ORCID Profile
0000-0002-0679-6666
Current Organisation
Lancaster University
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Publisher: Elsevier BV
Date: 03-2020
DOI: 10.1016/J.SCITOTENV.2019.135906
Abstract: Transformative advances in metagenomics are providing an unprecedented ability to characterize the enormous ersity of microorganisms and invertebrates sustaining soil health and water quality. These advances are enabling a better recognition of the ecological linkages between soil and water, and the bio ersity exchanges between these two reservoirs. They are also providing new perspectives for understanding microorganisms and invertebrates as part of interacting communities (i.e. microbiomes and zoobiomes), and considering plants, animals, and humans as holobionts comprised of their own cells as well as erse microorganisms and invertebrates often acquired from soil and water. The Government of Canada's Genomics Research and Development Initiative (GRDI) launched the Ecobiomics Project to coordinate metagenomics capacity building across federal departments, and to apply metagenomics to better characterize microbial and invertebrate bio ersity for advancing environmental assessment, monitoring, and remediation activities. The Project has adopted standard methods for soil, water, and invertebrate s ling, collection and provenance of metadata, and nucleic acid extraction. High-throughput sequencing is located at a centralized sequencing facility. A centralized Bioinformatics Platform was established to enable a novel government-wide approach to harmonize metagenomics data collection, storage and bioinformatics analyses. Sixteen research projects were initiated under Soil Microbiome, Aquatic Microbiome, and Invertebrate Zoobiome Themes. Genomic observatories were established at long-term environmental monitoring sites for providing more comprehensive bio ersity reference points to assess environmental change.
Publisher: Frontiers Media SA
Date: 25-11-2019
Publisher: Wiley
Date: 14-02-2019
DOI: 10.1111/GEB.12898
Publisher: Wiley
Date: 24-05-2017
DOI: 10.1111/DDI.12570
Publisher: Wiley
Date: 19-03-2014
DOI: 10.1111/DDI.12196
Publisher: Wiley
Date: 13-10-2018
DOI: 10.1111/GEB.12637
Publisher: Wiley
Date: 10-03-2023
DOI: 10.1111/GEB.13648
Abstract: Aquatic insects comprise 64% of freshwater animal ersity and are widely used as bioindicators to assess water quality impairment and freshwater ecosystem health, as well as to test ecological hypotheses. Despite their importance, a comprehensive, global database of aquatic insect occurrences for mapping freshwater bio ersity in macroecological studies and applied freshwater research is missing. We aim to fill this gap and present the Global EPTO Database , which includes worldwide geo‐referenced aquatic insect occurrence records for four major taxa groups: Ephemeroptera, Plecoptera, Trichoptera and Odonata (EPTO). A total of 8,368,467 occurrence records globally, of which 8,319,689 (99%) are publicly available. The records are attributed to the corresponding drainage basin and sub‐catchment based on the Hydrography90m dataset and are accompanied by the elevation value, the freshwater ecoregion and the protection status of their location. The database covers the global extent, with 86% of the observation records having coordinates with at least four decimal digits (11.1 m precision at the equator) in the World Geodetic System 1984 (WGS84) coordinate reference system. S ling years span from 1951 to 2021. Ninety‐nine percent of the records have information on the year of the observation, 95% on the year and month, while 94% have a complete date. In the case of seven sub‐datasets, exact dates can be retrieved upon communication with the data contributors. Ephemeroptera, Plecoptera, Trichoptera and Odonata, standardized at the genus taxonomic level. We provide species names for 7,727,980 (93%) records without further taxonomic verification. The entire tab‐separated value (.csv) database can be downloaded and visualized at roject/epto_database/ . Fifty in idual datasets are also available at fred.igb‐berlin.de , while six datasets have restricted access. For the latter, we share metadata and the contact details of the authors.
