Relationships between estimated autozygosity and complex traits in the UK Biobank

<div><p>Inbreeding increases the risk of certain Mendelian disorders in humans but may also reduce fitness through its effects on complex traits and diseases. Such inbreeding depression is thought to occur due to increased homozygosity at causal variants that are recessive with respect to fitness. Until recently it has been difficult to amass large enough sample sizes to investigate the effects of inbreeding depression on complex traits using genome-wide single nucleotide polymorphism (SNP) data in population-based samples. Further, it is difficult to infer causation in analyses that relate degree of inbreeding to complex traits because confounding variables (e.g., education) may influence both the likelihood for parents to outbreed and offspring trait values. The present study used runs of homozygosity in genome-wide SNP data in up to 400,000 individuals in the UK Biobank to estimate the proportion of the autosome that exists in autozygous tracts—stretches of the genome which are identical due to a shared common ancestor. After multiple testing corrections and controlling for possible sociodemographic confounders, we found significant relationships in the predicted direction between estimated autozygosity and three of the 26 traits we investigated: age at first sexual intercourse, fluid intelligence, and forced expiratory volume in 1 second. Our findings corroborate those of several published studies. These results may imply that these traits have been associated with Darwinian fitness over evolutionary time. However, some of the autozygosity-trait relationships were attenuated after controlling for background sociodemographic characteristics, suggesting that alternative explanations for these associations have not been eliminated. Care needs to be taken in the design and interpretation of ROH studies in order to glean reliable information about the genetic architecture and evolutionary history of complex traits.</p></div

The importance of including habitat-specific behaviour in models of butterfly movement

Dispersal is a key process affecting population persistence and major factors affecting dispersal rates are the amounts, connectedness and properties of habitats in landscapes. We present new data on the butterfly Maniola jurtina in flower-rich and flower-poor habitats that demonstrates how movement and behaviour differ between sexes and habitat types, and how this effects consequent dispersal rates. Females had higher flight speeds than males but their total time in flight was four times less. The effect of habitat type was strong for both sexes, flight speeds were ~2.5x and ~1.7x faster on resource-poor habitats for males and females respectively, and flights were approximately 50% longer. With few exceptions females oviposited in the mown grass habitat, likely because growing grass offers better food for emerging caterpillars, but they foraged in the resource-rich habitat. It seems that females faced a trade-off between ovipositing without foraging in the mown grass or foraging without ovipositing where flowers were abundant. We show that taking account of habitat-dependent differences in activity, here categorised as flight or non-flight, is crucial to obtaining good fits of an individual-based model to observed movement. An important implication of this finding is that incorporating habitat-specific activity budgets is likely necessary for predicting longer-term dispersal in heterogeneous habitats as habitat-specific behaviour substantially influences the mean (>30% difference) and kurtosis (1.4x difference) of dispersal kernels. The presented IBMs provide a simple method to explicitly incorporate known activity and movement rates when predicting dispersal in changing and heterogeneous landscapes

Doomed drones? Using passage experiments and mathematical modelling to determine Deformed wing virus population dynamics in male honey bees

Funding: This research was funded by the BBSRC (Biotechnology and Biological Sciences Research Council), grant numbers: BB/M010996/1 and BB/R00305X/1. P.C.S was supported by the BBSRC, grant number: BB/S00243X/1.Varroa destructor is an ectoparasitic mite of honeybees which vectors a range of pathogenic viruses, the most notable being Deformed wing virus (DWV). Mites parasitise bees during pupal development and male honeybees, drones, have a longer development cycle than female workers (24 versus 21 days), allow for more progeny mites to develop per foundress (1.6–2.5 compared to 0.7–1.45). How this longer exposure time influences evolution of the transmitted virus population is unknown. Using uniquely tagged viruses recovered from cDNA we investigated the replication, competition and morbidity of DWV genotypes in drones. Assays examining virus replication and morbidity revealed drones are highly susceptible to both predominant genotypes of DWV. In virus passage studies using an equimolar inocula of major DNA genotypes and their recombinants, the recombinant form dominated but did not reach 100% of the virus population within 10 passages. Using an in-silico model of the virus–mite–bee system we examined bottlenecks during virus acquisition by the mite and subsequent injection of viruses into the host, which may play a significant role in shaping virus diversity. This study furthers our understanding of the variables influencing DWV diversity changes and provides insight into areas of future research in the mite–virus–bee system.Publisher PDFPeer reviewe

Comparing non-invasive surveying techniques for elusive, nocturnal mammals: a case study of the West European hedgehog (Erinaceus europaeus)

Monitoring changes in populations is fundamental for effective management. The West European hedgehog (Erinaceus europeaus) is of conservation concern in the UK because of recent substantial declines. Surveying hedgehogs is, however, problematic because of their nocturnal, cryptic behaviour. We compared the effectiveness of three methods (infra-red thermal camera, specialist search dog, spotlight) for detecting hedgehogs in three different habitats. Significantly more hedgehogs were detected, and at greater distance, using the camera and dog than the spotlight in amenity grassland and pasture; no hedgehogs were detected in woodland. Increasing ground cover reduced detection distances, with most detections (59.6%) associated with bare soil or mown grass; the dog was the only method that detected hedgehogs in vegetation taller than the target species’ height. The additional value of surveying with a detection dog is most likely to be realised in areas where badgers (Meles meles), an intra-guild predator, are and/or where sufficient ground cover is present; both would allow hedgehogs to forage further from refuge habitats such as hedgerows. Further consideration of the effectiveness of detection dogs for finding hedgehogs in nests, as well as developing techniques for monitoring this species in woodland, is warranted

