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 arrays such as the 1240K, 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 1240K capture, YMCA significantly improves the coverage and number of sites hit 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.Competing Interest StatementThe authors have declared no competing interest.Introduction Results and Discussion - Validating the performance of YMCA - Application of YMCA to YHG H2 as a case study - Identifying diagnostic SNPs for improved YHG H2 resolution Discussion Materials and Methods - Data - Contamination quality filtering - Method of Y Haplogroup Assignment - Comparing the Performance of our Y-capture Array Phylogenetic Tree Reconstructio

Ten millennia of hepatitis B virus evolution

Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between similar to 10,500 and similar to 400 years ago. We date the most recent common ancestor of all HBV lineages to between similar to 20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for similar to 4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic.Molecular Technology and Informatics for Personalised Medicine and Healt

A numerical algorithm for modelling boson-fermion stars in dilatonic gravity

We investigate numerically the class of models of the static spherically symmetric boson-fermion stars in the scalar-tensor theory of gravity with massive dilaton field. The proper mathematical model of such stars is interpreted as a nonlinear two-parametric eigenvalue problem. The first of the parameters is the unknown internal boundary (the radius of the fermionic part of the star) R sub s , and the second one represents the frequency OMEGA of the time oscillations of the boson field. To solve this problem, the whole space [0, infinity) is splitted into two domains: internal [0, R sub s] (inside the star) and external [R sub s , infinity) (outside the star). In each domain the physical model leads to two nonlinear boundary value problems in respect to metric functions, the functions describing the fermionic and bosonic matter, and the dilaton field. These boundary value problems have different dimensions inside and outside the star, respectively. The solutions in these regions are obtained separately and matched using the necessary algebraic continuity conditions including R sub s and OMEGA. The continuous analogue of the Newton method for solving both the nonlinear differential and algebraic problems is used. The corresponding linearized boundary value problems at each iteration are solved by means of spline-collocation scheme. In this way, we obtain the behaviour of the basic geometric quantities and functions describing a dilaton field and matter fields, which build the sta