Publisher: Elsevier BV
Date: 09-2017
Publisher: Proceedings of the National Academy of Sciences
Date: 26-03-2020
Abstract: The complexity and natural variability of ecosystems present a challenge for reliable detection of change due to anthropogenic influences. This issue is exacerbated by necessary trade-offs that reduce the quality and resolution of survey data for assessments at large scales. The Peace–Athabasca Delta (PAD) is a large inland wetland complex in northern Alberta, Canada. Despite its geographic isolation, the PAD is threatened by encroachment of oil sands mining in the Athabasca watershed and hydroelectric dams in the Peace watershed. Methods capable of reliably detecting changes in ecosystem health are needed to evaluate and manage risks. Between 2011 and 2016, aquatic macroinvertebrates were s led across a gradient of wetland flood frequency, applying both microscope-based morphological identification and DNA metabarcoding. By using multispecies occupancy models, we demonstrate that DNA metabarcoding detected a much broader range of taxa and more taxa per s le compared to traditional morphological identification and was essential to identifying significant responses to flood and thermal regimes. We show that family-level occupancy masks high variation among genera and quantify the bias of barcoding primers on the probability of detection in a natural community. Interestingly, patterns of community assembly were nearly random, suggesting a strong role of stochasticity in the dynamics of the metacommunity. This variability seriously compromises effective monitoring at local scales but also reflects resilience to hydrological and thermal variability. Nevertheless, simulations showed the greater efficiency of metabarcoding, particularly at a finer taxonomic resolution, provided the statistical power needed to detect change at the landscape scale.
Publisher: Wiley
Date: 24-06-2014
Publisher: Wiley
Date: 03-06-2019
DOI: 10.1111/DDI.12935
Publisher: Wiley
Date: 09-04-2023
Abstract: The delivery of consistent and accurate fine‐resolution data on bio ersity using metabarcoding promises to improve environmental assessment and research. Whilst this approach is a substantial improvement upon traditional techniques, critics note that metabarcoding data are suitable for establishing taxon occurrence, but not abundance. We propose a novel hierarchical approach to recovering abundance information from metabarcoding, and demonstrate this technique using benthic macroinvertebrates. To s le a range of abundance structures without introducing additional changes in composition, we combined seasonal surveys with fish‐exclusion experiments at Catamaran Brook in northern New Brunswick, Canada. Five monthly surveys collected 31 benthic s les for DNA metabarcoding ided between caged and control treatments. A further six s les per survey were processed using traditional morphological identification for comparison. By estimating the probability of detecting a single in idual, multispecies abundance models infer changes in abundance based on changes in detection frequency. Using replicate detections of 184 genera (and 318 species) from metabarcoding s les, our analysis identified changes in abundance arising from both seasonal dynamics and the exclusion of fish predators. Counts obtained from morphological s les were highly variable, a feature that limited the opportunity for more robust comparison, and emphasizing the difficulty standard methods also face to detect changes in abundance. Our approach is the first to demonstrate how quantitative estimates of abundance can be made using metabarcoding, both among species within sites as well as within species among sites. Many s les are required to capture true abundance patterns, particularly in streams where counts are highly variable, but few studies can afford to process entire s les. Our approach allows study of responses across whole communities, and at fine taxonomic resolution. We discuss how ecological studies can use additional s ling to capture changes in abundance at fine resolution, and how this can complement broad‐scale biomonitoring using DNA metabarcoding.
Publisher: Wiley
Date: 30-03-2016
DOI: 10.1002/ECE3.2104
Publisher: Cold Spring Harbor Laboratory
Date: 18-03-2019
DOI: 10.1101/578591
Abstract: An ongoing challenge for ecological studies has been the collection of data with high precision and accuracy at a sufficient scale to detect effects relevant to management of critical global change processes. A major hurdle for many workflows has been the time-consuming and challenging process of sorting and identification of organisms, but the rapid development of DNA metabarcoding as a bio ersity observation tool provides a potential solution. As high-throughput sequencing becomes more rapid and cost-effective, a ‘big data’ revolution is anticipated, based on higher and more accurate taxonomic resolution, more efficient detection, and greater s le processing capacity. These advances have the potential to lify the power of ecological studies to detect change and diagnose its cause, through a methodology termed ‘Biomonitoring 2.0’. Despite its promise, the unfamiliar terminology and pace of development in high-throughput sequencing technologies has contributed to a growing concern that an unproven technology is supplanting tried and tested approaches, lowering trust among potential users, and reducing uptake by ecologists and environmental management practitioners. While it is reasonable to exercise caution, we argue that any criticism of new methods must also acknowledge the shortcomings and lower capacity of current observation methods. Broader understanding of the statistical properties of metabarcoding data will help ecologists to design, test and review evidence for new hypotheses. We highlight the uncertainties and challenges underlying DNA metabarcoding and traditional methods for compositional analysis, focusing on issues of taxonomic resolution, s le similarity, taxon misidentification, s le contamination, and taxon abundance. Using the ex le of freshwater benthic ecosystems, one of the most widely-applied non-microbial applications of DNA metabarcoding to date, we explore the ability of this new technology to improve the quality and utility of ecological data, recognising that the issues raised have widespread applicability across all ecosystem types.
