Subdividing Y-chromosome haplogroup R1a1 reveals Norse Viking dispersal lineages in Britain

The influence of Viking-Age migrants to the British Isles is obvious in archaeological and place-names evidence, but their demographic impact has been unclear. Autosomal genetic analyses support Norse Viking contributions to parts of Britain, but show no signal corresponding to the Danelaw, the region under Scandinavian administrative control from the ninth to eleventh centuries. Y-chromosome haplogroup R1a1 has been considered as a possible marker for Viking migrations because of its high frequency in peninsular Scandinavia (Norway and Sweden). Here we select ten Y-SNPs to discriminate informatively among hg R1a1 sub-haplogroups in Europe, analyse these in 619 hg R1a1 Y chromosomes including 163 from the British Isles, and also type 23 short-tandem repeats (Y-STRs) to assess internal diversity. We find three specifically Western-European sub-haplogroups, two of which predominate in Norway and Sweden, and are also found in Britain; starlike features in the STR networks of these lineages indicate histories of expansion. We ask whether geographical distributions of hg R1a1 overall, and of the two sub-lineages in particular, correlate with regions of Scandinavian influence within Britain. Neither shows any frequency difference between regions that have higher (≥10%) or lower autosomal contributions from Norway and Sweden, but both are significantly overrepresented in the region corresponding to the Danelaw. These differences between autosomal and Y-chromosomal histories suggest either male-specific contribution, or the influence of patrilocality. Comparison of modern DNA with recently available ancient DNA data supports the interpretation that two sub-lineages of hg R1a1 spread with the Vikings from peninsular Scandinavia

The Y-Chromosome Tree Bursts into Leaf: 13,000 High-Confidence SNPs Covering the Majority of Known Clades

Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51x, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analyzing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of nonsynonymous variants in 15 MSY single-copy genes

A global analysis of Y-chromosomal haplotype diversity for 23 STR loci

In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.Peer reviewe

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The annual PIMS Graduate Industrial Math Modelling Camp (GIMMC) is held in one of the PIMS universitie

Performance of the Low Energy Ion Ring at CERN with Lead Ions in 2022

2022 was a performance consolidation year for the Low Energy Ion Ring (LEIR) at CERN that demonstrated its capability of delivering the target beam parameters required for high luminosity production in the LHC in a reproducible and reliable way. The main steps that have led to the high performance reach of this beam, together with the machine stability improvements deployed, are detailed in this paper

Review of LEIR operation in 2018

During run 2 (2015-2018) the LEIR machine experienced several important improvements in terms of extracted intensity, driven by the LHC Injectors Upgrade (LIU) project requirements. In 2018 the machine not only gave another step forward in extracted intensity, but also demonstrated that it could deliver the LIU target intensity in a reproducible and reliable way. The main steps that allowed the high performance reach of the NOMINAL beam and improvements to the machine stability are detailed in this paper. This work is also intended to be a reference for the restart after the Long Shutdown 2

The Y-Chromosome Tree Bursts into Leaf: 13,000 High-Confidence SNPs Covering the Majority of Known Clades

Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51×, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analyzing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of nonsynonymous variants in 15 MSY single-copy genes.status: publishe

Linac3, LEIR and PS Performance with Ions in 2021 and Prospects for 2022

CERN accelerators underwent a period of long shutdown from the end of 2018 to 2020. During this time frame, significant hardware and software upgrades have been put in place to increase the performance of both proton and ion accelerator chains in the High Luminosity LHC era. In the context of the CERN lead ion chain, 2021 has been mainly devoted to restore the injectors’ performance and to successfully prove the slip-stacking technique in SPS. In this paper we summarise the key milestones of the ion beam commissioning and the achieved beam performance for the Linac 3 (including the source), LEIR and PS accelerators, together with an outlook on 2022 operation

Evaluating the effect of forest loss and agricultural expansion on Sumatran tigers from scat surveys

Sumatran tigers (Panthera tigris sumatrae) are a critically endangered carnivore restricted to the island of Sumatra, and like many other large mammals on the Indonesian archipelago, they are threatened by high levels of poaching and widespread habitat degradation. Here, we conduct the first range-wide assessment of Sumatran tiger genetics using scat surveys and show that the wild population retains levels of genetic heterozygosity comparable to mainland tigers. However, the population also exhibits signs of subdivision due to the unprecedented rates of deforestation and land conversion in the last 30–40 years. The fact that this subspecies retains such levels of heterozygosity despite high rates of habitat loss and increasing isolation suggests a form of genetic extinction debt with an elevated risk of extinction if no action is taken within the next 30–100 years (see Kenney et al., 2014). However, the inherent time delay in extinction debt provides opportunities for conservation if habitat quality can be improved and connections between existing population fragments can be made. Our study highlights the importance of genetic studies for providing baseline information to improve the population management of highly threatened carnivore species. Mitigating further habitat degradation and expansion of oil palm and other cash crops in this region would improve the viability not only of Sumatran tiger populations, but of other threatened large mammal species as well