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1. The application of whole genome capture (WGC) methods to ancient DNA (aDNA) promises to increase the efficiency of ancient genome sequencing. 2. We compared the performance of two recently developed WGC methods in enriching human aDNA within Illumina libraries built using both double-stranded (DSL) and single-stranded (SSL) build protocols. Although both methods effectively enriched aDNA, one consistently produced marginally better results, giving us the opportunity to further explore the parameters influencing WGC experiments. 3. Our results suggest that bait length has an important influence on library enrichment. Moreover, we show that WGC biases against the shorter molecules that are enriched in SSL preparation protocols. Therefore application of WGC to such samples is not recommended without future optimization. Lastly, we document the effect of WGC on other features including clonality, GC composition and repetitive DNA content of captured libraries. 4. Our findings provide insights for researchers planning to perform WGC on aDNA, and suggest future tests and optimization to improve WGC efficiency.

Bell, Lee-Thorp and Elkerton (2009) have recently published an isotopic investigation of the origins of 18 men whose remains were found in the wreck of the Mary Rose, Henry VIII’s warship, which sank in 1545. They conclude that a high proportion of the ship’s crew were foreigners and that this may have contributed to confusion onboard ship and the sinking of the vessel. We have re-evaluated the data of Bell et al. and conclude that only one of the 18 sailors demonstrably spent his childhood outside the British Isles.

Most ancient specimens contain very low levels of endogenous DNA, precluding the shotgun sequencing of many interesting samples because of cost. Ancient DNA (aDNA) libraries often contain

Inger Winkelmann ... et al., Despite its charismatic appeal to both scientists and the general public, remarkably little is known about the giant squid Architeuthis, one of the largest of the invertebrates. Although specimens of Architeuthis are becoming more readily available owing to the advancement of deep-sea fishing techniques, considerable controversy exists with regard to topics as varied as their taxonomy, biology and even behaviour. In this study, we have characterized the mitochondrial genome (mitogenome) diversity of 43 Architeuthis samples collected from across the range of the species, in order to use genetic information to provide new and otherwise difficult to obtain insights into the life of this animal. The results show no detectable phylogenetic structure at the mitochondrial level and, furthermore, that the level of nucleotide diversity is exceptionally low. These observations are consistent with the hypotheses that there is only one global species of giant squid, Architeuthis dux (Steenstrup, 1857), and that it is highly vagile, possibly dispersing through both a drifting paralarval stage and migration of larger individuals. Demographic history analyses of the genetic data suggest that there has been a recent population expansion or selective sweep, which may explain the low level of genetic diversity.

Alcohol Related Birth Defects (ARBD) are yet undocumented among past communities, although alcohol is the leading cause of non-heritable birth defects in the US today. We evaluate potential ARBD at Newton Plantation, Barbados (ca. 1660-1820), where earlier studies suggest frequent, community-wide consumption of lead-tainted rum by enslaved Africans. Skeletons excavated in 1997-1998 (n=45) were examined for congenital anomalies, using clinical/experimental descriptions to differentially diagnose possible ARBD. Enamel lead data served as a proxy for developmental exposure to tainted rum in a subsample (n=26). Elevated enamel lead (3.8μg/g), vertebral synostosis, and micrognathism in one subadult fit expectations for exposure. An adult male with low enamel lead (0.3μg/g) had congenital anomalies, but not those described with ethanol or lead exposures. Contrary to expectations, we did not identify ARBD in most individuals, including those with isotopic signatures of Barbadian origin who also showed consistently elevated dental lead levels. We discuss how such patterns may have emerged from timing of exposures and colonial medical practices, but underreporting remains a likely concern with ARBD, past and present. Ours is the first attempt to explore developmental signatures of alcohol use archeologically. We report the first possible case of ARBD from a past community.

Olalde, Iñigo et al., The spread of farming out of the Balkans and into the rest of Europe followed two distinct routes: An initial expansion represented by the Impressa and Cardial traditions, which followed the Northern Mediterranean coastline; and another expansion represented by the LBK (Linearbandkeramik) tradition, which followed the Danube River into Central Europe. Although genomic data now exist from samples representing the second migration, such data have yet to be successfully generated from the initial Mediterranean migration. To address this, we generated the complete genome of a 7,400-year-old Cardial individual (CB13) from Cova Bonica in Vallirana (Barcelona), as well as partial nuclear data from five others excavated from different sites in Spain and Portugal. CB13 clusters with all previously sequenced early European farmers and modern-day Sardinians. Furthermore, our analyses suggest that both Cardial and LBK peoples derived from a common ancient population located in or around the Balkan Peninsula. The Iberian Cardial genome also carries a discernible hunter–gatherer genetic signature that likely was not acquired by admixture with local Iberian foragers. Our results indicate that retrieving ancient genomes from similarly warm Mediterranean environments such as the Near East is technically feasible., The Centre for GeoGenetics is funded by the Danish National Research Foundation (DNRF94). Cova Bonica work is supported by Servei d’Arqueologia i Paleontologia (2014/100639), Generalitat de Catalunya (2014SGR-108), and Ministerio de Ciencia e Innovación (HAR2011-26193) projects. H.S. was supported by an ERC Synergy Grant (FP7/2007-2013/319209); C.L.-F. by a FEDER and Spanish Government Grant BFU2012-34157; and S.C. by a grant 2014 SGR 464 from Departament d’Economia i Coneixement (Generalitat de Catalunya). D.C.S-G. acknowledges support from the Generalitat Valenciana (VALi + d APOSTD/2014/123), the BBVA Foundation (I Ayudas a Investigadores, Innovadores y Creadores Culturales), and the European Union (FP7/2007-2013—MSCA-COFUND, no. 245743 via a Braudel-IFER-FMSH). I.O. was funded by a predoctoral fellowship from the Basque Government (DEUI), and M.S. and J.D. by postdoctoral grants from Fundação para a Ciência e a Tecnologia (FCT) and Juan de la Cierva Subprogram (JCI-2011-09543), respectively.