Publisher: Wiley
Date: 20-03-2019
DOI: 10.1111/ECOG.03994
Publisher: Cold Spring Harbor Laboratory
Date: 14-02-2023
DOI: 10.1101/2023.02.13.528257
Abstract: Despite decades of global commitments, and increasingly urgent warning of environmental instability, the demand for land to support economic production is still increasing. Isolated and disorganized actions will not be enough to avert ecosystem failures. As many developers are already required to compensate for their ecological impacts through restoration, many see markets trading bio ersity credits as a financial mechanism to counteract degradation and drive investment in conservation. The challenge stems from a desire to recognize the multidimensional nature of bio ersity that contributes to ecosystem integrity without making suitable offsets intractable to supply. Instead, most regulators have opted to streamline ecological assessment, and undermine ecological rigour, in favour of promoting offset supply and economic efficiency. As a result, all evidence suggests offset trading programs have so far failed to mitigate losses, let alone support “nature positive” outcomes. To overcome this disconnect, and support more effective and equitable bio ersity markets, we propose credits be defined by the irreplaceability of a site, a metric long-established in the domain of systematic conservation planning. Irreplaceability avoids the limitations of like-for-like trading, reduces costs of offsetting to developers and society, ensures farmers willing to sell are fairly rewarded for loss of earnings, and that sites critical to achieving conservation goals are safeguarded. We developed an ecological-economic model of a bio ersity offset market to demonstrate irreplaceability guarantees no net loss of bio ersity and is the most efficient metric for guiding investment toward the recovery of Nature.
Publisher: Elsevier BV
Date: 09-2019
DOI: 10.1016/J.SCITOTENV.2019.02.455
Abstract: A workshop was held in Wageningen, The Netherlands, in September 2017 to collate data and literature on three aquatic ecosystem types (agricultural drainage ditches, urban floodplains, and urban estuaries), and develop a general framework for the assessment of multiple stressors on the structure and functioning of these systems. An assessment framework considering multiple stressors is crucial for our understanding of ecosystem responses within a multiply stressed environment, and to inform appropriate environmental management strategies. The framework consists of two components: (i) problem identification and (ii) impact assessment. Both assessments together proceed through the following steps: 1) ecosystem selection 2) identification of stressors and quantification of their intensity 3) identification of receptors or sensitive groups for each stressor 4) identification of stressor-response relationships and their potential interactions 5) construction of an ecological model that includes relevant functional groups and endpoints 6) prediction of impacts of multiple stressors, 7) confirmation of these predictions with experimental and monitoring data, and 8) potential adjustment of the ecological model. Steps 7 and 8 allow the assessment to be adaptive and can be repeated until a satisfactory match between model predictions and experimental and monitoring data has been obtained. This paper is the preface of the MAEGA (Making Aquatic Ecosystems Great Again) special section that includes three associated papers which are also published in this volume, which present applications of the framework for each of the three aquatic systems.
Publisher: Wiley
Date: 05-12-2017
DOI: 10.1111/FWB.12874
Publisher: Elsevier BV
Date: 07-2023
Publisher: Springer Science and Business Media LLC
Date: 22-06-2017
Abstract: Understandably, given the fast pace of bio ersity loss, there is much interest in using Earth observation technology to track bio ersity, ecosystem functions and ecosystem services. However, because most bio ersity is invisible to Earth observation, indicators based on Earth observation could be misleading and reduce the effectiveness of nature conservation and even unintentionally decrease conservation effort. We describe an approach that combines automated recording devices, high-throughput DNA sequencing and modern ecological modelling to extract much more of the information available in Earth observation data. This approach is achievable now, offering efficient and near-real-time monitoring of management impacts on bio ersity and its functions and services.
Publisher: MDPI AG
Date: 28-02-2020
DOI: 10.3390/W12030651
Abstract: Reptiles are rarely included in urban freshwater bio ersity monitoring and conservation. We explored the global persistence of freshwater dependent turtles, lizards, crocodilians and snakes in cities with a population greater than 100,000 using species occurrence data in online databases from a five-year period (2013–2018). We then used ecological niche models to help identify the locations of suitable habitats for three freshwater reptile species in Sydney, Australia. Our Global analysis showed that sightings of a majority of known species of crocodilians and freshwater turtles were recorded in databases within this 5-year period in contrast to about one in three freshwater lizard species and one in ten freshwater snake species and that freshwater reptiles were observed within 50 km of the center of 40% of the 3525 cities. While global databases hold substantial recent species occurrence records for some regions, they contain very little data for large parts of the world. Modelling showed that potential suitable habitat for the three freshwater species in Sydney was distributed across areas with different levels of urban development. The persistence of populations of freshwater reptiles in and around a large proportion of the world’s cities show that this group can play an important role in urban bio ersity conservation.
