European domestic horses originated in two holocene refugia

The role of European wild horses in horse domestication is poorly understood. While the fossil record for wild horses in Europe prior to horse domestication is scarce, there have been suggestions that wild populations from various European regions might have contributed to the gene pool of domestic horses. To distinguish between regions where domestic populations are mainly descended from local wild stock and those where horses were largely imported, we investigated patterns of genetic diversity in 24 European horse breeds typed at 12 microsatellite loci. The distribution of high levels of genetic diversity in Europe coincides with the distribution of predominantly open landscapes prior to domestication, as suggested by simulation-based vegetation reconstructions, with breeds from Iberia and the Caspian Sea region having significantly higher genetic diversity than breeds from central Europe and the UK, which were largely forested at the time the first domestic horses appear there. Our results suggest that not only the Eastern steppes, but also the Iberian Peninsula provided refugia for wild horses in the Holocene, and that the genetic contribution of these wild populations to local domestic stock may have been considerable. In contrast, the consistently low levels of diversity in central Europe and the UK suggest that domestic horses in these regions largely derive from horses that were imported from the Eastern refugium, the Iberian refugium, or both.     

Leaf habit does not predict leaf functional traits in cerrado woody species

Plant species with a high leaf life span (LLS) commonly have a low specific leaf area (SLA), leaf nitrogen per unit mass (N), and phosphorous concentration (P), whereas species with low LLS have a high SLA, N and P. However, LLS tends to be longer in species growing in low-nutrient soils and, therefore, differences in LLS and other leaf traits may not be consistent with a plant classification according to leaf habit. Here we investigated whether leaf habit is consistent with leaf economic spectrum trade-offs in cerrado (a Neotropical savanna) woody species. We analyzed the SLA, N and P of 125 woody species with a distinct leaf habit (deciduous, semideciduous, brevideciduous or evergreen). We also gathered data on the LLS (33 species), maximum net photosynthesis per leaf area (A_area, 56 species) and per leaf mass (A_mass, 31 species), comprising the most extensive database analyzed so far for the cerrado. Differences among leaf habit groups were tested using generalized linear mixed models and ANOVA. We did not find differences in SLA and N among species with a distinct leaf habit, but deciduous species had a higher leaf P concentration than evergreens. Species did not differ in LLS and A_mass, but A_area varied among groups. Semideciduous species had higher A_area values than deciduous and brevideciduous species, but all other groups had similar A_area values. Because of the small difference in the LLS, SLA, leaf N, leaf P and maximum net photosynthesis, we argue that deciduous, brevideciduous, semideciduous and evergreen species may not constitute different functional groups in cerrado woody species.     

Sex-Differences and Temporal Consistency in Stickleback Fish Boldness

Behavioural traits that co-vary across contexts or situations often reflect fundamental trade-offs which individuals experience in different contexts (e.g. fitness trade-offs between exploration and predation risk). Since males tend to experience greater variance in reproductive success than females, there may be considerable fitness benefits associated with “bolder” behavioural types, but only recently have researchers begun to consider sex-specific and life-history strategies associated with these. Here we test the hypothesis that male three-spined sticklebacks (Gasterosteus aculeatus) show high risk but potentially high return behaviours compared to females. According to this hypothesis we predicted that male fish would show greater exploration of their environment in a foraging context, and be caught sooner by an experimenter than females. We found that the time fish spent out of cover exploring their environment was correlated over two days, and males spent significantly more time out of cover than females. Also, the order in which fish were net-caught from their holding aquarium by an experimenter prior to experiments was negatively correlated with the time spent out of cover during tests, and males tended to be caught sooner than females. Moreover, we found a positive correlation between the catch number prior to our experiments and nine months after, pointing towards consistent, long-term individual differences in behaviour.     

Validation of Two Rapid Diagnostic Tests for Visceral Leishmaniasis in Kenya

Background

Visceral leishmaniasis (VL) is a systemic parasitic disease that is fatal unless treated. In Kenya, national VL guidelines rely on microscopic examination of spleen aspirate to confirm diagnosis. As this procedure is invasive, it cannot be safely implemented in peripheral health structures, where non-invasive, accurate, easy to use diagnostic tests are needed.