Mechanisms matter: predicting the ecological impacts of global change

The ability of mechanistic models to reliably extrapolate to novel conditions could position them as the gold standard in understanding the impacts of global change, but exactly how mechanistic models can be used most effectively remains to be determined. In this issue, Desforges et al. present a mechanistic physiological model to understand the drivers of muskox population dynamics. We took this as an opportunity to discuss the potential for, and challenges of, using mechanistic models to predict ecological responses to environmental change

Managing hostile subsoils in the high rainfall zone of south-western Australia

This report is designed to complement existing information on the management of crops in the High Rainfall Zone of south-western Australia and to identify limitations for crop production arising from the soil properties in this area

Data on the movement behaviour of four species of grassland butterfly

This Data in Brief article describes data on the movement behaviour of four species of grassland butterflies collected over three years and at four sites in southern England. The datasets consist of the movement tracks of and recorded using standard methods and presented as steps distances and turning angles. Sites consisted of nectar-rich field margins, meadows, and mown short turf grasslands with minimal flowers. In total, 783 unique movement tracks were collected. The data were used for analysing the movement behaviour of the species and for parameterising individual-based movement models

Integrating the influence of weather into mechanistic models of butterfly movement

Understanding the factors influencing movement is essential to forecasting species persistence in a changing environment. Movement is often studied using mechanistic models, extrapolating short-term observations of individuals to longer-term predictions, but the role of weather variables such as air temperature and solar radiation, key determinants of ectotherm activity, are generally neglected. We aim to show how the effects of weather can be incorporated into individual-based models of butterfly movement thus allowing analysis of their effects. Methods: We constructed a mechanistic movement model and calibrated it with high precision movement data on a widely studied species of butterfly, the meadow brown (Maniola jurtina), collected over a 21-week period at four sites in southern England. Day time temperatures during the study ranged from 14.5 to 31.5⁰C and solar radiation from heavy cloud to bright sunshine. The effects of weather are integrated into the individual-based model through weather-dependent scaling of parametric distributions representing key behaviours: the durations of flight and periods of inactivity. Results: Flight speed was unaffected by weather, time between successive flights increased as solar radiation decreased, and flight duration showed a unimodal response to air temperature that peaked between approximately 23⁰C and 26⁰C. After validation, the model demonstrated that weather alone can produce a more than two-fold difference in predicted weekly displacement. Conclusions: Individual Based models provide a useful framework for integrating the effect of weather into movement models. By including weather effects we are able to explain a two-fold difference in movement rate of M. jurtina consistent with inter-annual variation in dispersal measured in population studies. Climate change for the studied populations is expected to decrease activity and dispersal rates since these butterflies already operate close to their thermal optimum

Phenological responses in a sycamore‐aphid‐parasitoid system and consequences for aphid population dynamics: a 20‐year case study

Species interactions have a spatio‐temporal component driven by environmental cues, which if altered by climate change can drive shifts in community dynamics. There is insufficient understanding of the precise time‐windows during which inter‐annual variation in weather drives phenological shifts and the consequences for mismatches between interacting species and resultant population dynamics – particularly for insects. We use a 20‐year study on a tri‐trophic system: sycamore Acer pseudoplatanus, two associated aphid species Drepanosiphum platanoidis and Periphyllus testudinaceus, and their hymenopteran parasitoids. Using a sliding window approach, we assess climatic drivers of phenology in all three trophic levels. We quantify the magnitude of resultant trophic mismatches between aphids and their plant hosts and parasitoids, and then model the impacts of these mismatches, direct weather effects and density dependence on local‐scale aphid population dynamics. Warmer temperatures in mid‐March to late‐April were associated with advanced sycamore budburst, parasitoid attack and (marginally) D. platanoidis emergence. The precise time‐window during which spring weather advances phenology varies considerably across each species. Crucially, warmer temperatures in late winter delayed the emergence of both aphid species. Seasonal variation in warming rates thus generate marked shifts in the relative timing of spring events across trophic levels and mismatches in the phenology of interacting species. Despite this, we found no evidence that aphid population growth rates were adversely impacted by the magnitude of mismatch with their host plants or parasitoids, or direct impacts of temperature and precipitation. Strong density dependence effects occurred in both aphid species and probably buffered populations, through density dependent compensation, from adverse impacts of the marked inter‐annual climatic variation that occurred during the study period. These findings explain the resilience of aphid populations to climate change and uncover a key mechanism, warmer winter temperatures delaying insect phenology, by which climate change drives asynchronous shifts between interacting species

The Mid-infrared Evolution of the FU Orionis Disk

We present new SOFIA-FORCAST observations obtained in 2016 February of the archetypal outbursting low-mass young stellar object FU Orionis, and we compare the continuum, solid-state, and gas properties with mid-infrared data obtained at the same wavelengths in 2004 with Spitzer-IRS. In this study, we conduct the first mid-infrared spectroscopic comparison of an FUor over a long time period. Over a 12-year period, UBVR monitoring indicates that FU Orionis has continued its steady decrease in overall brightness by ~14%. We find that this decrease in luminosity occurs only at wavelengths ≾20 μm. In particular, the continuum shortward of the silicate emission complex at 10 μm exhibits a ~12% (~3σ) drop in flux density but no apparent change in slope; both the Spitzer and SOFIA spectra are consistent with a 7200 K blackbody. Additionally, the detection of water absorption is consistent with the Spitzer spectrum. The silicate emission feature at 10 μm continues to be consistent with unprocessed grains, unchanged over 12 years. We conclude that either the accretion rate in FU Orionis has decreased by ~12–14% over this time baseline or the inner disk has cooled, but the accretion disk remains in a superheated state outside the innermost region