High genetic diversity and low differentiation reflect the ecological versatility of the African leopard

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Fences can support restoration in human‐dominated ecosystems when rewilding with large predators

The use of fences in conservation can be controversial, as artificial barriers constrain natural behavior and ecological dynamics. However, in the case of large predators inhabiting protected areas within a hostile human‐dominated landscape, predators may remain at low densities if they face high mortality upon leaving the reserve. In turn, this may compromise the potential for density‐dependent effects such as top‐down regulation of prey species abundance. We simulate the hypothetical reintroduction of gray wolves (Canis lupus) to reserves in their former range (Scottish Highlands), with the objectives of identifying parameters that allow a viable wolf population and the potential for direct top‐down forcing of red deer (Cervus elaphus) densities. We examine the extent to which the number of dispersing wolves leaving the protected area influences whether these objectives are achieved. Our simulations confirm that source‐sink population dynamics can result in a self‐perpetuating wolf population, but one that never achieves densities needed for strong top‐down forcing. When wolf density is weakly controlled by intraspecific competition, strong top‐down forcing occurs when 20% of dispersing wolves or less leave the population. When 20–35% of dispersing wolves leave, the strength of top‐down forcing is highly variable. The wolf population remained viable when 35–60% of dispersing wolves left, but then did not exert strong top‐down forcing. Wolves were vulnerable to extinction at greater than 60% disperser loss. Despite their negative connotations, fences (including semi‐permeable ones) could increase the potential for interspecific density‐dependent processes in some cases, thereby facilitating trophic rewilding.     

Localizing recent adaptive evolution in the human genome

Identifying genomic locations that have experienced selective sweeps is an important first step toward understanding the molecular basis of adaptive evolution. Using statistical methods that account for the confounding effects of population demography, recombination rate variation, and single-nucleotide polymorphism ascertainment, while also providing fine-scale estimates of the position of the selected site, we analyzed a genomic dataset of 1.2 million human single-nucleotide polymorphisms genotyped in African-American, European-American, and Chinese samples. We identify 101 regions of the human genome with very strong evidence (p < 10⁻⁵) of a recent selective sweep and where our estimate of the position of the selective sweep falls within 100 kb of a known gene. Within these regions, genes of biological interest include genes in pigmentation pathways, components of the dystrophin protein complex, clusters of olfactory receptors, genes involved in nervous system development and function, immune system genes, and heat shock genes. We also observe consistent evidence of selective sweeps in centromeric regions. In general, we find that recent adaptation is strikingly pervasive in the human genome, with as much as 10% of the genome affected by linkage to a selective sweep.     

Group Selection and Contribution of Minority Variants during Virus Adaptation Determines Virus Fitness and Phenotype

Understanding how a pathogen colonizes and adapts to a new host environment is a primary aim in studying emerging infectious diseases. Adaptive mutations arise among the thousands of variants generated during RNA virus infection, and identifying these variants will shed light onto how changes in tropism and species jumps can occur. Here, we adapted Coxsackie virus B3 to a highly permissive and less permissive environment. Using deep sequencing and bioinformatics, we identified a multi-step adaptive process to adaptation involving residues in the receptor footprints that correlated with receptor availability and with increase in virus fitness in an environment-specific manner. We show that adaptation occurs by selection of a dominant mutation followed by group selection of minority variants that together, confer the fitness increase observed in the population, rather than selection of a single dominant genotype.     

Assessing the Causal Relationship of Maternal Height on Birth Size and Gestational Age at Birth: A Mendelian Randomization Analysis

Background

Observational epidemiological studies indicate that maternal height is associated with gestational age at birth and fetal growth measures (i.e., shorter mothers deliver infants at earlier gestational ages with lower birth weight and birth length). Different mechanisms have been postulated to explain these associations. This study aimed to investigate the casual relationships behind the strong association of maternal height with fetal growth measures (i.e., birth length and birth weight) and gestational age by a Mendelian randomization approach.