Methodology

We evaluated the sensitivity, specificity and predictive values of two rapid diagnostic tests (RDT), DiaMed IT LEISH and Signal-KA, among consecutive patients with clinical suspicion of VL in two treatment centres located in Baringo and North Pokot District, Rift Valley province, Kenya. Microscopic examination of spleen aspirate was the reference diagnostic standard. Patients were prospectively recruited between May 2010 and July 2011.

Principal Findings

Of 251 eligible patients, 219 patients were analyzed, including 131 VL and 88 non-VL patients. The median age of VL patients was 16 years with predominance of males (66%). None of the tested VL patients were co-infected with HIV. Sensitivity and specificity of the DiaMed IT LEISH were 89.3% (95%CI: 82.7–94%) and 89.8% (95%CI: 81.5–95.2%), respectively. The Signal KA showed trends towards lower sensitivity (77.1%; 95%CI: 68.9–84%) and higher specificity (95.5%; 95%CI: 88.7–98.7%). Combining the tests did not improve the overall diagnostic performance, as all patients with a positive Signal KA were also positive with the DiaMed IT LEISH.

Conclusion/Significance

The DiaMed IT LEISH can be used to diagnose VL in Kenyan peripheral health facilities where microscopic examination of spleen aspirate or sophisticated serological techniques are not feasible. There is a crucial need for an improved RDT for VL diagnosis in East Africa.     

Environmental gradients predict the genetic population structure of a coral reef fish in the Red Sea

The relatively recent fields of terrestrial landscape and marine seascape genetics seek to identify the influence of biophysical habitat features on the spatial genetic structure of populations or individuals. Over the last few years, there has been accumulating evidence for the effect of environmental heterogeneity on patterns of gene flow and connectivity in marine systems. Here, we investigate the population genetic patterns of an anemonefish, Amphiprion bicinctus, along the Saudi Arabian coast of the Red Sea. We collected nearly one thousand samples from 19 locations, spanning approximately 1500 km, and genotyped them at 38 microsatellite loci. Patterns of gene flow appeared to follow a stepping‐stone model along the northern and central Red Sea, which was disrupted by a distinct genetic break at a latitude of approximately 19°N. The Red Sea is characterized by pronounced environmental gradients along its axis, roughly separating the northern and central from the southern basin. Using mean chlorophyll‐a concentrations as a proxy for this gradient, we ran tests of isolation by distance (IBD, R² = 0.52) and isolation by environment (IBE, R² = 0.64), as well as combined models using partial Mantel tests and multiple matrix regression with randomization (MMRR). We found that genetic structure across our sampling sites may be best explained by a combined model of IBD and IBE (Mantel: R² = 0.71, MMRR: R² = 0.86). Our results highlight the potential key role of environmental patchiness in shaping patterns of gene flow in species with pelagic larval dispersal. We support growing calls for the integration of biophysical habitat characteristics into future studies of population genetic structure.     

Active Case Finding of Tuberculosis (TB) in an Emergency Room in a Region with High Prevalence of TB in Brazil

Setting

Public hospital emergency room (ER) in Porto Alegre, Brazil, a setting with high prevalence of tuberculosis (TB) and human immunodeficiency virus (HIV) infection.

Objective

To determine the prevalence of PTB, using a symptom based active case finding (ACF) strategy in the ER of a public hospital in an area with high prevalence of TB and HIV, as well as variables associated with pulmonary TB diagnosis.

Methods

Cross sectional study. All patients ≥18 years seeking care at the ER were screened for respiratory symptoms and those with cough ≥2 weeks were invited to provide a chest radiograph and two unsupervised samples of sputum for acid-fast bacilli smear and culture.

