Review of “The Archaeology of Andean Pastoralism” edited by José M. Capriles and Nicholas

Book details Capriles J M and Tripcevich N (eds.) The Archaeology of Andean Pastoralism Albuquerque: University of New Mexico Press; 2016. 280 pages, 87 figures, 25 tables ISBN 978-0-8263-5702-

Rabbits and the Specious Origins of Domestication

Rabbits are commonly thought to have been domesticated in ∼AD600 by French monks. Using historical and archaeological records, and genetic methods, we demonstrate that this is a misconception and the general inability to date domestication stems from both methodological biases and the lack of appreciation of domestication as a continuum

The selection landscape and genetic legacy of ancient Eurasians

The Holocene (beginning around 12,000 years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for the dietary, physical and mental health of present-day populations. Using a dataset of more than 1,600 imputed ancient genomes 1, we modelled the selection landscape during the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify key selection signals related to metabolism, including that selection at the FADS cluster began earlier than previously reported and that selection near the LCT locus predates the emergence of the lactase persistence allele by thousands of years. We also find strong selection in the HLA region, possibly due to increased exposure to pathogens during the Bronze Age. Using ancient individuals to infer local ancestry tracts in over 400,000 samples from the UK Biobank, we identify widespread differences in the distribution of Mesolithic, Neolithic and Bronze Age ancestries across Eurasia. By calculating ancestry-specific polygenic risk scores, we show that height differences between Northern and Southern Europe are associated with differential Steppe ancestry, rather than selection, and that risk alleles for mood-related phenotypes are enriched for Neolithic farmer ancestry, whereas risk alleles for diabetes and Alzheimer’s disease are enriched for Western hunter-gatherer ancestry. Our results indicate that ancient selection and migration were large contributors to the distribution of phenotypic diversity in present-day Europeans

Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events

The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back to 40 Ma. Recent studies, however, suggest that much of Sulawesi's fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric datasets derived from Sulawesi's three largest mammals: the babirusa, anoa and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Ma to 2-3 Ma), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (approx. 1-2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years

Origins and genetic legacy of prehistoric dogs

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

The LUX-ZEPLIN (LZ) Experiment

We describe the design and assembly of the LUX-ZEPLIN experiment, a direct detection search for cosmic WIMP dark matter particles. The centerpiece of the experiment is a large liquid xenon time projection chamber sensitive to low energy nuclear recoils. Rejection of backgrounds is enhanced by a Xe skin veto detector and by a liquid scintillator Outer Detector loaded with gadolinium for efficient neutron capture and tagging. LZ is located in the Davis Cavern at the 4850' level of the Sanford Underground Research Facility in Lead, South Dakota, USA. We describe the major subsystems of the experiment and its key design features and requirements

The LUX-ZEPLIN (LZ) radioactivity and cleanliness control programs

LUX-ZEPLIN (LZ) is a second-generation direct dark matter experiment with spin-independent WIMP-nucleon scattering sensitivity above 1.4×10−48cm2 for a WIMP mass of 40GeV/c2 and a 1000days exposure. LZ achieves this sensitivity through a combination of a large 5.6t fiducial volume, active inner and outer veto systems, and radio-pure construction using materials with inherently low radioactivity content. The LZ collaboration performed an extensive radioassay campaign over a period of six years to inform material selection for construction and provide an input to the experimental background model against which any possible signal excess may be evaluated. The campaign and its results are described in this paper. We present assays of dust and radon daughters depositing on the surface of components as well as cleanliness controls necessary to maintain background expectations through detector construction and assembly. Finally, examples from the campaign to highlight fixed contaminant radioassays for the LZ photomultiplier tubes, quality control and quality assurance procedures through fabrication, radon emanation measurements of major sub-systems, and bespoke detector systems to assay scintillator are presented

Palaeogenomics of animal domestication: computational modelling of ancestry, demography and selection

The study of animal domestication is in the midst of a genomic revolution, as technological advances dramatically increase the availability of DNA sequence data from ancient and modern domestic populations. For the first time, palaeogenomic datasets are being produced of sufficient size and scope to directly observe anthropological and evolutionary processes through time; from the emergence of domestic animals in the Neolithic, to the formation of modern breeds in the Victorian era. This thesis applies computational modelling of ancient and modern DNA to infer ancestry, demography, and selection in domestic cattle (Bos taurus), horses (Equus ferus caballus), and dogs (Canis familiaris). Chapter 1 reviews the substantial contribution palaeogenomics has made to the study of animal domestication, and details the latest theoretical and empirical advances, alongside individual profiles of sixteen major domestic species. Chapter 2 reconstructs the allele frequency trajectories of genetic variants linked to quantitative traits in genome-wide associations studies (GWAS) of cattle and horses. Using a Bayesian modelling approach, and a dataset of more than 350 ancient genomes spread across the last 10,000 years, the age of the allele under selection for thousands of GWAS variants is inferred, along with the selection coefficients for hundreds of polygenic traits. Chapter 3 analyses the first ancient genome-wide DNA from pre-contact North American dogs. Admixture analyses show that the earliest American dogs were not independently domesticated, and originated from a population of arctic dogs in Eastern Siberia. These dogs likely accompanied humans during the peopling of the continent, and rapidly diversified after their arrival, until their sudden replacement following the arrival of European colonists. Remarkably, their most closely related living relatives are now an 8,000-year-old contagious cancer clone known as Canine Transmissible Venereal Tumour (CTVT). Chapter 4 presents an ancestry analysis of a rare breed of humpless, dwarf shorthorn cattle from the remote island of Socotra, in the Arabian Sea. Admixture analyses show that contrary to published hypotheses, these cattle are predominantly Eurasian taurine (Bos taurus) in ancestry, with only minimal African taurine heritage, and preliminary results indicate possible admixture with a basal clade of zebu cattle (Bos indicus).</p

Rabbits and the specious origins of domestication

Rabbits are commonly thought to have been domesticated in ∼AD600 by French monks. Using historical and archaeological records, and genetic methods, we demonstrate that this is a misconception and the general inability to date domestication stems from both methodological biases and the lack of appreciation of domestication as a continuum