Methods and Findings

We conducted a Mendelian randomization analysis using phenotype and genome-wide single nucleotide polymorphism (SNP) data of 3,485 mother/infant pairs from birth cohorts collected from three Nordic countries (Finland, Denmark, and Norway). We constructed a genetic score based on 697 SNPs known to be associated with adult height to index maternal height. To avoid confounding due to genetic sharing between mother and infant, we inferred parental transmission of the height-associated SNPs and utilized the haplotype genetic score derived from nontransmitted alleles as a valid genetic instrument for maternal height. In observational analysis, maternal height was significantly associated with birth length (p = 6.31 × 10⁻⁹), birth weight (p = 2.19 × 10⁻¹⁵), and gestational age (p = 1.51 × 10⁻⁷). Our parental-specific haplotype score association analysis revealed that birth length and birth weight were significantly associated with the maternal transmitted haplotype score as well as the paternal transmitted haplotype score. Their association with the maternal nontransmitted haplotype score was far less significant, indicating a major fetal genetic influence on these fetal growth measures. In contrast, gestational age was significantly associated with the nontransmitted haplotype score (p = 0.0424) and demonstrated a significant (p = 0.0234) causal effect of every 1 cm increase in maternal height resulting in ~0.4 more gestational d. Limitations of this study include potential influences in causal inference by biological pleiotropy, assortative mating, and the nonrandom sampling of study subjects.

Conclusions

Our results demonstrate that the observed association between maternal height and fetal growth measures (i.e., birth length and birth weight) is mainly defined by fetal genetics. In contrast, the association between maternal height and gestational age is more likely to be causal. In addition, our approach that utilizes the genetic score derived from the nontransmitted maternal haplotype as a genetic instrument is a novel extension to the Mendelian randomization methodology in casual inference between parental phenotype (or exposure) and outcomes in offspring.     

Ecosystem properties of semiarid savanna grassland in West Africa and its relationship with environmental variability

The Dahra field site in Senegal, West Africa, was established in 2002 to monitor ecosystem properties of semiarid savanna grassland and their responses to climatic and environmental change. This article describes the environment and the ecosystem properties of the site using a unique set of in situ data. The studied variables include hydroclimatic variables, species composition, albedo, normalized difference vegetation index (NDVI), hyperspectral characteristics (350–1800 nm), surface reflectance anisotropy, brightness temperature, fraction of absorbed photosynthetic active radiation (FAPAR), biomass, vegetation water content, and land‐atmosphere exchanges of carbon (NEE) and energy. The Dahra field site experiences a typical Sahelian climate and is covered by coexisting trees (~3% canopy cover) and grass species, characterizing large parts of the Sahel. This makes the site suitable for investigating relationships between ecosystem properties and hydroclimatic variables for semiarid savanna ecosystems of the region. There were strong interannual, seasonal and diurnal dynamics in NEE, with high values of ~?7.5 g C m^?2 day^?1 during the peak of the growing season. We found neither browning nor greening NDVI trends from 2002 to 2012. Interannual variation in species composition was strongly related to rainfall distribution. NDVI and FAPAR were strongly related to species composition, especially for years dominated by the species Zornia glochidiata. This influence was not observed in interannual variation in biomass and vegetation productivity, thus challenging dryland productivity models based on remote sensing. Surface reflectance anisotropy (350–1800 nm) at the peak of the growing season varied strongly depending on wavelength and viewing angle thereby having implications for the design of remotely sensed spectral vegetation indices covering different wavelength regions. The presented time series of in situ data have great potential for dryland dynamics studies, global climate change related research and evaluation and parameterization of remote sensing products and dynamic vegetation models.     

Toward an Active and Stable Catalyst for Oxygen Evolution in Acidic Media: Ti‐Stabilized MnO2

Catalysts are required for the oxygen evolution reaction, which are abundant, active, and stable in acid. MnO₂ is a promising candidate material for this purpose. However, it dissolves at high overpotentials. Using first‐principles calculations, a strategy to mitigate this problem by decorating undercoordinated surface sites of MnO₂ with a stable oxide is developed here. TiO₂ stands out as the most promising of the different oxides in the simulations. This prediction is experimentally verified by testing sputter‐deposited thin films of MnO₂ and Ti–MnO₂. A combination of electrochemical measurements, quartz crystal microbalance, inductively coupled plasma mass spectrometry measurements, and X‐ray photoelectron spectroscopy is performed. Small amounts of TiO₂ incorporated into MnO₂ lead to a moderate improvement in stability, with only a small decrease in activity. This study opens up the possibility of engineering surface properties of catalysts so that active and abundant nonprecious metal oxides can be used in acid electrolytes.