Results

Among 31,267 admissions, 6,273 (20.1%) reported respiratory symptoms; 197 reported cough ≥2 weeks, of which pulmonary TB was diagnosed in 30. In multivariate analysis, the variables associated with a pulmonary tuberculosis diagnosis were: age (OR 0.94, 95% CI: 0.92–0.97; p<0.0001), sputum production (OR 0.18, 95% CI 0.06–0.56; p = 0.003), and radiographic findings typical of TB (OR 12.11, 95% CI 4.45–32.93; p<0.0001).

Conclusions

This study identified a high prevalence of pulmonary TB among patients who sought care at the emergency department of a tertiary hospital, emphasizing the importance of regular screening of all comers for active TB in this setting.     

Walk on the Wild Side: Estimating the Global Magnitude of Visits to Protected Areas

How often do people visit the world’s protected areas (PAs)? Despite PAs covering one-eighth of the land and being a major focus of nature-based recreation and tourism, we don’t know. To address this, we compiled a globally-representative database of visits to PAs and built region-specific models predicting visit rates from PA size, local population size, remoteness, natural attractiveness, and national income. Applying these models to all but the very smallest of the world’s terrestrial PAs suggests that together they receive roughly 8 billion (8 x 109) visits/y—of which more than 80% are in Europe and North America. Linking our region-specific visit estimates to valuation studies indicates that these visits generate approximately US $600 billion/y in direct in-country expenditure and US $250 billion/y in consumer surplus. These figures dwarf current, typically inadequate spending on conserving PAs. Thus, even without considering the many other ecosystem services that PAs provide to people, our findings underscore calls for greatly increased investment in their conservation.Enjoyment of nature, much of it in protected areas (PAs), is recognised as the most prominent cultural ecosystem service [1–3], yet we still lack even a rough understanding of its global magnitude and economic significance. Large-scale assessments have been restricted to regional or biome-specific investigations [4–8] (but see [9]). There are good reasons for this. Information on visit rates is limited, widely scattered, and confounded by variation in methods [10,11]. Likewise, estimates of the value of visits vary greatly—geographically, among methods, and depending on the component of value being measured [12–14]. Until now, these problems have prevented data-driven analysis of the worldwide scale of nature-based recreation and tourism. But with almost all the world’s governments committed (through the Aichi Biodiversity Targets [15]) to integrating biodiversity into national accounts, policymakers require such gaps in our knowledge of natural capital to be filled.We tackled this shortfall in our understanding of a major ecosystem service by focusing on terrestrial PAs, which cover one-eighth of the land [16] and are a major focus of nature-based recreation and tourism. We compiled data on visit rates to over 500 PAs and built region-specific models, which predicted variation in visitation in relation to the properties of PAs and to local socioeconomic conditions. Next, we used these models to estimate visit rates to all but the smallest of the world’s terrestrial PAs. Last, by summing these estimates by region and combining the totals with region-specific medians for the value of nature visits obtained from the literature, we derived approximate estimates of the global extent and economic significance of PA visitation.Given the scarcity of data on visits to PAs, our approach was to use all available information (although we excluded marine and Antarctic sites, and International Union for Conservation of Nature (IUCN) Category I PAs where tourism is typically discouraged; for further details of data collection and analysis see Materials and Methods). This generated a database of visitor records for 556 PAs spread across 51 countries and included 2,663 records of annual visit numbers over our best-sampled ten-year period (1998–2007) (S1 Table). Mean annual visit rates for individual PAs in this sample ranged from zero to over 10 million visits/y, with a median across all sampled PAs of 20,333 visits/y.We explored this variation by modelling it in relation to a series of biophysical and socioeconomic variables that might plausibly predict visit rates (after refs [6,7,17]): PA size, local population size, PA remoteness, a simple measure of the attractiveness of the PA’s natural features, and national income (see Materials and Methods for a priori predictions). For each of five major regions, we performed univariate regressions (S2 Table) and then built generalised linear models (GLMs) in an effort to predict variation in observed visit rates. While the GLMs had modest explanatory power within regions (S3 Table), together they accounted for 52.9% of observed global variation in visit rates. Associations with individual GLM variables—controlling for the effects of other variables—differed regionally in their strength but broadly matched our predictions (S1 Fig.). Visit rates increased with local population size (in Europe), decreased with remoteness (everywhere apart from Asia/Australasia), increased with natural attractiveness (in North and Latin America), and increased with national income (everywhere else). Controlling for these