A Reanalysis of Eurasian Population History: Ancient DNA Evidence of Population Affinities

Mitochondrial hypervariable region I genetic data from ancient populations at two sites from Asia, Linzi in Shandong (northern China) and Egyin Gol in Mongolia, were reanalyzed to detect population affinities. Data from a total of 51 modern populations were used to generate distance measures (Fst's) to the two ancient populations. The tests first analyzed relationships at the regional level, and then compiled the top regional matches for an overall comparison to the two probe populations. The reanalysis showed that the Egyin Gol and Linzi populations have clear distinctions in genetic affinity. The Egyin Gol population as a whole appears to bear close affinities with modern populations of northern East Asia. The Linzi population does seem to have some genetic affinities with the West as suggested by the original analysis, though the original attribution of "European-like" seems to be misleading. This study suggests that the Linzi individuals are potentially related to early Iranians, who are thought to have been widespread in parts of Central Eurasia and the steppe regions in the first millennium BC, though some significant admixture between a number of populations of varying origin cannot be ruled out. The study also examines the effect of sequence length on this type of genetic data analysis and provides analysis and explanation for the results of previous studies on the Linzi sample as compared to this one.Comment: Keywords: d-loop, China, Mongolia, aDNA, mtDNA, Irania

U5a1 Mitochondrial DNA Haplotype Identified in Eneolithic Skeleton from Shatar Chuluu, Mongolia

The mitochondrial haplotype U5a1 was identified from an Eneolithic grave associated with the Afanasievo archaeological culture in Bayankhongor Province, Erdenetsogt Township, at the site of Shatar Chuluu. This is the earliest appearance of a mtDNA haplotype associated with modern European populations on the Mongol Steppe. This evidence demonstrations that people with “western” mtDNA lived on the Mongol Steppe east of the Altai Mountains before the Bronze Age and refutes the notion that the Altai Mountains were a substantial barrier to gene flow and definitively expands the acknowledged range of the Afanasievo archaeological culture

Molecular identification of parasites in an intestinal coprolite from a mummified religious dignitary of the Piraino Mother Church crypt, Sicily

Intestinal contents were sampled from a spontaneously enhanced mummy from the Sepulcher of the Priests of the Piraino Mother Church in the Province of Messina, Sicily. This adult male mummy, Piraino 1, is an unidentified religious dignitary dating from the late-18th to mid-19th centuries. Immunological and molecular diagnostics were used to test for common and clinically significant parasites. A morphological diagnosis of Trichuris trichiura (whipworm) was confirmed genetically. A previously undetected Enterobius vermicularis (pinworm) infection was also identified genetically. These data indicate that the Piraino 1 individual was simultaneously infected with multiple intestinal parasite species indicative of poor hygiene. This study also emphasizes the importance of utilizing multiple diagnostic techniques to detect pathogens from archaeological contexts

Patterns of mtDNA Diversity in Northwestern North America

The mitochondrial DNA (mtDNA) haplogroups of 54 full-blooded modern and 64 ancient Native Americans from northwestern North America were determined. The control regions of 10 modern and 30 ancient individuals were sequenced and compared. Within the Northwest, the frequency distribution for haplogroup A is geographically structured, with haplogroup A decreasing with distance from the Pacific Coast. The haplogroup A distribution suggests that a prehistoric population intrusion from the subarctic and coastal region occurred on the Columbia Plateau in prehistoric times. Overall, the mtDNA pattern in the Northwest suggests significant amounts of gene flow among Northwest Coast, Columbia Plateau, and Great Basin populations

Mitochondrial Genetic Diversity and its Determinants in Island Melanesia

For a long time, many physical anthropologists and human geneticists considered Island Melanesian populations to be genetically impoverished, dominated by the effects of random genetic drift because of their small sizes, internally very homogeneous, and therefore of little relevance in reconstructing past human migrations. This view is changing. Here we present the developing detailed picture of mitochondrial DNA (mtDNA) variation in eastern New Guinea and Island Melanesia that reflects linguistic distinctions within the region as well as considerable island-by-island isolation. It also appears that the patterns of variation reflect marital migration distinctions between bush and beach populations. We have identified a number of regionally specific mtDNA variants. We also question the widely accepted hypothesis that the mtDNA variant referred to as the ‘Polynesian Motif’ (or alternatively the ‘Austronesian Motif’) developed outside this region somewhere to the west. It may well have first appeared among certain non-Austronesian speaking groups in eastern New Guinea or the Bismarcks. Overall, the developing mtDNA pattern appears to be more easily reconciled with that of other genetic and biometric variables

