Genetic Signatures of Strong Recent Positive Selection at the Lactase Gene

In most human populations, the ability to digest lactose contained in milk usually disappears in childhood, but in European-derived populations, lactase activity frequently persists into adulthood (Scrimshaw and Murray 1988). It has been suggested (Cavalli-Sforza 1973; Hollox et al. 2001; Enattah et al. 2002; Poulter et al. 2003) that a selective advantage based on additional nutrition from dairy explains these genetically determined population differences (Simoons 1970; Kretchmer 1971; Scrimshaw and Murray 1988; Enattah et al. 2002), but formal population-genetics–based evidence of selection has not yet been provided. To assess the population-genetics evidence for selection, we typed 101 single-nucleotide polymorphisms covering 3.2 Mb around the lactase gene. In northern European–derived populations, two alleles that are tightly associated with lactase persistence (Enattah et al. 2002) uniquely mark a common (∼77%) haplotype that extends largely undisrupted for >1 Mb. We provide two new lines of genetic evidence that this long, common haplotype arose rapidly due to recent selection: (1) by use of the traditional FST measure and a novel test based on pexcess, we demonstrate large frequency differences among populations for the persistence-associated markers and for flanking markers throughout the haplotype, and (2) we show that the haplotype is unusually long, given its high frequency—a hallmark of recent selection. We estimate that strong selection occurred within the past 5,000–10,000 years, consistent with an advantage to lactase persistence in the setting of dairy farming; the signals of selection we observe are among the strongest yet seen for any gene in the genome

Preferential dust sources: a geomorphological classification designed for use in global dust-cycle models

We present a simple theoretical land-surface classification that can be used to determine the location and temporal behaviour of preferential sources of terrestrial dust emissions. The classification also provides information about the likely nature of the sediments, their erodibility and the likelihood that they will generate emissions under given conditions. The scheme is based on the dual notions of geomorphic type and connectivity between geomorphic units. We demonstrate that the scheme can be used to map potential modern-day dust sources in the Chihuahuan Desert, the Lake Eyre Basin and the Taklamakan. Through comparison with observed dust emissions, we show that the scheme provides a reasonable prediction of areas of emission in the Chihuahuan Desert and in the Lake Eyre Basin. The classification is also applied to point source data from the Sahara to enable comparison of the relative importance of different land surfaces for dust emissions. We indicate how the scheme could be used to provide an improved characterisation of preferential dust sources in global dust-cycle models

Recovery of 29-s Oscillations in HST/FOS Eclipse Observations of the Cataclysmic Variable UX Ursae Majoris

[abridged abstract] Low amplitude (~=0.5%) 29-s oscillations have been detected in HST/FOS eclipse observations of the nova-like cataclysmic variable UX UMa. These are the same dwarf nova-type oscillations that were originally discovered in this system by Warner & Nather in 1972. The oscillations are sinusoidal to within the small observational errors and undergo an approximately -360 degree phase shift during eclipses. Their amplitudes are highest at pre-eclipse orbital phases and exhibit a rather gradual eclipse whose shape is roughly similar to UX~UMa's overall light curve. Oscillation spectra derived from pre-eclipse data segments are extremely blue, whereas mid-eclipse oscillation spectra are much redder. We suggest that the ultimate source of the oscillations is a hot, compact region near disk center, but that a significant fraction of the observed, modulated flux is due to reprocessing of the light emitted by this source in the accretion disk atmosphere. The compact source is occulted at orbital phases near mid-eclipse, leaving only part of the more extended reprocessing region(s) to produce the weak oscillations that persist even at conjunction. The highly sinusoidal oscillation pulse shape does not permit the identification of the compact component in this model with emission produced by a rotating disturbance in the inner disk or in an equatorial boundary layer, and a standard intermediate polar model can also be ruled out. A model invoking magnetically controlled accretion onto differentially rotating WD surface layers may be viable, but needs more theoretical work.Comment: 28 pages, including 9 figures; to appear in the ApJ (Vol. 499

Don’t turn your back on the symptoms of psychosis : a proof-of-principle, quasi-experimental public health trial to reduce the duration of untreated psychosis in Birmingham, UK

