Genomic, Evolutionary and Functional Analyses of Diapause in Drosophila Melanogaster

Understanding the genetic basis of adaptation has been and remains to be one major goal of ecological and evolutionary genetics. The variation in diapause propensity in the model organism Drosophila melanogaster represents different life-history strategies underlying adaptation to regular and widespread environmental heterogeneity, thus provides an ideal model to study the genetic control of ecologically important complex phenotype. This work employs global genomic and transcriptomic approaches to identify genetic polymorphisms co-segregating with diapause propensity, as well as genes that are differentially regulated at the transcriptional level as a function of the diapause phenotype. I show that genetic polymorphisms co-segregating with diapause propensity are found throughout all major chromosomes, demonstrating that diapause is a multi-genic trait. I show that diapause in D. melanogaster is an actively regulated phenotype at the transcriptional level, suggesting that diapause is not a simple physiological or reproductive quiescence. I also demonstrate that genetic polymorphisms co-segregating with diapause propensity, as well as genes differentially expressed as a function of diapause are enriched for clinally varying and seasonal oscillating SNPs, supporting the hypothesis that natural variation in diapause propensity underlies adaptation to spatially and temporally varying selective pressures. In addition to global genomic and transcriptomic screens, I also performed functional analysis of one candidate polymorphism on the gene Crystalllin, which represents an intersection of multiple global screens related to seasonal adaptation. I show that this polymorphism affects patterns of gene expression and a subset of fitness-related phenotypes including diapause, in an environment-specific manner. Taken together, this work provide a holistic view of the genetic basis of a complex trait underlying climatic adaptation in wild populations of D. melanogaster, linking genetic polymorphism, gene regulation, organismal phenotype, population dynamics and environmental parameters

Upside-down fluxes Down Under: CO2 net sink in winter and net source in summer in a temperate evergreen broadleaf forest

Predicting the seasonal dynamics of ecosystem carbon fluxes is challenging in broadleaved evergreen forests because of their moderate climates and subtle changes in canopy phenology. We assessed the climatic and biotic drivers of the seasonality of net ecosystem–atmosphere CO2 exchange (NEE) of a eucalyptus-dominated forest near Sydney, Australia, using the eddy covariance method. The climate is characterised by a mean annual precipitation of 800mm and a mean annual temperature of 18°C, hot summers and mild winters, with highly variable precipitation. In the 4-year study, the ecosystem was a sink each year (−225gCm−2yr−1 on average, with a standard deviation of 108gCm−2yr−1); inter-annual variations were not related to meteorological conditions. Daily net C uptake was always detected during the cooler, drier winter months (June through August), while net C loss occurred during the warmer, wetter summer months (December through February). Gross primary productivity (GPP) seasonality was low, despite longer days with higher light intensity in summer, because vapour pressure deficit (D) and air temperature (Ta) restricted surface conductance during summer while winter temperatures were still high enough to support photosynthesis. Maximum GPP during ideal environmental conditions was significantly correlated with remotely sensed enhanced vegetation index (EVI; r2 = 0.46) and with canopy leaf area index (LAI; r2= 0.29), which increased rapidly after mid-summer rainfall events. Ecosystem respiration (ER) was highest during summer in wet soils and lowest during winter months. ER had larger seasonal amplitude compared to GPP, and therefore drove the seasonal variation of NEE. Because summer carbon uptake may become increasingly limited by atmospheric demand and high temperature, and because ecosystem respiration could be enhanced by rising temperatures, our results suggest the potential for large-scale seasonal shifts in NEE in sclerophyll vegetation under climate change.The Australian Education Investment Fund, Australian Terrestrial Ecosystem Research Network, Australian Research Council and Hawkesbury Institute for the Environment at Western Sydney University supported this work. We thank Jason Beringer, Helen Cleugh, Ray Leuning and Eva van Gorsel for advice and support. Senani Karunaratne provided soil classification details

Synthetic transactivation screening reveals ETV4 as broad coactivator of hypoxia-inducible factor signaling

