Detecting genetic variants under selection using FST outlier analysis (OA) and environmental association analyses (EAAs) are popular approaches that provide insight into the genetic basis of local ...adaptation. Despite the frequent use of OA and EAA approaches and their increasing attractiveness for detecting signatures of selection, their application to field‐based empirical data have not been synthesized. Here, we review 66 empirical studies that use Single Nucleotide Polymorphisms (SNPs) in OA and EAA. We report trends and biases across biological systems, sequencing methods, approaches, parameters, environmental variables and their influence on detecting signatures of selection. We found striking variability in both the use and reporting of environmental data and statistical parameters. For example, linkage disequilibrium among SNPs and numbers of unique SNP associations identified with EAA were rarely reported. The proportion of putatively adaptive SNPs detected varied widely among studies, and decreased with the number of SNPs analysed. We found that genomic sampling effort had a greater impact than biological sampling effort on the proportion of identified SNPs under selection. OA identified a higher proportion of outliers when more individuals were sampled, but this was not the case for EAA. To facilitate repeatability, interpretation and synthesis of studies detecting selection, we recommend that future studies consistently report geographical coordinates, environmental data, model parameters, linkage disequilibrium, and measures of genetic structure. Identifying standards for how OA and EAA studies are designed and reported will aid future transparency and comparability of SNP‐based selection studies and help to progress landscape and evolutionary genomics.
There is a lack of common surveillance systems providing comparable figures and temporal trends of the prevalence of overweight (OW), obesity and related risk factors among European preschool and ...school children. Comparability of available data is limited in terms of sampling design, methodological approaches and quality assurance. The IDEFICS (Identification and prevention of Dietary- and lifestyle-induced health Effects in Children and infantS) study provides one of the largest European data sets of young children based on state-of-the-art methodology.
To assess the European distribution of weight status according to different classification systems based on body mass index (BMI) in children (2.0-9.9 years). To describe the prevalence of weight categories by region, sex, age and socioeconomic position.
Between 2007 and 2010, 18,745 children from eight European countries participated in an extensive, highly standardised protocol including, among other measures, anthropometric examinations and parental reports on socio-demographic characteristics.
The combined prevalence of OW/obesity ranges from more than 40% in southern Europe to less than 10% in northern Europe. Overall, the prevalence of OW was higher in girls (21.1%) as compared with boys (18.6%). The prevalence of OW shows a negative gradient with social position, with some variation of the strength and consistency of this association across Europe. Overall, population groups with low income and/or lower education levels show the highest prevalence of obesity. The use of different reference systems to classify OW results in substantial differences in prevalence estimates and can even reverse the reported difference between boys and girls.
There is a higher prevalence of obesity in populations from southern Europe and in population groups with lower education and income levels. Our data confirm the need to develop and reinforce European public health policies to prevent early obesity and to reduce these health inequalities and regional disparities.
Summary
Drug‐induced liver injury (DILI) is often caused by innate and adaptive host immune responses. Characterization of inflammatory infiltrates in the liver may improve understanding of the ...underlying pathogenesis of DILI. This study aimed to enumerate and characterize leucocytes infiltrating liver tissue from subjects with acute DILI (n = 32) versus non‐DILI causes of acute liver injury (n = 25). Immunostains for CD11b/CD4 (Kupffer and T helper cells), CD3/CD20 (T and B cells) and CD8/CD56 T cytotoxic and natural killer (NK) cells were evaluated in biopsies from subjects with acute DILI, either immunoallergic (IAD) or autoimmune (AID) and idiopathic autoimmune (AIH) and viral hepatitis (VH) and correlated with clinical and pathological features. All biopsies showed numerous CD8+ T cells and macrophages. DILI cases had significantly fewer B lymphocytes than AIH and VH and significantly fewer NK cells than VH. Prominent plasma cells were unusual in IAD (three of 10 cases), but were associated strongly with AIH (eight of nine) and also observed in most with AID (six of nine). They were also found in five of 10 cases with VH. Liver biopsies from subjects with DILI were characterized by low counts of mature B cells and NK cells in portal triads in contrast to VH. NK cells were found only in cases of VH, whereas AIH and VH both showed higher counts of B cells than DILI. Plasma cells were associated most strongly with AIH and less so with AID, but were uncommon in IAD.
The aim of the study was to assess the associations of individual and combined physical fitness components with single and clustering of cardio-metabolic risk factors in children.
