Wide-area mapping of small-scale features in agricultural landscapes using airborne remote sensing

Natural and semi-natural habitats in agricultural landscapes are likely to come under increasing pressure with the global population set to exceed 9 billion by 2050. These non-cropped habitats are primarily made up of trees, hedgerows and grassy margins and their amount, quality and spatial configuration can have strong implications for the delivery and sustainability of various ecosystem services. In this study high spatial resolution (0.5 m) colour infrared aerial photography (CIR) was used in object based image analysis for the classification of non-cropped habitat in a 10,029 ha area of southeast England. Three classification scenarios were devised using 4 and 9 class scenarios. The machine learning algorithm Random Forest (RF) was used to reduce the number of variables used for each classification scenario by 25.5 % ± 2.7%. Proportion of votes from the 4 class hierarchy was made available to the 9 class scenarios and where the highest ranked variables in all cases. This approach allowed for misclassified parent objects to be correctly classified at a lower level. A single object hierarchy with 4 class proportion of votes produced the best result (kappa 0.909). Validation of the optimum training sample size in RF showed no significant difference between mean internal out-of-bag error and external validation. As an example of the utility of this data, we assessed habitat suitability for a declining farmland bird, the yellowhammer (Emberiza citronella), which requires hedgerows associated with grassy margins. We found that ∼22% of hedgerows were within 200 m of margins with an area >183.31 m2. The results from this analysis can form a key information source at the environmental and policy level in landscape optimisation for food production and ecosystem service sustainability

Insulin Resistance Exacerbates Genetic Predisposition to Nonalcoholic Fatty Liver Disease in Individuals Without Diabetes

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149741/1/hep41353.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149741/2/hep41353_am.pd

Hundreds of variants clustered in genomic loci and biological pathways affect human height

Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P < 0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.

Mixed-species plantations of eucalyptus with nitrogen fixing trees: a review

Mixed-species plantations of Eucalyptus with a nitrogen (N2) fixing species have the potential to increase productivity while maintaining soil fertility, compared to Eucalyptus monocultures. However, it is difficult to predict combinations of species and sites that will lead to these benefits. We review the processes and interactions occurring in mixed plantations, 5 and the influence of species or site attributes, to aid the selection of successful combinations of species and sites. Successful mixtures, where productivity is increased over that of monocultures, have often developed stratified canopies, such that the less shade-tolerant species overtops the more shadetolerant species. Successful mixtures also have significantly higher rates of N and P cycling than 10 Eucalyptus monocultures. It is therefore important to select N2-fixing species with readily decomposable litter and high rates of nutrient cycling, as well as high rates of N2-fixation. While the dynamics of N2-fixation in tree stands are not well understood, it appears as though eucalypts can benefit from fixed N as early as the first or second year following plantation establishment. A meta-analysis of 18 published studies revealed several trials in which mixtures were significantly 15 (

Impact of Rare and Common Genetic Variants on Diabetes Diagnosis by Hemoglobin A1c in Multi-Ancestry Cohorts: The Trans-Omics for Precision Medicine Program

Hemoglobin A1c (HbA1c) is widely used to diagnose diabetes and assess glycemic control in individuals with diabetes. However, nonglycemic determinants, including genetic variation, may influence how accurately HbA1c reflects underlying glycemia. Analyzing the NHLBI Trans-Omics for Precision Medicine (TOPMed) sequence data in 10,338 individuals from five studies and four ancestries (6,158 Europeans, 3,123 African-Americans, 650 Hispanics, and 407 East Asians), we confirmed five regions associated with HbA1c (GCK in Europeans and African-Americans, HK1 in Europeans and Hispanics, FN3K and/or FN3KRP in Europeans, and G6PD in African-Americans and Hispanics) and we identified an African-ancestry-specific low-frequency variant (rs1039215 in HBG2 and HBE1, minor allele frequency (MAF) = 0.03). The most associated G6PD variant (rs1050828-T, p.Val98Met, MAF = 12% in African-Americans, MAF = 2% in Hispanics) lowered HbA1c (−0.88% in hemizygous males, −0.34% in heterozygous females) and explained 23% of HbA1c variance in African-Americans and 4% in Hispanics. Additionally, we identified a rare distinct G6PD coding variant (rs76723693, p.Leu353Pro, MAF = 0.5%; −0.98% in hemizygous males, −0.46% in heterozygous females) and detected significant association with HbA1c when aggregating rare missense variants in G6PD. We observed similar magnitude and direction of effects for rs1039215 (HBG2) and rs76723693 (G6PD) in the two largest TOPMed African American cohorts, and we replicated the rs76723693 association in the UK Biobank African-ancestry participants. These variants in G6PD and HBG2 were monomorphic in the European and Asian samples. African or Hispanic ancestry individuals carrying G6PD variants may be underdiagnosed for diabetes when screened with HbA1c. Thus, assessment of these variants should be considered for incorporation into precision medicine approaches for diabetes diagnosis

