Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe

Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.

Genomic History of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus

Here, we report genome-wide data analyses from 110 ancient Near Eastern individuals spanning the Late Neolithic to Late Bronze Age, a period characterized by intense interregional interactions for the Near East. We find that 6^th millennium BCE populations of North/Central Anatolia and the Southern Caucasus shared mixed ancestry on a genetic cline that formed during the Neolithic between Western Anatolia and regions in today's Southern Caucasus/Zagros. During the Late Chalcolithic and/or the Early Bronze Age, more than half of the Northern Levantine gene pool was replaced, while in the rest of Anatolia and the Southern Caucasus, we document genetic continuity with only transient gene flow. Additionally, we reveal a genetically distinct individual within the Late Bronze Age Northern Levant. Overall, our study uncovers multiple scales of population dynamics through time, from extensive admixture during the Neolithic period to long-distance mobility within the globalized societies of the Late Bronze Age. VIDEO ABSTRACT.

A migration-driven model for the historical spread of leprosy in medieval Eastern and Central Europe

Leprosy was rare in Europe during the Roman period, yet its prevalence increased dramatically in medieval times. We examined human remains, with paleopathological lesions indicative of leprosy, dated to the 6th-11th century AD, from Central and Eastern Europe and Byzantine Anatolia. Analysis of ancient DNA and bacterial cell wall lipid biomarkers revealed Mycobacterium leprae in skeletal remains from 6th-8th century Northern Italy, 7th-11th century Hungary, 8th-9th century Austria, the Slavic Greater Moravian Empire of the 9th-10th century and 8th-10th century Byzantine samples from Northern Anatolia. These data were analyzed alongside findings published by others. M. leprae is an obligate human pathogen that has undergone an evolutionary bottleneck followed by clonal expansion. Therefore M. leprae genotypes and sub-genotypes give information about the human populations they have infected and their migration. Although data are limited, genotyping demonstrates that historical M. leprae from Byzantine Anatolia, Eastern and Central Europe resembles modern strains in Asia Minor rather than the recently characterized historical strains from North West Europe. The westward migration of peoples from Central Asia in the first millennium may have introduced different M. leprae strains into medieval Europe and certainly would have facilitated the spread of any existing leprosy. The subsequent decline of M. leprae in Europe may be due to increased host resistance. However, molecular evidence of historical leprosy and tuberculosis co-infections suggests that death from tuberculosis in leprosy patients was also a factor.

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.