This 2-year ...longitudinal study included a total of 1635 European children aged 6-11 years. The test battery included cardio-respiratory fitness (20-m shuttle run test), upper-limb strength (handgrip test), lower-limb strength (standing long jump test), balance (flamingo test), flexibility (back-saver sit-and-reach) and speed (40-m sprint test). Metabolic risk was assessed through z-score standardization using four components: waist circumference, blood pressure (systolic and diastolic), blood lipids (triglycerides and high-density lipoprotein) and insulin resistance (homeostasis model assessment). Mixed model regression analyses were adjusted for sex, age, parental education, sugar and fat intake, and body mass index.
Physical fitness was inversely associated with clustered metabolic risk (P<0.001). All coefficients showed a higher clustered metabolic risk with lower physical fitness, except for upper-limb strength (β=0.057; P=0.002) where the opposite association was found. Cardio-respiratory fitness (β=-0.124; P<0.001) and lower-limb strength (β=-0.076; P=0.002) were the most important longitudinal determinants. The effects of cardio-respiratory fitness were even independent of the amount of vigorous-to-moderate activity (β=-0.059; P=0.029). Among all the metabolic risk components, blood pressure seemed not well predicted by physical fitness, while waist circumference, blood lipids and insulin resistance all seemed significantly predicted by physical fitness.
Poor physical fitness in children is associated with the development of cardio-metabolic risk factors. Based on our results, this risk might be modified by improving mainly cardio-respiratory fitness and lower-limb muscular strength.
Climate change is testing the resilience of forests worldwide pushing physiological tolerance to climatic extremes. Plant functional traits have been shown to be adapted to climate and have evolved ...patterns of trait correlations (similar patterns of distribution) and coordinations (mechanistic trade‐off). We predicted that traits would differentiate between populations associated with climatic gradients, suggestive of adaptive variation, and correlated traits would adapt to future climate scenarios in similar ways.
We measured genetically determined trait variation and described patterns of correlation for seven traits: photochemical reflectance index (PRI), normalized difference vegetation index (NDVI), leaf size (LS), specific leaf area (SLA), δ13C (integrated water‐use efficiency, WUE), nitrogen concentration (NCONC), and wood density (WD). All measures were conducted in an experimental plantation on 960 trees sourced from 12 populations of a key forest canopy species in southwestern Australia.
Significant differences were found between populations for all traits. Narrow‐sense heritability was significant for five traits (0.15–0.21), indicating that natural selection can drive differentiation; however, SLA (0.08) and PRI (0.11) were not significantly heritable. Generalized additive models predicted trait values across the landscape for current and future climatic conditions (>90% variance). The percent change differed markedly among traits between current and future predictions (differing as little as 1.5% (δ13C) or as much as 30% (PRI)). Some trait correlations were predicted to break down in the future (SLA:NCONC, δ13C:PRI, and NCONC:WD).
Synthesis: Our results suggest that traits have contrasting genotypic patterns and will be subjected to different climate selection pressures, which may lower the working optimum for functional traits. Further, traits are independently associated with different climate factors, indicating that some trait correlations may be disrupted in the future. Genetic constraints and trait correlations may limit the ability for functional traits to adapt to climate change.
We tested whether functional traits of an important tree species in southwestern Australia were genetically determined and able to undergo selection. Our results suggest that some traits are heritable (Water Use Efficiency) while others are not (SLA), indicating that in the future, under different climates, selection will differentially effect traits. Therefore, it is likely that current trait combinations will change with climate.
The aim of this study is to present age- and sex-specific reference values of insulin, glucose, glycosylated haemoglobin (HbA1c) and the homeostasis model assessment to quantify insulin resistance ...(HOMA-IR) for pre-pubertal children.
The reference population consists of 7074 normal weight 3- to 10.9-year-old pre-pubertal children from eight European countries who participated in at least one wave of the IDEFICS ('identification and prevention of dietary- and lifestyle-induced health effects in children and infants') surveys (2007-2010) and for whom standardised laboratory measurements were obtained. Percentile curves of insulin (measured by an electrochemiluminescence immunoassay), glucose, HbA1c and HOMA-IR were calculated as a function of age stratified by sex using the general additive model for location scale and shape (GAMLSS) method.
Levels of insulin, fasting glucose and HOMA-IR continuously show an increasing trend with age, whereas HbA1c shows an upward trend only beyond the age of 8 years. Insulin and HOMA-IR values are higher in girls of all age groups, whereas glucose values are slightly higher in boys. Median serum levels of insulin range from 17.4 and 13.2 pmol l(-1) in 3-<3.5-year-old girls and boys, respectively, to 53.5 and 43.0 pmol l(-1) in 10.5-<11-year-old girls and boys. Median values of glucose are 4.3 and 4.5 mmol l(-1) in the youngest age group and 49.3 and 50.6 mmol l(-1) in the oldest girls and boys. For HOMA-IR, median values range from 0.5 and 0.4 in 3-<3.5-year-old girls and boys to 1.7 and 1.4 in 10.5-<11-year-old girls and boys, respectively.
