Search

Ancient DNA has revealed multiple episodes of admixture in human prehistory during geographic expansions associated with cultural innovations. One important example is the expansion of Neolithic agricultural groups out of the Near East into Europe, and their consequent admixture with Mesolithic hunter-gatherers. Ancient genomes from this period provide an opportunity to study the role of admixture in providing new genetic variation for selection to act upon, and also to identify genomic regions that resisted hunter-gatherer introgression and may thus contribute to agricultural adaptations. We used genome-wide DNA from 728 individuals spanning Mesolithic and Neolithic Europe to infer ancestry deviations in the genomes of admixed individuals, and to test for natural selection after admixture using a new method based on testing for deviations from a genome-wide null distribution. We find that the region around the pigmentation-associated gene SLC24A5 shows the greatest overrepresentation of Neolithic ancestry in the genome (|Z| = 3.45). In contrast, we find the greatest overrepresentation of Mesolithic local ancestry across the key immunity locus that is the Major Histocompatibility Complex (MHC; |Z| > 4) which also shows allele frequency deviations indicative of a selective sweep following admixture (p =1×10−29). This could reflect negative frequency dependent selection on MHC alleles common in Neolithic populations, or that Mesolithic alleles were positively selected for and facilitated adaptation by Neolithic populations to pathogens, new diets, or other environmental factors. Our results extend previous results that highlight immune function and pigmentation as targets of adaptation in more recent populations to selection processes in the Stone Age, and demonstrate that admixture facilitated selection by contributing new genetic variation.

Extinct lineages of Yersinia pestis, the causative agent of the plague, have been identified in several individuals from Central Europe and Asia between 5,000 and 3,500 years before present (BP). One of these, the ‘LNBA lineage’ (Late Neolithic and Bronze Age), has been suggested to have spread into Central Europe with human groups expanding from the Eurasian steppes. Here, we show that LNBA plague was spread to Europe’s northwestern periphery by sequencing Yersinia pestis genomes from two individuals dating to ~4,000 cal BP from an unusual mass burial context in Somerset, England, UK. This represents the earliest evidence of plague in Britain documented to date. These British Yersinia pestis genomes belong to a sublineage previously observed in two Bronze Age individuals from Central Europe that had lost the putative virulence factor yapC. This sublineage is later found in Central Asia ~3,600 BP. While the severity of disease is currently unclear, the wide geographic distribution within a few centuries suggests substantial transmissibility.

Frantz, Laurent/0000-0001-8030-3885; Ersmark, Erik/0000-0003-4186-7498; Sjogren, Karl-Goran/0000-0003-1791-3175; Bergstrom, Anders/0000-0002-4096-9268 WOS:000583031800042 PubMed ID: 33122379 Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry. SciLifeLab National Projects; Erik Philip Sorensen Foundation; Francis Crick Institute from Cancer Research UK [FC001595]; UK Medical Research CouncilMedical Research Council UK (MRC); Wellcome TrustWellcome Trust [210119/Z/18/Z]; European Research CouncilEuropean Research Council (ERC) [852558]; Wellcome Trust Investigator awardWellcome Trust [217223/Z/19/Z]; Vallee Foundation; Social Sciences and Humanities Research Council of CanadaSocial Sciences and Humanities Research Council of Canada (SSHRC) [SSHRC IG 435-2014-0075]; State Assignment of the Sobolev Institute of Geology and Mineralogy; ZIN RAS [AAA-A19119032590102-7]; Smithsonian's Peter Buck Postdoctoral Fellowship; AHRC [AH/J001406/1]; SNIC-UPPMAX [b2016004]; UOXF ARC facilityAustralian Research Council; Wolfson College (University of Oxford); ERCEuropean Research Council (ERC) [ERC-2013-StG-337574-UNDEAD]; Natural Environmental Research CouncilNERC Natural Environment Research Council [NE/K005243/1, NE/K003259/1]; NERC Radiocarbon Facility [NF/2016/2/4] Ancient genome sequencing was supported by SciLifeLab National Projects and the Erik Philip Sorensen Foundation (to P.S.). A.B., T.D., and P.S. were supported by the Francis Crick Institute core funding (FC001595) from Cancer Research UK, the UK Medical Research Council, and the Wellcome Trust. P.S. was also supported by the European Research Council (grant no. 852558), a Wellcome Trust Investigator award (217223/Z/19/Z) and the Vallee Foundation. R.J.L. was supported by the Social Sciences and Humanities Research Council of Canada (#SSHRC IG 435-2014-0075). Y.K. was supported by State Assignment of the Sobolev Institute of Geology and Mineralogy. M.S. was supported by ZIN RAS (state assignment no. AAA-A19119032590102-7). A.T.L. was supported by the Smithsonian's Peter Buck Postdoctoral Fellowship. Archaeological work in Serbia was supported by AHRC grant AH/J001406/1. Computations were supported by SNIC-UPPMAX (b2016004) and the UOXF ARC facility. L.F. was supported by the Wellcome Trust (grant 210119/Z/18/Z) and by Wolfson College (University of Oxford). G.L. was supported by the ERC (grant ERC-2013-StG-337574-UNDEAD). G.L. and K.D. were supported by the Natural Environmental Research Council (grants NE/K005243/1 and NE/K003259/1). Dating was supported by the NERC Radiocarbon Facility (NF/2016/2/4).

In the last two decades, genomic analyses have enriched the study of the biology of selenium in many ways. These include the identification of selenoproteins in prokaryotic and eukaryotic genomes, the discovery of genetic variants that mediate humans and other vertebrates' adaptations to their selenium nutritional histories, and the association of specific genotypes with common and rare human selenium disorders. We briefly review these computational, evolutionary and association studies and their contribution to the genomics of selenium, selenocysteine and selenoproteins in the 200th anniversary of the discovery of this trace element.

Based on a paper presented at the 30th UKSG Conference, Warwick, April 2007 Given huge advances in information technology over the past 20 years, why do students still use textbooks when there are much better ways to deliver courseware digitally? This article explores the evolution of the textbook and examines why, despite huge investments by publishers, today’s students are spending less on textbooks and are not yet using electronic resources to replace them, relying instead on free handouts and Google. This is in stark contrast to the progress that has been made in professional markets where publishers like Thomson, Reed and Wolters Kluwer now derive the majority of their revenues from digital products and services.Academics, it is argued, need to embrace digital courseware solutions, librarians need to offer new services and market themselves more effectively, and publishers need to think beyond e-books to deliver superior learning solutions.