Background: Reducing the duration of untreated psychosis (DUP) is an aspiration of international guidelines for first episode psychosis; however, public health initiatives have met with mixed results. Systematic reviews suggest that greater focus on the sources of delay within care pathways, (which will vary between healthcare settings) is needed to achieve sustainable reductions in DUP (BJP 198: 256-263; 2011). Methods/Design: A quasi-experimental trial, comparing a targeted intervention area with a ‘detection as usual’ area in the same city. A proof-of–principle trial, no a priori assumptions are made regarding effect size; key outcome will be an estimate of the potential effect size for a definitive trial. DUP and number of new cases will be collected over an 18-month period in target and control areas and compared; historical data on DUP collected in both areas over the previous three years, will serve as a benchmark. The intervention will focus on reducing two significant DUP component delays within the overall care pathway: delays within the mental health service and help-seeking delay. Discussion: This pragmatic trial will be the first to target known delays within the care pathway for those with a first episode of psychosis. If successful, this will provide a generalizable methodology that can be implemented in a variety of healthcare contexts with differing sources of delay. Trial registration: http://www.controlled-trials.com/ISRCTN45058713 Keywords: Public mental health campaign, First-episode psychosis, Early detection, Duration of untreated psychosis, Youth mental healt

Taphonomic and zooarchaeological investigations at the middle Pleistocene site of Ti's al Ghadah, western Nefud Desert, Saudi Arabia

In recent years, the Arabian Peninsula has emerged as a key region for elucidating hominin and faunal evolution and dispersals between Africa and Eurasia. Central to this research is the middle Pleistocene site of Ti's al Ghadah (TAG) which has yielded a diverse and abundant fossil faunal assemblage and the earliest chronometrically dated evidence for hominins in this part of the world. Here, we present the first detailed taphonomic study of the large Unit 5 fossil assemblage from the site. We aim to assess which actor/s were responsible for the accumulation of the assemblage and evaluate evidence that might be consistent with the accumulation of fauna by hominins. We also describe, for the first time, fossils and lithic artefacts from stratigraphic horizons not previously considered, providing taphonomic insights into their accumulation. The taphonomic work shows that the Unit 5 faunal assemblage was accumulated by ambush predators, likely large felids and hominins, in a lake side environment, and that carcasses were subsequently scavenged by more durophagus carnivores such as hyenas and canids. Less can be reliably said regarding the newly described fossil assemblages given their poor preservation and significant wind abrasion, but large carnivores again appear to have played a role, and hominins probably played a role in the accumulation of at least one of these. This study provides the first detail insights into the interplay between hominins, carnivores, and herbivores in Arabia, and suggests that watering holes have been a focus on the Arabian landscape for resources since the middle Pleistocene

Incorporation of metals into calcite in a deep anoxic granite aquifer

Understanding metal scavenging by calcite in deep aquifers in granite is of importance for deciphering and modeling hydrochemical fluctuations and water–rock interaction in the upper crust and for retention mechanisms associated with underground repositories for toxic wastes. Metal scavenging into calcite has generally been established in the laboratory or in natural environments that cannot be unreservedly applied to conditions in deep crystalline rocks, an environment of broad interest for nuclear waste repositories. Here, we report a microanalytical study of calcite precipitated over a period of 17 years from anoxic, low-temperature (14 °C), neutral (pH: 7.4–7.7), and brackish (Cl: 1700–7100 mg/L) groundwater flowing in fractures at >400 m depth in granite rock. This enabled assessment of the trace metal uptake by calcite under these deep-seated conditions. Aquatic speciation modeling was carried out to assess influence of metal complexation on the partitioning into calcite. The resulting environment-specific partition coefficients were for several divalent ions in line with values obtained in controlled laboratory experiments, whereas for several other ions they differed substantially. High absolute uptake of rare earth elements and U(IV) suggests that coprecipitation into calcite can be an important sink for these metals and analogousactinides in the vicinity of geological repositories

Low-fidelity DNA synthesis by the L979F mutator derivative of Saccharomyces cerevisiae DNA polymerase ζ