Our study provides the first standardised reference values for an international European children's population and provides the, up to now, largest data set of healthy pre-pubertal children to model reference percentiles for markers of insulin resistance. Our cohort shows higher values of Hb1Ac as compared with a single Swedish study while our percentiles for the other glucose metabolic markers are in good accordance with previous studies.
To provide sex- and age-specific percentile values for levels of physical activity (PA) and sedentary time of European children aged 2.0-10.9 years from eight European countries (Sweden, Germany, ...Hungary, Italy, Cyprus, Spain, Belgium and Estonia).
Free-living PA and sedentary time were objectively assessed using ActiGraph GT1M or ActiTrainer activity monitors in all children who had at least 3 days' worth of valid accelerometer data, with at least 8 h of valid recording time each day. The General Additive Model for Location Scale and Shape was used for calculating percentile curves.
Reference values for PA and sedentary time in the European children according to sex and age are displayed using smoothed percentile curves for 7684 children (3842 boys and 3842 girls). The figures show similar trends in boys and girls. The percentage of children complying with recommendations regarding moderate-to-vigorous physical activity (MVPA) is also presented and varied considerably between sexes and country. For example, the percentage of study participants who were physically active (as assessed by MVPA) for 60 or more minutes per day ranged from 2.0% (Cyprus) to 14.7% (Sweden) in girls and from 9.5% (Italy) to 34.1% (Belgium) in boys.
This study provides the most up-to-date sex- and age-specific reference data on PA in young children in Europe. The percentage compliance to MVPA recommendations for these European children varied considerably between sexes and country and was generally low. These results may have important implications for public health policy and PA counselling.
Drought adaptation is critical to many tree species persisting under climate change, however our knowledge of the genetic basis for trees to adapt to drought is limited. This knowledge gap impedes ...our fundamental understanding of drought response and application to forest production and conservation. To improve our understanding of the genomic determinants, architecture, and trait constraints, we assembled a reference genome and detected ~ 6.5 M variants in 432 phenotyped individuals for the foundational tree Corymbia calophylla. We found 273 genomic variants determining traits with moderate heritability (h.sup.2.sub.SNP = 0.26-0.64). Significant variants were predominantly in gene regulatory elements distributed among several haplotype blocks across all chromosomes. Furthermore, traits were constrained by frequent epistatic and pleiotropic interactions. Our results on the genetic basis for drought traits in Corymbia calophylla have several implications for the ability to adapt to climate change: (1) drought related traits are controlled by complex genomic architectures with large haplotypes, epistatic, and pleiotropic interactions; (2) the most significant variants determining drought related traits occurred in regulatory regions; and (3) models incorporating epistatic interactions increase trait predictions. Our findings indicate that despite moderate heritability drought traits are likely constrained by complex genomic architecture potentially limiting trees response to climate change.
To estimate the prevalence of the metabolic syndrome (MetS) using reference standards obtained in European children and to develop a quantitative MetS score and describe its distribution in children.
...Population-based survey in eight European countries, including 18745 children 2.0 to 10.9 years, recruited during a second survey. Anthropometry (weight, height and waist circumference), blood pressure and serum-fasting triglycerides, HDL cholesterol, glucose and insulin were measured. We applied three widely accepted definitions of the pediatric MetS and we suggest a new definition, to guide pediatricians in decisions about close monitoring or even intervention (values of at least three of the MetS components exceeding the 90th or 95th percentile, respectively). We used a z-score standardisation to calculate a continuous score combining the MetS components.
Among the various definitions of MetS, the highest prevalence (5.5%) was obtained with our new definition requiring close observation (monitoring level). Our more conservative definition, requiring pediatric intervention gives a prevalence of 1.8%. In general, prevalences were higher in girls than in boys. The prevalence of metabolic syndrome is highest among obese children. All definitions classify a small percentage of thin or normal weight children as being affected. The metabolic syndrome score shows a positive trend with age, particularly regarding the upper percentiles of the score.
According to different definitions of pediatric MetS, a non-negligible proportion of mostly prepubertal children are classified as affected. We propose a new definition of MetS that should improve clinical guidance. The continuous score developed may also serve as a useful tool in pediatric obesity research. It has to be noted, however, that the proposed cutoffs are based on a statistical definition that does not yet allow to quantify the risk of subsequent disease.
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