SummarySeveral major migrations and population turnover events during the later Stone Age (after c. 11,000 cal. BP) are believed to have shaped the contemporary population genetic diversity in Eurasia. While the genetic impacts of these migrations have been investigated on regional scales, a detailed understanding of their spatiotemporal dynamics both within and between major geographic regions across Northern Eurasia remains largely elusive. Here, we present the largest shotgun-sequenced genomic dataset from the Stone Age to date, representing 317 primarily Mesolithic and Neolithic individuals from across Eurasia, with associated radiocarbon dates, stable isotope data, and pollen records. Using recent advances, we imputed >1,600 ancient genomes to obtain accurate diploid genotypes, enabling previously unachievable fine-grained population structure inferences. We show that 1) Eurasian Mesolitic hunter-gatherers were more genetically diverse than previously known, and deeply divergent between the west and the east; 2) Hitherto genetically undescribed hunter-gatherers from the Middle Don region contributed significant ancestry to the later Yamnaya steppe pastoralists; 3) The genetic impact of the transition from Mesolithic hunter-gatherers to Neolithic farmers was highly distinct, east and west of a “Great Divide” boundary zone extending from the Black Sea to the Baltic, with large-scale shifts in genetic ancestry to the west. This include an almost complete replacement of hunter-gatherers in Denmark, but no substantial shifts during the same period further to the east; 4) Within-group relatedness changes substantially during the Neolithic transition in the west, where clusters of Neolithic farmer-associated individuals show overall reduced relatedness, while genetic relatedness remains high until ~4,000 BP in the east, consistent with a much longer persistence of smaller localised hunter-gatherer groups; 5) A fast-paced second major genetic transformation beginning around 5,000 BP, with Steppe-related ancestry reaching most parts of Europe within a 1,000 years span. Local Neolithic farmers admixed with incoming pastoralists in most parts of Europe, whereas Scandinavia experienced another near-complete population replacement, with similar dramatic turnover-patterns also evident in western Siberia; 6) Extensive regional differences in the ancestry components related to these early events remain visible to this day, even within countries (research conducted using the UK Biobank resource). Neolithic farmer ancestry is highest in southern and eastern England while Steppe-related ancestry is highest in the Celtic populations of Scotland, Wales, and Cornwall. Overall, our findings show that although the Stone-Age migrations have been important in shaping contemporary genetic diversity in Eurasia, their dynamics and impact were geographically highly heterogeneous.

Sánchez-Quinto, Federico et al.-- Data can be downloaded from http://www.ibe.upf-csic.es/ibe/research/research-groups/lalueza-fox.html, The genetic background of the European Mesolithic and the extent of population replacement during the Neolithic [1-10] is poorly understood, both due to the scarcity of human remains from that period [11-18] and the inherent methodological difficulties of ancient DNA research. However, advances in sequencing technologies are both increasing data yields and providing supporting evidence for data authenticity, such as nucleotide misincorporation patterns [19-22]. We use these methods to characterize both the mitochondrial DNA genome and generate shotgun genomic data from two exceptionally well-preserved 7,000-year-old Mesolithic individuals from La Braña-Arintero site in León (Northwestern Spain) [23]. The mitochondria of both individuals are assigned to U5b2c1, a haplotype common among the small number of other previously studied Mesolithic individuals from Northern and Central Europe. This suggests a remarkable genetic uniformity and little phylogeographic structure over a large geographic area of the pre-Neolithic populations. Using Approximate Bayesian Computation, a model of genetic continuity from Mesolithic to Neolithic populations is poorly supported. Furthermore, analyses of 1.34% and 0.53% of their nuclear genomes, containing about 50,000 and 20,000 ancestry informative SNPs, respectively, show that these two Mesolithic individuals are not related to current populations from either the Iberian Peninsula or Southern Europe. © 2012 Elsevier Ltd All rights reserved., C.L.-F., O.R., and F.S.-Q. are supported by a grant from the Ministerio de Ciencia e Innovación of Spain (BFU2009-06974). H.S., L.O., M.C.A.-A., and M.T.P.G acknowledge the Marie Curie Actions, Danish National Research Foundation, and Danish Council for Independent Research for support.

Ancient steppes for human equestrians The Eurasian steppes reach from the Ukraine in Europe to Mongolia and China. Over the past 5000 years, these flat grasslands were thought to be the route for the ebb and flow of migrant humans, their horses, and their languages. de Barros Damgaard et al. probed whole-genome sequences from the remains of 74 individuals found across this region. Although there is evidence for migration into Europe from the steppes, the details of human movements are complex and involve independent acquisitions of horse cultures. Furthermore, it appears that the Indo-European Hittite language derived from Anatolia, not the steppes. The steppe people seem not to have penetrated South Asia. Genetic evidence indicates an independent history involving western Eurasian admixture into ancient South Asian peoples. Science , this issue p. eaar7711