Explore research activities in the Biodiversity Assessment and Tool Development theme related to terrestrial ecosystems. Names shown indicate authors or co-authors involved from the Centre of Conservation and Restoration Science.
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Taxonomic & Functional Biodiversity Assessment
To assess biodiversity, taxonomic diversity, the “fingerprint” (who you are), and functional diversity, “the footprint” (what you do), are measured. Understanding the significance of the presence of a species, population, community, and the consequence of their loss is fundamental for the science and application of conservation and restoration.
Projects
Optimisation of moorland bird surveys project
Easter Beltie Ecological Restoration Monitoring Research
Investigating the prevalence and diversity of bacterial endosymbionts in Scottish hoverfly populations
Online Plant Identification Training for Water of Leith Conservation Trust
Scotland-India Antimicrobial Resistance in the Environment Network (SIAMREN)
Nubian Ibex Genetics in Oman
Publications
Raccoons contraband: The metazoan parasite fauna of free-ranging raccoons in central Europe (2023), International Journal for Parasitology: Parasites and Wildlife; (Rueckert)
Pollinator-flower interactions in gardens during the covid 19 pandemic lockdown of 2020 (2022), Journal of Pollination Ecology; (Ballantyne)
The plant rhizosheath-root niche is an edaphic "mini-oasis"in hyperarid deserts with enhanced microbial competition (2022), ISME Communications; (Fusi)
Fluctuating Habitats: Ecological Relevance of Environmental Variability and Predictability on Species, Communities, and Ecosystems (2022), Frontiers in Ecology and Evolution; (Fusi)
Expert range maps of global mammal distributions harmonised to three taxonomic authorities (2022), Journal of Biogeography; (Gilchrist)
Bacterial communities in soils as indicators of the potential of syenite as an agromineral (2022), Pesquisa Agropecuária Brasileira; (Singleton)
Contrasting Effects of Local Environmental and Biogeographic Factors on the Composition and Structure of Bacterial Communities in Arid Monospecific Mangrove Soils (2022), Microbiology Spectrum; (Fusi)
Multi-scale habitat selection and spatial analysis reveals a mismatch between the wintering distribution of a threatened population of Taiga Bean Geese Anser fabalis and its protected area (2022), Bird Study; (Briers, White)
Editorial: New Approaches to Understanding Vector Borne Diseases in Domestic and Wild animals (2022), Frontiers in Veterinary Science; (Wheelhouse)
Aridity modulates belowground bacterial community dynamics in olive tree (2021), Environmental Microbiology; (Fusi)
Parasites, pathogens, and other symbionts of copepods (2021), Trends in Parasitology; (Rueckert)
Genetic diversity of the Nubian ibex in Oman as revealed by mitochondrial DNA (2021), Royal Society Open Science; (White)
Compartmentalization of bacterial and fungal microbiomes in the gut of adult honeybees (2021), npj Biofilms and Microbiomes; (Fusi)
Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans (2021), BMC Biology; (Rueckert)
Quantification of Ammonia Oxidizing Bacterial Abundances in Environmental Samples by Quantitative-PCR (2021), ; (Blaud)
Monitoring soil microbial communities using molecular tools: DNA extraction methods may offset long-term management effects (2021), European Journal of Soil Science; (Blaud)
Pollinator importance networks illustrate the crucial value of bees in a highly speciose plant community (2020), Scientific Reports; (Ballantyne)
Edaphic factors and plants influence denitrification in soils from a long-term arable experiment (2020), Scientific Reports; (Blaud)
Hydrolytic Profile of the Culturable Gut Bacterial Community Associated with Hermetia illucens (2020), Frontiers in Microbiology; (Fusi)
Affordable and robust phenotyping framework to analyse root system architecture of soil-grown plants (2020), Plant Journal; (Giuffrida)
Effects of urease and nitrification inhibitors on soil N, nitrifier abundance and activity in a sandy loam soil (2020), Biology and Fertility of Soils; (Blaud)
Developmental stages and gut microenvironments influence gut microbiota dynamics in the invasive beetle Popillia japonica Newman (Coleoptera: Scarabaeidae) (2019), Environmental Microbiology; (Fusi)
The pH optimum of soil exoenzymes adapt to long term changes in soil pH (2019), Soil Biology and Biochemistry; (Blaud)
Evolution: Parallel Paths to Parasitism in the Apicomplexa (2019), Current Biology; (Rueckert)
The symbiotic spectrum: where do the gregarines fit? (2019), Trends in Parasitology; (Rueckert)
The role of fungi in heterogeneous sediment microbial networks (2019), Scientific Reports; (Fusi)
Microbes associated with fresh produce: sources, types and methods to reduce spoilage and contamination (2019), ; (Singleton)
Consistent bacterial selection by date palm root system across heterogeneous desert oasis agroecosystems (2019), Scientific Reports; (Fusi)
Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes (2019), Journal of Eukaryotic Microbiology; (Rueckert)
Analysing the effect of dietary prebiotics and probiotics on gut bacterial richness and diversity of Asian snakehead fingerlings using T-RFLP method (2018), Aquaculture Research; (Blaud)
Consistent patterns of high alpha and low beta diversity in tropical parasitic and free-living protists (2018), Molecular Ecology; (Rueckert)
Spatial zoning of microbial functions and plant-soil nitrogen dynamics across a riparian area in an extensively grazed livestock system (2018), Soil Biology and Biochemistry; (Blaud)
Sources and contamination routes of microbial pathogens to fresh produce during field cultivation: A review (2018), Food Microbiology; (Singleton)
The stage of soil development modulates rhizosphere effect along a High Arctic desert chronosequence (2018), The ISME Journal; (Fusi)
Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality (2018), Microbiome; (Fusi)
The abundance of nitrogen cycle genes and potential greenhouse gas fluxes depends on land use type and little on soil aggregate size (2018), Applied Soil Ecology; (Blaud)
Animal Behaviour & Evolution
Animal Behaviour includes how animals move, interact with other organisms/species, and with their environment. Behaviour can be inherited as well as learned, and often increases an organism’s survival and reproduction. Behavioural adaptations can improve species’ resilience to changing environments.
