School of BioSciences - Research Publications

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    Modelling temperature-driven changes in species associations across freshwater communities
    Perrin, SW ; van der Veen, B ; Golding, N ; Finstad, AG (WILEY, 2021-10-20)
    Due to global climate change-induced shifts in species distributions, estimating changes in community composition through the use of Species Distribution Models has become a key management tool. Being able to determine how species associations change along environmental gradients is likely to be pivotal in exploring the magnitude of future changes in species' distributions. This is particularly important in connectivity-limited ecosystems, such as freshwater ecosystems, where increased human translocation is creating species associations over previously unseen environmental gradients. Here, we use a large-scale presence-absence dataset of freshwater fish from lakes across the Fennoscandian region in a Joint Species Distribution Model, to measure the effect of temperature on species associations. We identified a trend of negative associations between species tolerant of cold waters and those tolerant of warmer waters, as well as positive associations between several more warm-tolerant species, with these associations often shifting depending on local temperatures. Our results confirm that freshwater ecosystems can expect to see a large-scale shift towards communities dominated by more warm-tolerant species. While there remains much work to be done to predict exactly where and when local extinctions may take place, the model implemented provides a starting-point for the exploration of climate-driven community trends. This approach is especially informative in regards to determining which species associations are most central in shaping future community composition, and which areas are most vulnerable to local extinctions.
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    Establishment of Wolbachia Strain wAlbB in Malaysian Populations of Aedes aegypti for Dengue Control
    Nazni, WA ; Hoffmann, AA ; NoorAfizah, A ; Cheong, YL ; Mancini, MV ; Golding, N ; Kamarul, GMR ; Arif, MAK ; Thohir, H ; NurSyamimi, H ; ZatilAqmar, MZ ; NurRuqqayah, M ; NorSyazwani, A ; Faiz, A ; Irfan, F-RMN ; Rubaaini, S ; Nuradila, N ; Nizam, NMN ; Irwan, SM ; Endersby-Harshman, NM ; White, VL ; Ant, TH ; Herd, CS ; Hasnor, AH ; AbuBakar, R ; Hapsah, DM ; Khadijah, K ; Kamilan, D ; Lee, SC ; Paid, YM ; Fadzilah, K ; Topek, O ; Gill, BS ; Lee, HL ; Sinkins, SP (CELL PRESS, 2019-12-16)
    Dengue has enormous health impacts globally. A novel approach to decrease dengue incidence involves the introduction of Wolbachia endosymbionts that block dengue virus transmission into populations of the primary vector mosquito, Aedes aegypti. The wMel Wolbachia strain has previously been trialed in open releases of Ae. aegypti; however, the wAlbB strain has been shown to maintain higher density than wMel at high larval rearing temperatures. Releases of Ae. aegypti mosquitoes carrying wAlbB were carried out in 6 diverse sites in greater Kuala Lumpur, Malaysia, with high endemic dengue transmission. The strain was successfully established and maintained at very high population frequency at some sites or persisted with additional releases following fluctuations at other sites. Based on passive case monitoring, reduced human dengue incidence was observed in the release sites when compared to control sites. The wAlbB strain of Wolbachia provides a promising option as a tool for dengue control, particularly in very hot climates.
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    Data Integration for Large-Scale Models of Species Distributions
    Isaac, NJB ; Jarzyna, MA ; Keil, P ; Dambly, LI ; Boersch-Supan, PH ; Browning, E ; Freeman, SN ; Golding, N ; Guillera-Arroita, G ; Henrys, PA ; Jarvis, S ; Lahoz-Monfort, J ; Pagel, J ; Pescott, OL ; Schmucki, R ; Simmonds, EG ; O'Hara, RB (ELSEVIER SCIENCE LONDON, 2020-01-01)
    With the expansion in the quantity and types of biodiversity data being collected, there is a need to find ways to combine these different sources to provide cohesive summaries of species' potential and realized distributions in space and time. Recently, model-based data integration has emerged as a means to achieve this by combining datasets in ways that retain the strengths of each. We describe a flexible approach to data integration using point process models, which provide a convenient way to translate across ecological currencies. We highlight recent examples of large-scale ecological models based on data integration and outline the conceptual and technical challenges and opportunities that arise.
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    steps: Software for spatially and temporally explicit population simulations
    Visintin, C ; Briscoe, NJ ; Woolley, SNC ; Lentini, PE ; Tingley, R ; Wintle, BA ; Golding, N ; Graham, L (WILEY, 2020-02-25)
    Species population dynamics are driven by spatial and temporal changes in the environment, anthropogenic activities and conservation management actions. Understanding how populations will change in response to these drivers is fundamental to a wide range of ecological applications, but there are few open-source software options accessible to researchers and managers that allow them to predict these changes in a flexible and transparent way. We introduce an open-source, multi-platform r package, steps, that models spatial changes in species populations as a function of drivers of distribution and abundance, such as climate, disturbance, landscape dynamics and species ecological and physiological requirements. To illustrate the functionality of steps, we model the population dynamics of the greater glider Petauroides volans, an arboreal Australian mammal. We demonstrate how steps can be used to simulate population responses of the glider to forest dynamics and management with the types of data commonly used in ecological analyses. steps expands on the features found in existing software packages, can easily incorporate a range of spatial layers (e.g. habitat suitability, vegetation dynamics and disturbances), facilitates integrated and transparent analyses within a single platform and produces interpretable outputs of changes in species' populations through space and time. Further, steps offers both ready-to-use, built-in functionality, as well as the ability for advanced users to define their own modules for custom analyses. Thus, we anticipate that steps will be of significant value to environment and wildlife managers and researchers from a broad range of disciplines.
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    Reconstructing the early global dynamics of under-ascertained COVID-19 cases and infections
    Russell, T ; Russell, T ; Golding, N ; Hellewell, J ; Abbott, S ; Wright, L ; Pearson, C ; Pearson, C ; Zandvoort, KV ; Jarvis, C ; Gibbs, H ; Liu, Y ; Eggo, R ; Edmunds, J ; Kucharski, A ( 2020-07-08)