Publisher: Wiley
Date: 23-12-2015
DOI: 10.1111/FWB.12515
Publisher: Elsevier BV
Date: 05-2016
Publisher: Wiley
Date: 25-09-2013
DOI: 10.1111/DDI.12007
Publisher: Frontiers Media SA
Date: 09-01-2020
Publisher: Elsevier BV
Date: 09-2019
DOI: 10.1016/J.SCITOTENV.2019.03.497
Abstract: In September 2017, a workshop was held at Wageningen University and Research to determine the current state of knowledge of multiple stressor effects on aquatic ecosystems and to assess how to improve prediction of these effects. We developed a theoretical framework that integrates species-level responses to stressors to predict how these effects propagate through higher levels of biological organisation. Here, we present the application of the framework for drainage ditch ecosystems in the Netherlands. We used food webs to assess single and multiple stressor effects of common stressors on ditch communities. We reviewed the literature for the effects of targeted stressors (nutrients, pesticides, dredging and mowing, salinization, and siltation) on each functional group present in the food web and qualitatively assessed the relative sensitivity of groups. Using this information, we created a stressor-response matrix of positive and negative direct effects of each stressor-functional group combination. Fungicides, salinization, and sedimentation were identified as particularly detrimental to most groups, although destructive management practices, such as dredging with almost complete community removal, would take precedence depending on frequency. Using the stressor-response matrix we built, first, a series of conceptual null models of single stressor effects on food web structure and, second, a series of additive null models to illustrate potential paired-stressor effects. We compared these additive null models with published studies of the same pairs of combined single stressors to explore more complex interactions. Our approach serves as a first-step to considering multiple stressor scenarios in systems that are understudied or data-poor and as a baseline from which more complex models that include indirect effects and quantitative data may be developed. We make specific suggestions for appropriate management strategies that could be taken to support the bio ersity of these systems for in idual stressors and their combined impacts.
Publisher: Wiley
Date: 22-11-2016
DOI: 10.1111/ELE.12696
Abstract: Based on the sensitivity of species to ongoing climate change, and numerous challenges they face tracking suitable conditions, there is growing interest in species' capacity to adapt to climatic stress. Here, we develop and apply a new generic modelling approach (AdaptR) that incorporates adaptive capacity through physiological limits, phenotypic plasticity, evolutionary adaptation and dispersal into a species distribution modelling framework. Using AdaptR to predict change in the distribution of 17 species of Australian fruit flies (Drosophilidae), we show that accounting for adaptive capacity reduces projected range losses by up to 33% by 2105. We identify where local adaptation is likely to occur and apply sensitivity analyses to identify the critical factors of interest when parameters are uncertain. Our study suggests some species could be less vulnerable than previously thought, and indicates that spatiotemporal adaptive models could help improve management interventions that support increased species' resilience to climate change.
Publisher: Public Library of Science (PLoS)
Date: 13-02-2014
Publisher: Wiley
Date: 15-06-2012
Publisher: Frontiers Media SA
Date: 08-11-2019
Publisher: The Royal Society
Date: 10-03-2008
Abstract: There are two major competing explanations for the counter-intuitive presence of bright coloration in certain orb-web spiders. Bright coloration could lure insect prey to the web vicinity, increasing the spider's foraging success. Alternatively, the markings could function as disruptive camouflage, making it difficult for the insect prey to distinguish spiders from background colour variation. We measured the prey capture rates of wasp spiders, Argiope bruennichi , that were blacked out, shielded from view using a leaf fragment, or left naturally coloured. Naturally coloured spiders caught over twice the number of prey as did either blacked-out or leaf-shielded spiders, and almost three times as many orthopteran prey. Spectrophotometer measurements suggest that the bright yellow bands on the spider's abdomen are visible to insect prey, but not the banding on the legs, which could disguise the spider's outline. Thus, our results provide strong support for the hypothesis that bright coloration in the wasp spider acts as a visual lure for insect prey and weak support for the hypothesis that the arrangement of the banding pattern across the spider's body disguises the presence of the spider on the web.
Publisher: Elsevier
Date: 2018
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Alex Bush.