Investigation of Ancient DNA from Western Siberia and the Sargat Culture

Mitochondrial DNA from 14 archaeological samples at the Ural State University in Yekaterinburg, Russia, was extracted to test the feasibility of ancient DNA work on their collection. These samples come from a number of sites that fall into two groupings. Seven samples are from three sites, dating to the 8th–12th century AD, that belong to a northern group of what are thought to be Ugrians, who lived along the Ural Mountains in northwestern Siberia. The remaining seven samples are from two sites that belong to a southern group representing the Sargat culture, dating between roughly the 5th century BC and the 5th century AD, from southwestern Siberia near the Ural Mountains and the present-day Kazakhstan border. The samples are derived from several burial types, including kurgan burials. They also represent a number of different skeletal elements and a range of observed preservation. The northern sites repeatedly failed to amplify after multiple extraction and amplification attempts, but the samples from the southern sites were successfully extracted and amplified. The sequences obtained from the southern sites support the hypothesis that the Sargat culture was a potential zone of intermixture between native Ugrian and/or Siberian populations and steppe peoples from the south, possibly early Iranian or Indo-Iranian, which has been previously suggested by archaeological analysis

Investigation of Ancient DNA from Western Siberia and the Sargat Culture

Mitochondrial DNA from 14 archaeological samples at the Ural State University in Yekaterinburg, Russia, was extracted to test the feasibility of ancient DNA work on their collection. These samples come from a number of sites that fall into two groupings. Seven samples are from three sites, dating to the 8th–12th century AD, that belong to a northern group of what are thought to be Ugrians, who lived along the Ural Mountains in northwestern Siberia. The remaining seven samples are from two sites that belong to a southern group representing the Sargat culture, dating between roughly the 5th century BC and the 5th century AD, from southwestern Siberia near the Ural Mountains and the present-day Kazakhstan border. The samples are derived from several burial types, including kurgan burials. They also represent a number of different skeletal elements and a range of observed preservation. The northern sites repeatedly failed to amplify after multiple extraction and amplification attempts, but the samples from the southern sites were successfully extracted and amplified. The sequences obtained from the southern sites support the hypothesis that the Sargat culture was a potential zone of intermixture between native Ugrian and/or Siberian populations and steppe peoples from the south, possibly early Iranian or Indo-Iranian, which has been previously suggested by archaeological analysis

Tuberculosis in the New World: a study of ribs from the Schild Mississippian population, West-Central Illinois

Vertebral lesions have been the main evidence for infection by the Mycobacterium tuberculosis complex (MTC) in paleopathology. Skeletal involvement is expected in a small percentage of infected individuals. Recently, several authors report a correlation between rib lesions and tuberculosis (TB) complex infection. This study tests the hypothesis that rib lesions can serve as a useful marker for MTC infection within the Mississippian Schild skeletal collection from West-Central Illinois. Ribs from 221 adults and juveniles were examined, and affected individuals were tested for TB complex infection. DNA from rib samples of affected individuals was amplified with primers targeting the IS6110 insertion element, which is common to all members of the TB complex. Although it cannot allow discrimination between different species of TB, IS6110 is present in many copies within their genomes, and its presence is thus an indication of MTC infection. The results support the use of rib lesions as a marker for TB infection. Additionally, we demonstrate that MTC DNA can be recovered from ribs that lack lesions in individuals who have lesions of other bones. We recommend that an examination of ribs be incorporated into investigations for TB

A pilot study into the effects of X-ray and computed tomography exposure on the amplification of DNA from bone

This research investigates the intersection of radiography and aDNA, two commonly used methods in bioarchaeology. The goal of this project was to investigate the effects of radiation on the ability to amplify DNA from bone. Bones (n = 124) from domestic pig (Sus scrofa) feet were randomly sorted into a control group and four treatment groups: (1) single exposure X-ray; (2) single exposure CT; (3) multiple exposures X-ray; and (4) multiple exposures CT. Number of PCR cycles required to amplify DNA in 100 bp, 200 bp and 400 bp segments were used as a proxy for the amount of available DNA. In the 200 bp CT sample, distal phalanges required significantly more amplification cycles than did the other bones and were removed from analysis. Results suggest that in general radiation exposure fragments DNA thereby decreasing the amount that is amplifiable. While these results are suggestive, further research is required to elucidate the degree to which radiation fragments DNA in archaeological specimens