The human prolyl-4-hydroxylase domain (PHD) proteins 1–3 are known as cellular oxygen sensors, acting via the degradation of hypoxia-inducible factor (HIF) α-subunits. PHD2 and PHD3 genes are inducible by HIFs themselves, suggesting a negative feedback loop that involves PHD abundance. To identify novel regulators of the PHD2 gene, an expression array of 704 transcription factors was screened by a method that allows distinguishing between HIF-dependent and HIF-independent promoter regulation. Among others, the E-twenty six transcription factor ETS translocation variant 4 (ETV4) was found to contribute to PHD2 gene expression particularly under hypoxic conditions. Mechanistically, complex formation between ETV4 and HIF-1/2α was observed by mammalian two-hybrid and fluorescence resonance energy transfer analysis. HIF-1α domain mapping, CITED2 overexpression and factor inhibiting HIF depletion experiments provided evidence for cooperation between HIF-1α and p300/CBP in ETV4 binding. Chromatin immunoprecipitation confirmed ETV4 and HIF-1α corecruitment to the PHD2 promoter. Of 608 hypoxically induced transcripts found by genome-wide expression profiling, 7.7% required ETV4 for efficient hypoxic induction, suggesting a broad role of ETV4 in hypoxic gene regulation. Endogenous ETV4 highly correlated with PHD2, HIF-1/2α and several established markers of tissue hypoxia in 282 human breast cancer tissue samples, corroborating a functional interplay between the ETV4 and HIF pathways

Global application of an unoccupied aerial vehicle photogrammetry protocol for predicting aboveground biomass in non‐forest ecosystems

P. 1-15Non-forest ecosystems, dominated by shrubs, grasses and herbaceous plants, provide ecosystem services including carbon sequestration and forage for grazing, and are highly sensitive to climatic changes. Yet these ecosystems are poorly represented in remotely sensed biomass products and are undersampled by in situ monitoring. Current global change threats emphasize the need for new tools to capture biomass change in non-forest ecosystems at appropriate scales. Here we developed and deployed a new protocol for photogrammetric height using unoccupied aerial vehicle (UAV) images to test its capability for delivering standardized measurements of biomass across a globally distributed field experiment. We assessed whether canopy height inferred from UAV photogrammetry allows the prediction of aboveground biomass (AGB) across low-stature plant species by conducting 38 photogrammetric surveys over 741 harvested plots to sample 50 species. We found mean canopy height was strongly predictive of AGB across species, with a median adjusted R2 of 0.87 (ranging from 0.46 to 0.99) and median prediction error from leave-one-out cross-validation of 3.9%. Biomass per-unit-of-height was similar within but different among, plant functional types. We found that photogrammetric reconstructions of canopy height were sensitive to wind speed but not sun elevation during surveys. We demonstrated that our photogrammetric approach produced generalizable measurements across growth forms and environmental settings and yielded accuracies as good as those obtained from in situ approaches. We demonstrate that using a standardized approach for UAV photogrammetry can deliver accurate AGB estimates across a wide range of dynamic and heterogeneous ecosystems. Many academic and land management institutions have the technical capacity to deploy these approaches over extents of 1–10 ha−1. Photogrammetric approaches could provide much-needed information required to calibrate and validate the vegetation models and satellite-derived biomass products that are essential to understand vulnerable and understudied non-forested ecosystems around the globe.S

Unravelling spatio-temporal water balance patterns in topographically complex landscapes

© 2017 Dr. Daniel MetzenThe Budyko framework for understanding how precipitation (P) is partitioned into evapotranspiration (ET) and streamflow has been shown to be remarkably robust at large spatial scales. The Budyko model simply uses P and potential ET as variables. However, at smaller spatial scales additional predictor variables are required to partition precipitation. In steep uplands, topography appears to exert strong control on the water balance at the hillslope scale. Organization of vegetation suggest heterogeneity in the water balance at these scales. This topographic control though is poorly characterized in most environments and therefore not well represented in models. The aim of this thesis is to quantify the effect of local topography (aspect and drainage position) on forest water balance as a first step towards a down-scaling of the Budyko model in steep upland terrain. Six intensively instrumented sited were established on three drainage positions and two aspects in mixed species eucalypt forests (MSEF), with all other variables remaining constant. Continuously monitored water balances were extrapolated across a ~70 ha catchment using a Random Forest model and LiDAR characterization of stand density and structure. The study demonstrated that spatial vegetation patterns emerged in response to topographic control on water-availability via soil depth, water redistribution and sub-canopy radiation loads. Moreover, short-term variations of overstory transpiration (To) were driven by atmospheric forcing, whereas seasonal and annual To patterns were explained by sapwood area index (As, R^2:0.89). Understory and forest floor evapotranspiration (ETu) was controlled by sub-canopy short-wave radiation. Further, the combined effect of aspect and drainage position on water balance partitioning markedly diverged along the south and north-facing transect. All plots on northern aspects had a positive water balance (P> ET), whereas only the ridge plot on the south-facing slope had a positive water balance, while the lower hillslope had higher ET rates than rainfall inputs.ET measurements from the distributed plots could be up-scaled using terrain and vegetation information derived from LiDAR and unveiled strong spatial variability of To (4.5-fold), ETu (3.5-fold) and total ET rates (2-fold) over as little as 200 m distance. The observed ET range corresponds to eucalypt forests typically located >100s of kilometers apart, with the lower end similar to arid open woodlands in Western Australia and the upper end to tall mountain ash forests in the Victorian highlands. Predicting ET using the Budyko framework revealed strongly biased ET estimates in relation to landscape position, where ~18% of the catchment area plotted above the theoretical water limit, confirming the importance of topographic water redistribution. Further, model residuals were explained well by As and terrain patterns. My thesis presented strong links between vegetation patterns, topography, soil depth and energy and water fluxes in upland MSEF. Ultimately, the study demonstrated the potential of remotely sensed vegetation and terrain patterns to infer and scale water-balance patterns in heterogeneous upland forests

