Canary islands aborigin sex determination based on mandible parameters contrasted by amelogenin analysis

Sex determination using mandible parameters is population dependent. In order to assess which measurements better characterize sex in prehispanic individuals from the Canary Islands, we blindly contrasted the results obtained by visual inspection and osteometric measurements with those obtained by molecular sexing using amelogenin ancient DNA analysis on teeth from the same material. Unambiguous sex classification was achieved by amplification of sex specific amelogenin alleles in 56 out of 76 mandibles (73.78% of the cases). Visual inspection led to a correct diagnosis in 66.04% of cases, with a greater proportion of errors for female (54.17%) than male (17.24%) mandibles. Osteometric measurements were able to assign sex correctly in 72.2% in the best of cases (mandibular height), a proportion similar to that obtained using a discriminant function (71.2%). By logistic regression analysis, ramus breadth, index ramus breadth/ramus height and mandibular length were the parameters independently related with a mistaken diagnosis of female sex, whereas bigonial width, ramus height and mandibular length were the parameters more closely and independently related to a mistaken diagnosis of male sex. In conclusion, diagnosis based on visual examination of the mandible or on its metric measurement only serves to roughly estimate sex with an accuracy of around 70% or less, at least among the prehispanic population from Gran Canaria. Amplification of amelogenin alleles leads to unambiguous identification of male and female alleles in 73.68% of cases, at least among the prehispanic population from Gran Canaria.     

Mitochondrial DNA Analysis of Ancient Domestic Goats in the Southern Caucasus: A Preliminary Result from Neolithic Settlements at Göytepe and Hacı Elamxanlı Tepe

This study presents preliminary results of mitochondrial DNA analyses of modern and ancient domestic goats in the southern Caucasus in order to examine their phylogenetic relationship with modern and ancient goats. For this purpose, seven ancient samples were obtained from two early agricultural villages in west Azerbaijan (Göytepe and Hacı Elamxanlı tepe, dated to ca. 6000–5500 cal bc , the Pottery Neolithic period), in addition to five modern goat samples in the same region. In the study, mitochondrial DNA segments of the control region (216 bp for the Neolithic samples and 481 bp for the modern samples) were amplified, and phylogenetic analyses were performed using previously published reference DNA sequences. As a result, all the haplotypes found in this study were grouped in the haplogroup A of goats. The finding of the haplogroup A among domestic goats in the southern Caucasus in the early sixth millennium bc can be interpreted as part of the geographic expansion of this lineage from the areas of initial domestication to surrounding areas that include also South and Southeast Europe. In the southern Caucasus, the haplogroup A probably continued to be a major lineage among domestic goats since their emergence in this area to the present. In contrast, this lineage has not been detected among local wild goats including Capra aegagrus , indicating the external origin of domestic goats. This possibility is consistent with archaeological records that indicate sudden appearance of agricultural lifeways in the southern Caucasus and cultural connections with northern Mesopotamia. Copyright © 2016 John Wiley & Sons, Ltd.     

Biosocial archaeology of the Early Neolithic: Synthetic analyses of a human skeletal population from the LBK cemetery of Vedrovice,Czech Republic

Bioarchaeology is a powerful tool in the examination of prehistoric collections of human skeletal remains. Application of a few bioarchaeological techniques (ancient DNA, carbon and nitrogen stable isotopes, and dental micro-wear) to the human osteological remains from the Early Neolithic LBK settlement of Vedrovice (Moravia), has allowed us to reconstruct not only broad cultural patterns but also the life histories of the individuals with insights into diet, migrations, ancestry, personal identity, social position and life experience. Vedrovice acted as a gateway settlement for a farming community with close ties to western Hungary and northeast Bohemia. The individuals showed clear differences in status and migration histories, giving glimpses of more complex social practices and patterns than could have been determined through the traditional culture-historical studies.     

Accurate sex identification of ancient human remains using DNA shotgun sequencing

Accurate identification of the biological sex of ancient remains is vital for critically testing hypotheses about social structure in prehistoric societies. However, morphological methods are imprecise for juvenile individuals and fragmentary remains, and molecular methods that rely on particular sex-specific marker loci such as the amelogenin gene suffer from allelic dropout and sensitivity to modern contamination. Analyzing shotgun sequencing data from 14 present-day humans of known biological sex and 16 ancient individuals from a time span of 100 to ∼70,000 years ago, we show that even relatively sparse shotgun sequencing (about 100,000 human sequences) can be used to reliably identify chromosomal sex simply by considering the ratio of sequences aligning to the X and Y chromosomes, and highlight two examples where the genetic assignments indicate morphological misassignment. Furthermore, we show that accurate sex identification of highly degraded remains can be performed in the presence of substantial amounts of present-day contamination by utilizing the signature of cytosine deamination, a characteristic feature of ancient DNA.     

Sex identification of ancient DNA samples using a microfluidic device

A microfluidic device has been developed for the sex identification of ancient DNA samples and works by manipulating liquids within an environment of micrometer dimensions. In this work a range of microfluidic DNA extraction methods were evaluated for their compatibility with ancient DNA samples, and the use of streptavidin-coated super paramagnetic particles to isolate biotin-labeled abasic sites within damaged DNA was shown to be the most reproducible. Polymerase chain reaction-based DNA amplification was possible on the microfluidic device when less than 50 pg of template DNA was added. As a proof-of-principle, powdered bone samples were analysed using the integrated methodology developed. Following conventional capillary gel electrophoresis, two out of the three samples produced positive amplification results and were successfully identified as female. These sex identifications were corroborated by independent Amelogenin, anthropological and Y chromosome analysis. The work reported here is the first step in the development of a complete miniaturized microfluidic system that would enable on-site ancient DNA analysis.     