    Background

    Asymptomatic or subclinical SARS-CoV-2 infections are often unreported, which means that confirmed case counts may not accurately reflect underlying epidemic dynamics. Understanding the level of ascertainment (the ratio of confirmed symptomatic cases to the true number of symptomatic individuals) and undetected epidemic progression is crucial to informing COVID-19 response planning, including the introduction and relaxation of control measures. Estimating case ascertainment over time allows for accurate estimates of specific outcomes such as seroprevalence, which is essential for planning control measures.

    Methods

    Using reported data on COVID-19 cases and fatalities globally, we estimated the proportion of symptomatic cases (i.e. any person with any of fever >= 37.5°C, cough, shortness of breath, sudden onset of anosmia, ageusia or dysgeusia illness) that were reported in 210 countries and territories, given those countries had experienced more than ten deaths. We used published estimates of the baseline case fatality ratio (CFR), which was adjusted for delays and under-ascertainment, then calculated the ratio of this baseline CFR to an estimated local delay-adjusted CFR to estimate the level of under-ascertainment in a particular location. We then fit a Bayesian Gaussian process model to estimate the temporal pattern of under-ascertainment.

    Results

    Based on reported cases and deaths, we estimated that, during March 2020, the median percentage of symptomatic cases detected across the 84 countries which experienced more than ten deaths ranged from 2.4% (Bangladesh) to 100% (Chile). Across the ten countries with the highest number of total confirmed cases as of 6th July 2020, we estimated that the peak number of symptomatic cases ranged from 1.4 times (Chile) to 18 times (France) larger than reported. Comparing our model with national and regional seroprevalence data where available, we find that our estimates are consistent with observed values. Finally, we estimated seroprevalence for each country. As of the 7th June, our seroprevalence estimates range from 0% (many countries) to 13% (95% CrI: 5.6% – 24%) (Belgium).