Miombo woodland under threat : Consequences for tree diversity and carbon storage

Agriculture is expanding rapidly in the miombo woodlands of sub-Saharan Africa. Clear felling results in the loss of species and ecosystem services. The remaining woodland is used as a vital support system for the farming communities, and the impact of this utilisation on biodiversity and ecosystem service provision is not clear. Understanding these effects will aid the development of effective, sustainable land management strategies for multiple outcomes, including biodiversity conservation and resource utilisation. This study provides new data on miombo woodland tree species diversity, structure and carbon storage from a 8766km2 landscape in south-western Tanzania, which is undergoing rapid conversion to tobacco cultivation.Human utilisation of the woodland was classified by ground surveys which recorded evidence of use (e.g. cut poles and timber, removal of bark and roots, access routes). Nine sites were surveyed and categorised into three groups: high, medium and low utilisation. To determine the effect of utilisation on the tree community stem density, diameter at breast height, tree species richness and carbon storage were recorded. In the low utilisation sites carbon storage was similar to that found in other miombo woodlands (28tHa-1), and the Shannon Wiener diversity score for tree species diversity was 3.44. However, in the high utilisation sites, tree species diversity (2.86) and carbon storage declined (14.6tHa-1). In areas of moderate utilisation diversity and carbon storage were maintained, but the structure of the woodland was affected, with a reduction of Class 1 (Diameter at Breast Height (DBH)<10cm) stems, demonstrating low recruitment which leads to a reduction in sustainability. Tree species richness and abundance demonstrated an intermediate disturbance effect in relation to utilisation, with highest levels at medium utilisation sites.Key miombo woodland species from the subfamily Caesalpinioideae in the two genera Brachystegia and Julbernardia were present in all sites, but the frequency of Brachystegia species declined by 60% from low to high utilisation. The IUCN near-threatened timber species Pterocarpus angolensis, highly protected in Tanzania, was harvested throughout the study site, and the majority of trees recorded were immature (DBH. ≤. 20. cm), suggesting that it is commercially extinct for the foreseeable future.These findings illustrate that in miombo woodlands with low to medium utilisation levels key miombo species are retained, and tree species diversity and carbon storage remains optimal. Sustainable land management plans need to regulate utilisation within miombo landscapes and retain areas of woodland. This will ensure their long term viability, and continue to support the 100. million people who are reliant on miombo woodlands for their goods and services

Multi-ancestry genome-wide association study accounting for gene-psychosocial factor interactions identifies novel loci for blood pressure traits

Psychological and social factors are known to influence blood pressure (BP) and risk of hypertension and associated cardiovascular diseases. To identify novel BP loci, we carried out genome-wide association meta-analyses of systolic, diastolic, pulse, and mean arterial BP, taking into account the interaction effects of genetic variants with three psychosocial factors: depressive symptoms, anxiety symptoms, and social support. Analyses were performed using a two-stage design in a sample of up to 128,894 adults from five ancestry groups. In the combined meta-analyses of stages 1 and 2, we identified 59 loci (p value &lt; 5e−8), including nine novel BP loci. The novel associations were observed mostly with pulse pressure, with fewer observed with mean arterial pressure. Five novel loci were identified in African ancestry, and all but one showed patterns of interaction with at least one psychosocial factor. Functional annotation of the novel&nbsp;loci supports a major role for genes implicated in the immune response (PLCL2), synaptic function and neurotransmission (LIN7A and PFIA2), as well as genes previously implicated in neuropsychiatric or stress-related disorders (FSTL5 and CHODL). These findings underscore the importance of considering psychological and social factors in gene discovery for BP, especially in non-European populations

Genetic determinants of telomere length from 109,122 ancestrally diverse whole-genome sequences in TOPMed

Genetic studies on telomere length are important for understanding age-related diseases. Prior GWAS for leukocyte TL have been limited to European and Asian populations. Here, we report the first sequencing-based association study for TL across ancestrally-diverse individuals (European, African, Asian and Hispanic/Latino) from the NHLBI Trans-Omics for Precision Medicine (TOPMed) program. We used whole genome sequencing (WGS) of whole blood for variant genotype calling and the bioinformatic estimation of telomere length in n=109,122 individuals. We identified 59 sentinel variants (p-value OBFC1indicated the independent signals colocalized with cell-type specific eQTLs for OBFC1 (STN1). Using a multi-variant gene-based approach, we identified two genes newly implicated in telomere length, DCLRE1B (SNM1B) and PARN. In PheWAS, we demonstrated our TL polygenic trait scores (PTS) were associated with increased risk of cancer-related phenotypes