To probe Pol ζ functions in vivo via its error signature, here we report the properties of Saccharomyces cerevisiae Pol ζ in which phenyalanine was substituted for the conserved Leu-979 in the catalytic (Rev3) subunit. We show that purified L979F Pol ζ is 30% as active as wild-type Pol ζ when replicating undamaged DNA. L979F Pol ζ shares with wild-type Pol ζ the ability to perform moderately processive DNA synthesis. When copying undamaged DNA, L979F Pol ζ is error-prone compared to wild-type Pol ζ, providing a biochemical rationale for the observed mutator phenotype of rev3-L979F yeast strains. Errors generated by L979F Pol ζ in vitro include single-base insertions, deletions and substitutions, with the highest error rates involving stable misincorporation of dAMP and dGMP. L979F Pol ζ also generates multiple errors in close proximity to each other. The frequency of these events far exceeds that expected for independent single changes, indicating that the first error increases the probability of additional errors within 10 nucleotides. Thus L979F Pol ζ, and perhaps wild-type Pol ζ, which also generates clustered mutations at a lower but significant rate, performs short patches of processive, error-prone DNA synthesis. This may explain the origin of some multiple clustered mutations observed in vivo

Homo sapiens in Arabia by 85,000 years ago.

Understanding the timing and character of the expansion of Homo sapiens out of Africa is critical for inferring the colonization and admixture processes that underpin global population history. It has been argued that dispersal out of Africa had an early phase, particularly ~130-90 thousand years ago (ka), that reached only the East Mediterranean Levant, and a later phase, ~60-50 ka, that extended across the diverse environments of Eurasia to Sahul. However, recent findings from East Asia and Sahul challenge this model. Here we show that H. sapiens was in the Arabian Peninsula before 85 ka. We describe the Al Wusta-1 (AW-1) intermediate phalanx from the site of Al Wusta in the Nefud desert, Saudi Arabia. AW-1 is the oldest directly dated fossil of our species outside Africa and the Levant. The palaeoenvironmental context of Al Wusta demonstrates that H. sapiens using Middle Palaeolithic stone tools dispersed into Arabia during a phase of increased precipitation driven by orbital forcing, in association with a primarily African fauna. A Bayesian model incorporating independent chronometric age estimates indicates a chronology for Al Wusta of ~95-86 ka, which we correlate with a humid episode in the later part of Marine Isotope Stage 5 known from various regional records. Al Wusta shows that early dispersals were more spatially and temporally extensive than previously thought. Early H. sapiens dispersals out of Africa were not limited to winter rainfall-fed Levantine Mediterranean woodlands immediately adjacent to Africa, but extended deep into the semi-arid grasslands of Arabia, facilitated by periods of enhanced monsoonal rainfall

The greening of Arabia: multiple opportunities for human occupation of the Arabian peninsula during the Late Pleistocene inferred from an ensemble of climate model simulations

Climate models are potentially useful tools for addressing human dispersals and demographic change. The Arabian Peninsula is becoming increasingly significant in the story of human dispersals out of Africa during the Late Pleistocene. Although characterised largely by arid environments today, emerging climate records indicate that the peninsula was wetter many times in the past, suggesting that the region may have been inhabited considerably more than hitherto thought. Explaining the origins and spatial distribution of increased rainfall is challenging because palaeoenvironmental research in the region is in an early developmental stage. We address environmental oscillations by assembling and analysing an ensemble of five global climate models (CCSM3, COSMOS, HadCM3, KCM, and NorESM). We focus on precipitation, as the variable is key for the development of lakes, rivers and savannas. The climate models generated here were compared with published palaeoenvironmental data such as palaeolakes, speleothems and alluvial fan records as a means of validation. All five models showed, to varying degrees, that the Arabia Peninsula was significantly wetter than today during the Last Interglacial (130 ka and 126/125 ka timeslices), and that the main source of increased rainfall was from the North African summer monsoon rather than the Indian Ocean monsoon or from Mediterranean climate patterns. Where available, 104 ka (MIS 5c), 56 ka (early MIS 3) and 21 ka (LGM) timeslices showed rainfall was present but not as extensive as during the Last Interglacial. The results favour the hypothesis that humans potentially moved out of Africa and into Arabia on multiple occasions during pluvial phases of the Late Pleistocene