    Conclusions

    We found substantial under-ascertainment of symptomatic cases, particularly at the peak of the first wave of the SARS-CoV-2 pandemic, in many countries. Reported case counts will therefore likely underestimate the rate of outbreak growth initially and underestimate the decline in the later stages of an epidemic. Although there was considerable under-reporting in many locations, our estimates were consistent with emerging serological data, suggesting that the proportion of each country’s population infected with SARS-CoV-2 worldwide is generally low.

    Funding

    Wellcome Trust, Bill & Melinda Gates Foundation, DFID, NIHR, GCRF, ARC.
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    Factors influencing the residency of bettongs using one-way gates to exit a fenced reserve
    Moyses, J ; Hradsky, B ; Tuft, K ; Moseby, K ; Golding, N ; Wintle, B (Wiley, 2020-11)
    Understanding the conditions under which small native Australian mammals can persist in the presence of introduced predators remains a key challenge to conservation ecologists. Bettong‐specific one‐way gates were used at a predator‐free reserve in South Australia to allow the burrowing bettong (Bettongia lesueur) – a small potoroid, listed as ‘vulnerable’ nationally – to disperse out of the reserve. We conducted a field experiment to explore the conditions affecting residence time of bettongs that left the reserve. We monitored bettong and mammalian predator activity outside the fence using track surveys across 18 sites over two seasons. We examined the effect of supplementary feeding as a strategy for increasing residence time, as well as the influence of predator presence and habitat quality, using linear mixed models. Bettong activity was positively associated with supplementary feeding, midstorey vegetation cover and shelter availability. After gates were closed, bettong activity near gates declined to almost zero the following weeks, likely either due to death from predation or due to movement away from the sites. To a small extent, mammalian predators were more likely to be present at sites with high bettong activity. Further research on conditions to support persistence of burrowing bettongs and other small mammals, including understanding minimum necessary predator control effort, is required before successful establishment of populations outside of fences can occur.
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    Assessing biophysical and socio-economic impacts of climate change on regional avian biodiversity
    Kapitza, S ; Van Ha, P ; Kompas, T ; Golding, N ; Cadenhead, NCR ; Bal, P ; Wintle, BA (NATURE PORTFOLIO, 2021-02-08)
    Climate change threatens biodiversity directly by influencing biophysical variables that drive species' geographic distributions and indirectly through socio-economic changes that influence land use patterns, driven by global consumption, production and climate. To date, no detailed analyses have been produced that assess the relative importance of, or interaction between, these direct and indirect climate change impacts on biodiversity at large scales. Here, we apply a new integrated modelling framework to quantify the relative influence of biophysical and socio-economically mediated impacts on avian species in Vietnam and Australia and we find that socio-economically mediated impacts on suitable ranges are largely outweighed by biophysical impacts. However, by translating economic futures and shocks into spatially explicit predictions of biodiversity change, we now have the power to analyse in a consistent way outcomes for nature and people of any change to policy, regulation, trading conditions or consumption trend at any scale from sub-national to global.
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    Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus (vol 4, pg 854, 2019)
    Kraemer, MUG ; Reiner, RC ; Brady, OJ ; Messina, JP ; Gilbert, M ; Pigott, DM ; Yi, D ; Johnson, K ; Earl, L ; Marczak, LB ; Shirude, S ; Weaver, ND ; Bisanzio, D ; Perkins, TA ; Lai, S ; Lu, X ; Jones, P ; Coelho, GE ; Carvalho, RG ; Van Bortel, W ; Marsboom, C ; Hendrickx, G ; Schaffner, F ; Moore, CG ; Nax, HH ; Bengtsson, L ; Wetter, E ; Tatem, AJ ; Brownstein, JS ; Smith, DL ; Lambrechts, L ; Cauchemez, S ; Linard, C ; Faria, NR ; Pybus, OG ; Scott, TW ; Liu, Q ; Yu, H ; Wint, GRW ; Hay, SI ; Golding, N (NATURE PUBLISHING GROUP, 2019-05-01)