The role of canids in ritual and domestic contexts: new ancient DNA insights from complex hunter–gatherer sites in prehistoric Central California

This study explores the interrelationship between the genus Canis and hunter–gatherers through a case study of prehistoric Native Americans in the San Francisco Bay-Sacramento Delta area. A distinctive aspect of the region's prehistoric record is the interment of canids, variously classified as coyotes, dogs, and wolves. Since these species are difficult to distinguish based solely on morphology, ancient DNA analysis was employed to distinguish species. The DNA study results, the first on canids from archaeological sites in California, are entirely represented by domesticated dogs (including both interments and disarticulated samples from midden deposits). These results, buttressed by stable isotope analyses, provide new insight into the complex interrelationship between humans and canids in both ritual and prosaic contexts, and reveal a more prominent role for dogs than previously envisioned.     

Kinship and mobility in 11th-century A.D. Gammertingen,Germany: an interdisciplinary approach

Excavation in and around a Medieval church in Gammertingen, Germany, revealed the skeletal remains of eight individuals dating to the 10th and 11th century AD. Archaeologists hypothesized that the individuals were the first members of a family later known as the Counts of Gammertingen, a medieval high nobility family. In an interdisciplinary approach, Strontium isotope and ancient DNA techniques were performed in order to test the hypothesis that the church was used as a family burial site and to investigate the provenance of family members. Seven of the eight individuals can be placed in a three-generation genealogy. The isotope analyses establish that the eighth individual had a different birthplace and possibly became a member of the Counts of Gammertingen through marriage. Further, genetic data revealed that distant relatives of the paternal lineage are still present in this area today. Thus, the combined results lead to a very detailed knowledge about a 1000-year old noble family.     

Next generation sequencing of DNA in 3300-year-old charred cereal grains

We investigated whether ‘next generation’ methods can be used to sequence ancient DNA molecules in charred cereal grains. We prepared a DNA extract from a mixed sample of barley, einkorn, emmer and broomcorn millet, taken from a 3300-year-old assemblage of charred cereal grains from Assiros Toumba, Greece. Using the SOLiD 5500 system, we obtained 21,112,844 unique sequence reads. Of these, 178,779 had a 75% or greater nucleotide sequence similarity with one or more entries in the full nucleotide sequence database; 496 of these matches were to previously reported sequences from barley, einkorn, emmer, broomcorn millet or related species such as hexaploid wheat. The unique reads were also compared with a database comprising only wheat sequences. This analysis identified 1658 charred grain sequences that had 90% or greater similarity with segments of the wheat genome. The presence of barley, wheat and millet sequences in the next generation dataset confirms the presence of ancient DNA in this charred grain assemblage. Enrichment of extracts by hybridization capture or equivalent methods is likely to enable sequences to be obtained for entire genes and other genomic regions of interest.     

Latitudinal variation in a photoperiod response gene in European barley: insight into the dynamics of agricultural spread from ‘historic’ specimens

Between ca. 6000 BC and ca. 500 BC, barley cultivation spread across the continent of Europe from the extreme south to the extreme north. Carbon-dating would suggest that this spread, and indeed the spread of crop cultivation generally, varied in its pace, with ‘delays’ at certain points along its route. Such delays in the spread of agriculture have been explained as resulting from the slow assimilation of agricultural practices by existing indigenous human populations or as the time taken for the crops to adapt to novel climatic conditions, such as altered temperature regimes and day-lengths. A mutant form of the photoperiod response gene, Ppd-H1, causes barley to be non-responsive to long days, while the wild-type responsive form allows plants to flower in response to long days. We sequenced this gene in 65 ‘historic’ barley accessions, from the late 19th and early 20th centuries, in order to explore the potential role of environmental adaptation in the spread of agriculture. We chose to use ‘historic’ material, to complement the richer patterns in extant genetic lines, by spreading the data range in both time and space. Our ‘historic’ barley data shows a latitudinal divide in the Ppd-H1 gene similar to that found in extant lines, but with clearer geographical resolution, and extending northwards into the Arctic Circle. We discuss the implications of our results in relation to the dynamics of agricultural spread across Europe.     

Deficiencies and challenges in the study of ancient tuberculosis DNA

We explore the standards of research and reporting needed to justify the destructive analysis of archaeological human bone for biomolecular studies of ancient tuberculosis (TB). Acceptable standards in osteological interpretation have been met in some biomolecular papers, but there are also cases where insufficient care has been taken in distinguishing between pathognomonic lesions and those that are ‘consistent with’ a diagnosis of TB. Some biomolecular studies have failed to recognize that archaeological bones might be contaminated with environmental mycobacteria whose DNA could give rise to false positives in polymerase chain reactions directed at members of the Mycobacterium tuberculosis complex. The difficulties of applying spoligotyping to ancient DNA have also been underestimated and conclusions drawn from such analyses are often weakly supported. Assumptions that mycobacterial DNA preserves better than human DNA, and that contamination with modern DNA is less of a problem, has led in some cases to a laxity in research standards with insufficient attention paid to the need to authenticate ancient DNA results. We illustrate our concerns by reference to a recent paper reporting biomolecular detection of ancient TB DNA in skeletons from the eastern Mediterranean Neolithic settlement of Atlit-Yam. We are unconvinced that the skeletal evidence presented in this paper gives sufficient indication of TB to warrant destructive analysis, and we are concerned that during the biomolecular part of the project inadequate attention was paid to the possibility that results might be due to laboratory cross-contamination or to amplification of environmental mycobacterial DNA present in the bones.