variables, visit rates were highest in North America, lower in Asia/Australasia and Europe, and lowest in Africa and Latin America.To quantify how often people visit PAs as a whole, we used our region-specific GLMs to estimate visit rates to 94,238 sites listed in the World Database on Protected Areas (WDPA) [18]). We again excluded marine, Antarctic, and Category I PAs, as well as almost 40,000 extremely small sites which were below the size (10 ha) of the smallest PA in our sample (S2 Fig.). The limited power of our GLMs and significant errors in the WDPA mean our estimates of visit rates should be treated with caution for individual sites or (when aggregated to national level) for smaller countries. However, the larger-scale patterns they reveal are marked. Estimated median visit rates per PA (averaged within countries) are lowest in Africa (at around 3,000/y) and Latin America (4,000/y), and greatest in North America (350,000/y) (S3 Table). When visit rates are aggregated across all PAs within a country, pronounced regional differences in the numbers of PAs (with relatively few in Africa and Latin America) magnify these patterns and indicate that while many African countries have <100,000 PA visits/y, PAs in the United States receive a combined total of over 3 billion visits/y (Fig. 1). This variation is underscored when aggregate PA visit rates are standardised by the annual number of non-workdays and total population size of each region: across Europe we reckon there are ~5 PA visits/100 non-work person-days; for North America, the figure is ~10 visits/100 non-work person-days respectively, while for each other region our estimates are <0.3 visits/100 non-work person-days.Open in a separate windowFig 1Estimated total PA visit rates for each country.Totals (which are log₁₀-transformed) were derived by applying the relevant regional GLM (S3 Table) to all of a country’s terrestrial PAs (excluding those <10 ha, and marine and IUCN Category I PAs) listed in the WDPA [18]. Asterisks show countries for which we had visit rate observations.Summing our aggregate estimates of PA visits suggests that between them, the world’s terrestrial PAs receive approximately 8 billion visits/y. Of these, we estimate 3.8 billion visits/y are in Europe (where more than half of the PAs in the WDPA are located) and 3.3 billion visits/y are in North America (S3 Table). These numbers are strikingly large. However, given our confidence intervals (95% CIs for the global total: 5.4–18.5 billion/y) and considering several conservative aspects of our calculations (e.g., the exclusion of ~40,000 very small sites and the incomplete nature of the WDPA), we consider it implausible that there are fewer than 5 billion PA visits worldwide each year. Three national estimates support this view: 2.5 billion visitdays/y to US PAs in 1996 [4], >1 billion visits/y (albeit many of them cultural rather than nature-based) to China’s National Parks in 2006 [19], and 3.2–3.9 billion visits/y to all British “ecosystems” (most of which are not in PAs) in 2010 [7].Finally, what can be inferred about the economic significance of visits on this scale? Economists working on tourism distinguish two main, non-overlapping components of value [12]: direct expenditure by visitors (an element of economic impact, calculated from spending on fees, travel, accommodation, etc.); and consumer surplus (a measure of economic value which arises because many visitors would be prepared to pay more for their visit than they actually have to, and which is defined as the difference between what visitors would be prepared to pay for a visit and what they actually spend; consumer surplus is typically quantified using travel cost or contingent valuation methods). We conducted an extensive literature search to derive median (but conservative) figures for each type of value for each region (S4 Table). Applying these to our corresponding estimates of visit rates and summing across regions yields an estimate of global gross direct expenditure associated with PA visits (within-country only, and excluding indirect and induced expenditure) of ~US $600 billion/y worldwide (at 2014 prices). The corresponding figure for global consumer surplus is ~US $250 billion/y.Such numbers are unavoidably imprecise. Uncertainty in our modelled visit rates and the wide variation in published estimates of expenditure and consumer surplus mean that they could be out by a factor of two or more. However, comparison with calculations that visits to North American PAs alone have an economic impact of $350–550 billion/y [4] and that direct expenditure on all travel and tourism worldwide runs at $2,000 billion/y [20] suggests our figures are of the correct order of magnitude, and that the value of PA visitation runs into hundreds of billions of dollars annually.These results quantify, we believe for the first time, the scale of visits to the world’s PAs and their approximate economic significance. We currently spend <$10 billion/y in safeguarding PAs [21]—a figure which is widely regarded as grossly insufficient [21–25]. Even without considering the many other benefits which PAs provide [22], our estimates of the economic impact and value of PA visitation dwarf current expenditure—highlighting the risks of underinvestment in conservation, and suggesting substantially increased investments in protected area maintenance and expansion would yield substantial returns.     