The myth of the stupid believer : The negative religiousness-IQ nexus is not on general intelligence (g) and is likely a product of the relations between IQ and Autism Spectrum traits

Numerous studies have found a negative relationship between religiousness and IQ. It is in the region of - 0.2, according to meta-analyses. The reasons for this relationship are, however, unknown. It has been suggested that higher intelligence leads to greater attraction to science, or that it helps to override evolved cognitive dispositions such as for religiousness. Either way, such explanations assume that the religion-IQ nexus is on general intelligence (g), rather than some subset of specialized cognitive abilities. In other words, they assume it is a Jensen effect. Two large datasets comparing groups with different levels of religiousness show that their IQ differences are not on g and must, therefore, be attributed to specialized abilities. An analysis of the specialized abilities on which the religious and non-religious groups differ reveals no clear pattern. We cautiously suggest that this may be explicable in terms of autism spectrum disorder traits among people with high IQ scores, because such traits are negatively associated with religiousness

Generating spatially robust carbon budgets from flux tower observations

Estimating global terrestrial productivity is typically achieved by rescaling individual flux tower measurements, traditionally assumed to represent homogeneous areas, using gridded remote sensing and climate data. Using 154 locations from the FLUXNET2015 database, we demonstrate that variations in spatial homogeneity and nonuniform sampling patterns introduce variability in carbon budget estimates that propagate to the biome scale. We propose a practical solution to quantify the variability of vegetation characteristics and uniformity of sampling patterns and, moreover, account for contributions of sampling variations over heterogeneous surfaces to carbon budgets from flux towers. Our proposed space‐time‐equitable budgets reduce uncertainty related to heterogeneities, allow for more accurate attribution of physiological variations in productivity trends, and provide more representative grid cell averages for linking fluxes with gridded data products

TAVR : nemesis of NOACs?

Data on non-vitamin K antagonist oral anticoagulants (NOACs) in transcatheter aortic valve replacement (TAVR) patients are controversial. In patients without atrial fibrillation (AF), rivaroxaban showed enhanced ischemia and bleeding as compared to standard of care. ENVISAGE showed enhanced bleeding in AF patients as compared to vitamin K antagonist (VKA). Only apixaban was non-inferior but failed superiority regarding bleeding in AF patients after TAVR. One could hypothesize that this might be due to pharmacokinetics of NOACs. Therefore, we compared outcome in rivaroxaban/edoxaban (once-daily) and apixaban (twice-daily) treated patients. 568 patients with indication for permanent oral anticoagulation due to AF undergoing TAVR were analyzed via inverse probability of treatment weighting. Valve academic research consortium complications during 30-day follow-up were assessed. Bleeding complications were similar in once-daily and twice-daily NOACs (major: 22 (7.5%) vs. 14 (5.3%), p = 0.285; minor: 66 (22.4%) vs. 46 (17.4%), p = 0.133). Complications did not change when splitting the cohort in the different agents apixaban, rivaroxaban and edoxaban. These findings remained robust after multivariate analysis. In summary, twice-daily and once-daily NOACs did not differ regarding bleeding complications in a hypothesis generating real-world cohort of TAVR patients with AF