Ten millennia of hepatitis B virus evolution

[Figure: see text].

Emergence of human-adapted Salmonella enterica is linked to the Neolithization process

It has been hypothesized that the Neolithic transition towards an agricultural and pastoralist economy facilitated the emergence of human adapted pathogens. Here, we recovered eight Salmonella enterica subsp. enterica genomes from human skeletons of transitional foragers, pastoralists, and agro-pastoralists in western Eurasia that were up to 6,500 years old. Despite the high genetic diversity of S. enterica all ancient bacterial genomes clustered in a single previously uncharacterized branch that contains S. enterica adapted to multiple mammalian species. All ancient bacterial genomes from prehistoric (agro-)pastoralists fall within a part of this branch that also includes the human-specific S. enterica Paratyphi C, illustrating the evolution of a human pathogen over a period of five thousand years. Bacterial genomic comparisons suggest that the earlier ancient strains were not host specific, differed in pathogenic potential, and experienced convergent pseudogenization that accompanied their downstream host adaptation. These observations support the concept that the emergence of human adapted S. enterica is linked to human cultural transformations.

Amino acid 15 N analysis reveals change in the importance of freshwater resources between the hunter-gatherer and farmer in the Neolithic upper Tigris

OBJECTIVE

The inhabitants of several sites in the Upper Tigris Valley, such as Hakemi Use, domesticated animals and cereals during the Pottery Neolithic period, while the inhabitants in this valley were hunter-gatherers in the Pre-Pottery Neolithic period, consuming freshwater and terrestrial food resources. However, there is considerable uncertainty surrounding whether or not changes in dietary food composition accompanied the shift in food production away from foraging. In order to reveal the impact of the development of agriculture on the human diet over the Pre-Pottery and Pottery Neolithic periods in this region, we analyzed the isotopic compositions of amino acids from the farmers at the Hakemi Use Pottery Neolithic site, and compared them with those from the Pre-Pottery hunter-gatherers in the close region.

MATERIALS AND METHODS

Herein, we report the nitrogen isotopic compositions of amino acids, as well as both carbon and nitrogen isotopic compositions of bulk collagen, from human and faunal remains collected from Hakemi Use.

RESULTS

Whereas freshwater resources were consumed by hunter-gatherers in this region during the Pre-Pottery period, the δ¹⁵ N values of glutamic acid (δ¹⁵ N_Glu ) and phenylalanine (δ¹⁵ N_Phe ) suggest that freshwater food resources were rarely consumed by inhabitants following the development of agriculture.

DISCUSSION

Despite living in similar settings by the Tigris as its inhabitants during the Pre-Pottery period, the farmers of the Pottery Neolithic period depended less on freshwater resources for their diets relative to the hunter-gatherers of the Pre-Pottery Neolithic period.

Geometric morphometric study and cluster analysis of late Byzantine and modern human crania

Inter-population variation of cranial morphology, which plays an important role in human evolution studies and biological research, can be studied morphologically and metrically. Geometric morphometry compares body forms using specific landmarks determined by anatomical prominences. The aim of this study was to identify cranial shape differences between the crania of Byzantium period humans and modern humans. Variability in cranial shape was examined using the geometric morphometric technique based on landmark coordinates. Landmark coordinate data were collected from two-dimensional digital photogrammetry and were analyzed using generalized Procrustes analysis, hierarchical clustering and thin-plate spline analysis.

Why did the frequency of palatine torus increase in the ancient Anatolian populations?

The frequency of the palatine torus varies in various populations from different regions of the world. In this study, the change of frequency of palatine torus is examined using 387 skulls from 12 different ancient Anatolian populations in various periods ranging from the Early Bronze Age to the first quarter of the 20th century. While the frequency of palatine torus is 45% in the Early Bronze Age, this ratio steadily increases to 87% in the Ottoman Period and finally declines to 40% during the recent period. It was determined that the increase in the frequency of the palatine torus is statistically significant across different periods from the Early Bronze Age until the 20th century. Constituting a passageway between Asia and Europe and being located on the crossroads of the most important trade route of the Medieval Period, the Silk Road, Anatolia is known to have been subjected to recurring invasions and migrations since the 11th century A.D. Therefore, it is possible to say that, with the introduction of the Mongoloid influence in Anatolia, genetic flow has had a significant role in the observed increase in the frequency of this trait.

A new approach for calibrating dental caries frequency of skeletal remains

It is a fact that researchers make use of various calibration methods for calculating and correcting dental caries frequency. The lack of standardization and accuracy of such methods has made it difficult for the researchers to draw reliable and differentiated conclusions from caries frequencies. Besides, the number of studies on how far the calculation methods reflect the "real" caries frequency is very limited. In this study, various methods for calculating caries frequency in skeletal samples are discussed and a new calculation method is proposed for estimating "real" caries frequency. The Hardwick's correction, which is one of the methods discussed in this study, is not successful in estimating "real" caries frequency as it proposes standard values for different life styles and dietary habits. The decayed and missing index is also considered inefficient as it assumes that all antemortem tooth loss is due to caries. The caries correction factor, proposed by Lukacs, achieves more successful results by considering factors other than caries in antemortem tooth loss, but because it does not differentiate between the anterior and posterior tooth groups during calculation, the results to be obtained therefrom may deviate from actual figures. In order to correct any such deviation, the caries correction factor must be applied separately for the anterior and posterior teeth groups since the resistance of each group to cariogenic factors is different. All the methods outlined above do not consider the effects of postmortem tooth loss on caries frequency. As a result, these methods are still far from reflecting a reliable caries frequency. The application of a proportional correction factor--as a technique newly introduced here--corrects the deviation caused by postmortem tooth loss and achieves more realistic results.

A new correction procedure for calibrating dental caries frequency

The incisors and canines and the premolars and molars show differential resistance to cariogenic factors. The anterior teeth have a lower caries frequency than the posterior teeth. However, these tooth classes are lost differentially in postmortem stages due to their anatomical structures. This differential postmortem tooth loss distorts proportions between the anterior and posterior tooth classes. The disproportionality can affect the calculation of total caries prevalence. In this paper, we propose a new calibration procedure which removes this disproportionality and call it the proportional correction factor. For this procedure, the caries rates of anterior and posterior teeth are corrected by multiplying the anterior teeth by three-eighths and the posterior teeth by five-eighths. These fractions are derived from the human dental formula which contains three anterior and five posterior teeth by side. The correction factor is more effective if the proportion of anterior to the posterior teeth is extremely distorted. When this procedure is used with the caries correction factor, it provides a useful way to approach to an almost true caries prevalence.