We also amplified some short tandem repeats of the thirteen specimens. This study revealed that six of the thirteen individuals are indeed closely related. [source]

Confirmation of the presence of Mycobacterium tuberculosis complex-specific DNA in three archaeological specimens

Mark Spigelman
Abstract This journal published the first reported identification of Mycobacterium tuberculosis complex (MTB) DNA in ancient human remains but concerns were raised about the article two years after publication. These were based on methodology which, in the field of ancient DNA, was still developing. Here we present a re-examination of the 1993 research conducted on three specimens which exhibited palaeopathologies indicative of tuberculosis. The specimens were: an ulna from pre-European-contact Borneo, a spine from Byzantine Turkey, and a lumbar-sacral spine from 17th century Scotland. There was insufficient material to permit re-examination of all of the original samples. The earlier results were confirmed in two independent laboratories using different methodologies. MTB DNA complex-specific DNA amplicons were obtained, and sequenced in both laboratories, in a re-analysis of samples which supported the earlier findings. Copyright © 2002 John Wiley & Sons, Ltd. [source]

Ancient mitochondrial DNA analyses of Iberian sturgeons

A. Ludwig
Summary Today's European sturgeons are relics of erstwhile widely distributed populations, diminished mainly by overfishing and habitat changes over the centuries. While extinct European populations in the Baltic and North seas have been identified as Acipenser oxyrhinchus or A. sturio, a clear species determination on the Iberian Peninsula is still lacking. Plans to conserve existing populations and to re-introduce extinct wild populations in European rivers will benefit from information of historic population/genotype composition. In this study, we used techniques involving ancient DNA as well as morphological comparisons based on bony scutes to identify twelve samples from five archaeological sites (650bc,1500ad, one sample dated 10.1,11.8 ky) on the Iberian Peninsula. All amplified PCR products of bony scutes (n = 5) had the mitochondrial DNA haplotypes of European sturgeon. Neither mitochondrial haplotypes of A. naccarii nor mitochondrial haplotypes of A. oxyrinchus were found. [source]

Bacterial ancient DNA as an indicator of human presence in the past: its correlation with palynological and archaeological data,

Jacek Madeja
Abstract Palynological investigation is one of the most important tools for reconstructing past vegetation. Some plants have proved to be relatively sensitive indicators of human activity, but most of them are not specific. In this paper we propose a method which can be used for the verification of phases of anthropogenic impact on vegetation distinguished in pollen diagrams. In this work we adopted the existing molecular methods for tracking bacterial ancient DNA of Bifidobacterium and Bacteroides-Prevotella (known as human- and cow-specific genetic markers) in palynologically and archaeologically associated sediments. This method can be helpful in determining local human presence, especially in those time periods when pollen analysis has not always been very discriminating (Palaeolithic, Mesolithic) and at sites without archaeological evidence. Copyright © 2008 John Wiley & Sons, Ltd. [source]

THE STATE OF THE FIELD: Combining contemporary and ancient DNA in population genetic and phylogeographical studies

Abstract The analysis of ancient DNA in a population genetic or phylogeographical framework is an emerging field, as traditional analytical tools were largely developed for the purpose of analysing data sampled from a single time point. Markov chain Monte Carlo approaches have been successfully developed for the analysis of heterochronous sequence data from closed panmictic populations. However, attributing genetic differences between temporal samples to mutational events between time points requires the consideration of other factors that may also result in genetic differentiation. Geographical effects are an obvious factor for species exhibiting geographical structuring of genetic variation. The departure from a closed panmictic model require researchers to either exploit software developed for the analysis of isochronous data, take advantage of simulation approaches using algorithms developed for heterochronous data, or explore approximate Bayesian computation. Here, we review statistical approaches employed and available software for the joint analysis of ancient and modern DNA, and where appropriate we suggest how these may be further developed. [source]

Technical note: PCR analysis of minimum target amount of ancient DNA

Daniela Woide
Abstract The study of ancient DNA plays an important role in archaeological and palaeontological research as well as in pathology and forensics. Here, we present a new tool for ancient DNA analysis, which overcomes contamination problems, DNA degradation, and the negative effects of PCR inhibitors while reducing the amount of starting target material in the picogram range. Ancient bone samples from four Egyptian mummies were examined by combining laser microdissection, conventional DNA extraction, and low-volume PCR. Initially, several bone particles (osteons) in the micrometer range were extracted by laser microdissection. Subsequently, ancient DNA amplification was performed to verify our extraction method. Amelogenin and ,-actin gene specific fragments were amplified via low-volume PCR in a total reaction volume of 1 ,l. Results of microdissected mummy DNA samples were compared to mummy DNA, which was extracted using a standard DNA extraction method based on pulverization of bone material. Our results highlight the combination of laser microdissection and low-volume PCR as a promising new technique in ancient DNA analysis. Am J Phys Anthropol, 2010. © 2010 Wiley-Liss, Inc. [source]

Brief communication: Identification of the authentic ancient DNA sequence in a human bone contaminated with modern DNA

Abigail S. Bouwman
Abstract We present a method to distinguish authentic ancient DNA from contaminating DNA in a human bone. This is achieved by taking account of the spatial distribution of the various sequence families within the bone and the extent of degradation of the template DNAs, as revealed by the error content of the sequences. To demonstrate the veracity of the method, we handled two ancient human tibiae in order to contaminate them with modern DNA, and then subjected segments of the bones to various decontaminating treatments, including removal of the outer 1,2 mm, before extracting DNA, cloning, and obtaining a total of 107 mitochondrial DNA sequences. Sequences resulting from the deliberate contamination were located exclusively in the outer 1,2 mm of the bones, and only one of these 27 sequences contained an error that could be ascribed to DNA degradation. A second, much smaller set of relatively error-free sequences, which we ascribe to contamination during excavation or curation, was also located exclusively in the outer 1,2 mm. In contrast, a family of 72 sequences, displaying extensive degradation products but identifiable as haplogroup U5a1a, was distributed throughout one of the bones and represents the authentic ancient DNA content of this specimen. Am J Phys Anthropol, 2006. © 2006 Wiley-Liss, Inc. [source]

Long-term survival of ancient DNA in Egypt: Reply to Gilbert et al.

Albert R. Zink
First page of article [source]

Detection of bone glue treatment as a major source of contamination in ancient DNA analyses

Graeme J. Nicholson
Abstract Paleogenetic investigations of ancient DNA extracted from fossil material is for many reasons susceptible to falsification by the presence of more recent contamination from several sources. Gelatine-based bone glue that has been used extensively for nearly two centuries by curators to preserve hard tissues contributes nonauthentic DNA to paleontological material. This fact has been frequently neglected and is barely mentioned in the literature. Now paleogeneticists, curators, and conservators are faced with the problem that treatment of samples with adhesives and consolidants for conservatory purposes has seldom been recorded. Here, we show that racemization of amino acids, and in particular serine, is an excellent indicator for the treatment of paleontological samples with glue. Am J Phys Anthropol 118:117,120, 2002. © 2002 Wiley-Liss, Inc. [source]