    This Article was mistakenly not made Open Access when originally published; this has now been amended, and information about the Creative Commons Attribution 4.0 International License has been added into the 'Additional information' section.
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    Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus (vol 4, pg 854, 2019)
    Kraemer, MUG ; Reiner, RC ; Brady, OJ ; Messina, JP ; Gilbert, M ; Pigott, DM ; Yi, D ; Johnson, K ; Earl, L ; Marczak, LB ; Shirude, S ; Weaver, ND ; Bisanzio, D ; Perkins, TA ; Lai, S ; Lu, X ; Jones, P ; Coelho, GE ; Carvalho, RG ; Van Bortel, W ; Marsboom, C ; Hendrickx, G ; Schaffner, F ; Moore, CG ; Nax, HH ; Bengtsson, L ; Wetter, E ; Tatem, AJ ; Brownstein, JS ; Smith, DL ; Lambrechts, L ; Cauchemez, S ; Linard, C ; Faria, NR ; Pybus, OG ; Scott, TW ; Liu, Q ; Yu, H ; Wint, GRW ; Hay, SI ; Golding, N (NATURE PUBLISHING GROUP, 2019-05-01)
    In the version of this Article originally published, the affiliation for author Catherine Linard was incorrectly stated as '6Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK'. The correct affiliation is '9Spatial Epidemiology Lab (SpELL), Universite Libre de Bruxelles, Brussels, Belgium'. The affiliation for author Hongjie Yu was also incorrectly stated as '11Department of Statistics, Harvard University, Cambridge, MA, USA'. The correct affiliation is '15School of Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China'. This has now been amended in all versions of the Article.
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    Measurement of the Infection and Dissemination of Bluetongue Virus in Culicoides Biting Midges Using a Semi-Quantitative RT-PCR Assay and Isolation of Infectious Virus
    Veronesi, E ; Antony, F ; Gubbins, S ; Golding, N ; Blackwell, A ; Mertens, PPC ; Brownlie, J ; Darpel, KE ; Mellor, PS ; Carpenter, S ; Brown, JD (PUBLIC LIBRARY SCIENCE, 2013-08-05)
    BACKGROUND: Culicoides biting midges (Diptera: Ceratopogonidae) are the biological vectors of globally significant arboviruses of livestock including bluetongue virus (BTV), African horse sickness virus (AHSV) and the recently emerging Schmallenberg virus (SBV). From 2006-2009 outbreaks of BTV in northern Europe inflicted major disruption and economic losses to farmers and several attempts were made to implicate Palaearctic Culicoides species as vectors. Results from these studies were difficult to interpret as they used semi-quantitative RT-PCR (sqPCR) assays as the major diagnostic tool, a technique that had not been validated for use in this role. In this study we validate the use of these assays by carrying out time-series detection of BTV RNA in two colony species of Culicoides and compare the results with the more traditional isolation of infectious BTV on cell culture. METHODOLOGY/PRINCIPAL FINDINGS: A BTV serotype 1 strain mixed with horse blood was fed to several hundred individuals of Culicoides sonorensis (Wirth & Jones) and C. nubeculosus (Mg.) using a membrane-based assay and replete individuals were then incubated at 25°C. At daily intervals 25 Culicoides of each species were removed from incubation, homogenised and BTV quantified in each individual using sqPCR (Cq values) and virus isolation on a KC-C. sonorensis embryonic cell line, followed by antigen enzyme-linked immunosorbent assay (ELISA). In addition, comparisons were also drawn between the results obtained with whole C. sonorensis and with individually dissected individuals to determine the level of BTV dissemination. CONCLUSIONS/SIGNIFICANCE: Cq values generated from time-series infection experiments in both C. sonorensis and C. nubeculosus confirmed previous studies that relied upon the isolation and detection of infectious BTV. Implications on the testing of field-collected Culicoides as potential virus vectors by PCR assays and the use of such assays as front-line tools for use in diagnostic laboratories in this role are discussed.