Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, today infects a majority of adults globally1, yet no ancient HSV-1 genomes have yet been published. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups2, 3 has suggested that the virus co-diverged with anatomically modern humans migrating out of Africa4, although a much younger origin has also been proposed5. The lack of ancient HSV-1 genomes, high rates of recombination, and high mobility of humans in the modern era have impeded the understanding of HSV-1’s evolutionary history. Here we present three full ancient European HSV-1 genomes and one partial genome, dating to between the 3rd and 17th century CE, sequenced to up to 9.5× with paired human genomes up to 10.16×. These HSV-1 strains fall within modern Eurasian diversity. We estimate a mean mutation rate of 7.6 × 10-7Introduction Results - Retrieved genomes are likely from typical infections - Demographic history of HSV-1 in a global context Discussion Material and Methods - Ethics statement - Sampling - Generation of aDNA libraries - Sequencing - aDNA authentication - Metagenomic screening - Targeted capture of HSV-1 - Alignment of viral data to the reference sequence - Genotyping - HSV-1 linkage disequilibrium and population genetic analysis - Compilation of comparative HSV data - Preparation of genome sequences - HSV-1 phylogenetic analysis and recombination filtering - Phylogenetic dating - Alignment of human data to the reference sequence and quality control - Genetic sex estimation, mtDNA, and Y haplotyping - Human variant calling and imputation of genotype

Complex permittivity measurements for moisture and salinity characterization of building materials

In this paper, preliminary results of complex permittivity measurements of clay-brick material will be presented. The general aim of the experimental project is to correlate the measured permittivity of construction materials with the content of water and salt, in order to obtain information on the condition of ancient walls by using non-invasive techniques. The complex permittivity values reported in this paper have been obtained by waveguide measurements on samples of clay-brick dried and then immersed in demineralized water or in a saturated solution of demineralized water and NaCl

Genetic diversity at three palindromic sequences of the human Y chromosome

One of the most striking structural features of the male specific region of the human Y chromosome (MSY) is the presence, within the ampliconic sequences, of eight massive palindromes (P1-P8). Each palindrome is composed of two large inverted repeats (arms) separated by a small “spacer” sequence at the centre. These elements, ranging from 30 kb to 2.9 Mb, contain many testis-specific genes and typically exhibit > 99.9% intra-palindromic (arm-to-arm) sequence identity. It has been hypothesized that the high observed sequence similarity is due to abundant gene conversion events between the arms of each palindrome. Although the occurrence of arm-to-arm gene conversion has been clearly demonstrated, the effect of this molecular mechanism on the genetic diversity of palindromes, as well as its rate and extension, remain largely unexplored. To gain new insights into the evolutionary history of the human Y chromosome palindromic sequences and to shed light into the dynamics of intra-palindrome gene conversion, we analysed by high-coverage next- generation sequencing (50x) the shortest known palindromes (P6, P7 and P8) and their relative spacers (for a total of about 0.3 Mb) in 158 samples chosen to represent most of the independent evolutionary lineages (haplogroups) of the MSY. By this analysis we identified several gene conversion events and a peculiar mutational pattern of the palindrome arms with respect to the spacer. Moreover, we found few phylogenetically conserved paralogous sequence variants (PSVs), suggestive of a high arm-to-arm gene conversion activity. Because Y chromosomes are clonally inherited from father to son, it has been possible to capture their evolutionary relationships in a robust phylogenetic tree with known age of each node. By mapping gene conversion events across a Y tree based on thousands of stable mutations obtained from 3.3 Mb of single copy MSY sequences, we were able to calculate a precise Y-Y gene conversion rate for each of the palindromes here analysed

Human Y chromosome diversity and the peopling of the “Green Sahara” during the Holocene humid phase

In Africa, the human population dynamics have been heavily influenced by the Sahara desert, as suggested by the strong Y haplogroup differentiation between northern and sub-Saharan Africa. During the Holocene, the climatic changes of the “African humid period” led to the replacement of the desert with a fertile environment (the “Green Sahara”), which allowed human settlements as indicated by archeological and paleoanthropological evidences. To evaluate the extent and trajectories of human movements across the Sahara, we analyzed by NGS about 3.3 Mb of the X-degenerate portion of the Y chromosome in 104 subjects, focusing on haplogroups currently found both in northern Africa and in the sub-Saharan area. We identified 7,544 polymorphisms, which were used to reconstruct the phylogeny and to estimate the coalescence age of nodes. Informative markers were further analyzed in a wider set of about 5,000 Y chromosomes. Combining phylogeography and age estimates, we found that northern African and sub-Saharan lineages only coalesced within a 5-12 kya time frame, suggesting extensive human movements across the “Green Sahara” and subsequent isolation after the desertification

Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, infects a majority of adults globally. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups has suggested the virus codiverged with human migrations out of Africa, although a much younger origin has also been proposed. We present three full ancient European HSV-1 genomes and one partial genome, dating from the 3rd to 17th century CE, sequenced to up to 9.5× with paired human genomes up to 10.16×. Considering a dataset of modern and ancient genomes, we apply phylogenetic methods to estimate the age of sampled modern Eurasian HSV-1 diversity to 4.68 (3.87 to 5.65) ka. Extrapolation of estimated rates to a global dataset points to the age of extant sampled HSV-1 as 5.29 (4.60 to 6.12) ka, suggesting HSV-1 lineage replacement coinciding with the late Neolithic period and following Bronze Age migrations

Low Genetic Impact of the Roman Occupation of Britain in Rural Communities

Acknowledgements: We thank the support of the Cambridge Archaeological Unit, the other members of the After the Plague project (Piers Mitchell, Bram Mulder, and Jay Stock), the Estonian Biocentre and aDNA group for their help and expertise, and Stephen Hoper and Paula Reimer and the 14Chrono Centre at Queen's University Belfast for assistance with the radiocarbon dates. A.R. acknowledges support from the British Archaeological Association. This research has been conducted using the UK Biobank Resource under Application Number 54698. Data analyses were carried out with the facilities of the High-Performance Computing Center of the University of Tartu.Funder: St John's College, CambridgeAbstract The Roman period saw the empire expand across Europe and the Mediterranean, including much of what is today Great Britain. While there is written evidence of high mobility into and out of Britain for administrators, traders, and the military, the impact of imperialism on local, rural population structure, kinship, and mobility is invisible in the textual record. The extent of genetic change that occurred in Britain during the Roman military occupation remains underexplored. Here, using genome-wide data from 52 ancient individuals from eight sites in Cambridgeshire covering the period of Roman occupation, we show low levels of genetic ancestry differentiation between Romano-British sites and indications of larger populations than in the Bronze Age and Neolithic. We find no evidence of long-distance migration from elsewhere in the Empire, though we do find one case of possible temporary mobility within a family unit during the Late Romano-British period. We also show that the present-day patterns of genetic ancestry composition in Britain emerged after the Roman period.</jats:p

Low Genetic Impact of the Roman Occupation of Britain in Rural Communities

Acknowledgements: We thank the support of the Cambridge Archaeological Unit, the other members of the After the Plague project (Piers Mitchell, Bram Mulder, and Jay Stock), the Estonian Biocentre and aDNA group for their help and expertise, and Stephen Hoper and Paula Reimer and the 14Chrono Centre at Queen's University Belfast for assistance with the radiocarbon dates. A.R. acknowledges support from the British Archaeological Association. This research has been conducted using the UK Biobank Resource under Application Number 54698. Data analyses were carried out with the facilities of the High-Performance Computing Center of the University of Tartu.Funder: St John's College, CambridgeThe Roman period saw the empire expand across Europe and the Mediterranean, including much of what is today Great Britain. While there is written evidence of high mobility into and out of Britain for administrators, traders, and the military, the impact of imperialism on local, rural population structure, kinship, and mobility is invisible in the textual record. The extent of genetic change that occurred in Britain during the Roman military occupation remains underexplored. Here, using genome-wide data from 52 ancient individuals from eight sites in Cambridgeshire covering the period of Roman occupation, we show low levels of genetic ancestry differentiation between Romano-British sites and indications of larger populations than in the Bronze Age and Neolithic. We find no evidence of long-distance migration from elsewhere in the Empire, though we do find one case of possible temporary mobility within a family unit during the Late Romano-British period. We also show that the present-day patterns of genetic ancestry composition in Britain emerged after the Roman period

Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, infects a majority of adults globally. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups has suggested the virus codiverged with human migrations out of Africa, although a much younger origin has also been proposed. We present three full ancient European HSV-1 genomes and one partial genome, dating from the 3rd to 17th century CE, sequenced to up to 9.5× with paired human genomes up to 10.16×. Considering a dataset of modern and ancient genomes, we apply phylogenetic methods to estimate the age of sampled modern Eurasian HSV-1 diversity to 4.68 (3.87 to 5.65) ka. Extrapolation of estimated rates to a global dataset points to the age of extant sampled HSV-1 as 5.29 (4.60 to 6.12) ka, suggesting HSV-1 lineage replacement coinciding with the late Neolithic period and following Bronze Age migrations