Computational approach to suggest a new multi-target-directed ligand as a potential medication for Alzheimer’s disease

Abstract

Acetylcholinesterase (AChE) enzyme and myeloid differentiation 2 protein (MD2) are two critical proteins involved in Alzheimer’s disease (AD). Since the nature of the active site of AChE and the binding pocket of MD2 are similar, some ligands can inhibit both of them appropriately. Oxidative stress has also been known as an important cause of AD. Designing an effective common inhibitor with antioxidant activity to inhibit AChE and MD2 proteins is the main goal of this work. In this regard, we used tacrine molecule with a high ligand efficiency (LE) and dehydrozingerone (DHZ) with anti-inflammatory, antioxidant and anti-Alzheimer activities. Some modifications on DHZ structure can increase its antioxidant activity. So, tacrine molecule was combined with modified DHZ to present a new multi-target-directed ligand (MTDL). The ability of the designed ligand to inhibit AChE and MD2 proteins was confirmed by molecular docking, molecular dynamics (MD) simulation, and binding-free energy calculations. Therefore, the designed ligand can target two proteins involved in AD. It can also act as a potent antioxidant. In general, three important causative agents of AD are targeted by the designed ligand. Moreover, the inhibition of MD2, as the main source of oxidative stress, significantly reduces the production of free radicals.     

Unexpectedly broad target recognition of the CRISPR-mediated virus defence system in the archaeon Sulfolobus solfataricus

The hyperthermophilic archaeon Sulfolobus solfataricus carries an extensive array of clustered regularly interspaced short palindromic repeats (CRISPR) systems able to mediate DNA degradation of invading genetic elements when complementarity to the small CRISPR-derived (cr)RNAs is given. Studying virus defence in vivo with recombinant viral variants, we demonstrate here that an unexpectedly high number of mutations are tolerated between the CRISPR-derived guide RNAs (crRNAs) and their target sequences (protospacer). Up to 15 mismatches in the crRNA still led to ∼50% of DNA degradation, when these mutations were outside the ‘seed’ region. More than 15 mutations were necessary to fully abolished interference. Different from other CRISPR systems investigated in vivo, mutations outside the protospacer region indicated no need for a protospacer adjacent motif sequence to confer DNA interference. However, complementarity of only 3 nucleotides between the repeat-derived 5′ handle of the crRNA and nucleotides adjacent to the protospacer enabled self-recognition, i.e. protection of the host locus. Our findings show commonalities and differences among the various CRISPR-mediated defence systems and suggest that they should not merely be perceived as a ‘first-barrier-defence system’ but may be considered to have a broader mechanism that allows host cells to cope with viruses keeping them at reduced levels.     

Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographical distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the Late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single Late Pleistocene population. Both the geographical origin of this ancestral population and how it became widespread remain unknown. Here, we used a spatially and temporally explicit modelling framework to analyse a data set of 90 modern and 45 ancient mitochondrial wolf genomes from across the Northern Hemisphere, spanning the last 50,000 years. Our results suggest that contemporary wolf populations trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum, and that this process was most likely driven by Late Pleistocene ecological fluctuations that occurred across the Northern Hemisphere. This study provides direct ancient genetic evidence that long‐range migration has played an important role in the population history of a large carnivore, and provides insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because Late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.