Projects
Nubian Ibex Genetics in Oman
Publications
Mammalian predators and vegetated nesting habitat drive reduced protected area nesting success of Kentish plovers, Yellow Sea region, China (2023), Ecology and Evolution; (Pagani-Nunez)
The effect of urbanization and exposure to multiple environmental factors on life-history traits and breeding success of Barn Swallows (Hirundo rustica) across China (2022), Avian Research; (Pagani-Nunez)
A migratory divide spanning two continents is associated with genomic and ecological divergence (2022), Evolution; (Pagani-Nunez)
Avian predators taste reject mimetic prey in relation to their signal reliability (2022), Scientific Reports; (Pagani-Nunez)
Dynamic trait-niche relationships shape niche partitioning across habitat transformation gradients (2022), Basic and Applied Ecology; (Pagani-Nunez)
A comment on 'The adaptive value of gluttony: predators mediate the life history trade-offs of satiation threshold' by Pruitt & Krauel (2010) (2021), Journal of Evolutionary Biology; (Holman)
Sexual selection can partly explain low frequencies of Segregation Distorter alleles (2021), Proceedings of the Royal Society B: Biological Sciences; (Holman)
Breeding Great Tit Parus major Individuals have Moderately Consistent Foraging Niches Across Years (2021), Ardeola; (Pagani-Nunez)
Male-biased sexual selection, but not sexual dichromatism, predicts speciation in birds (2021), Evolution; (Holman)
The impact of urbanization on body size of Barn Swallows Hirundo rustica gutturalis (2021), Ecology and Evolution; (Pagani-Nunez)
Sexual selection affects the evolution of physiological and life history traits (2021), ; (Holman)
How to become a generalist species? Individual niche variation across habitat transformation gradients (2020), Frontiers in Ecology and Evolution; (Pagani-Nunez)
The truth is in the detail: predators attack aposematic prey with less aggression than other prey types (2020), Biological Journal of the Linnean Society; (Pagani-Nunez)
Differences in dietary specialization, habitat use and susceptibility to human disturbance influence feeding rates and resource partitioning between two migratory Numenius curlew species (2020), Estuarine, Coastal and Shelf Science; (Pagani-Nunez)
Sibling rivalry versus mother's curse: can kin competition facilitate a response to selection on male mitochondria? (2020), Proceedings of the Royal Society B: Biological Sciences; (Holman)
Social interactions in striped hyena inferred from camera trap data: is it more social than previously thought? (2020), Current Zoology; (Gilchrist)
Mother's curse and indirect genetic effects: Do males matter to mitochondrial genome evolution? (2020), Journal of Evolutionary Biology; (Holman)
Fitness consequences of the selfish supergene Segregation Distorter (2020), Journal of Evolutionary Biology; (Holman)
An X-linked meiotic drive allele has strong, recessive fitness costs in female Drosophila pseudoobscura (2019), Proceedings of the Royal Society B: Biological Sciences; (Holman)
Evolutionary simulations of Z-linked suppression gene drives (2019), Proceedings of the Royal Society B: Biological Sciences; (Holman)
Genetic, phenotypic and ecological differentiation suggests incipient speciation in two Charadrius plovers along the Chinese coast (2019), BMC Evolutionary Biology; (Pagani-Nunez)
Niches in the Anthropocene: passerine assemblages show niche expansion from natural to urban habitats (2019), Ecography; (Pagani-Nunez)
Comparative transcriptomics of social insect queen pheromones (2019), Nature Communications; (Holman)
A Comparison of Blood Biochemical Parameters as a Tool to Measure Welfare in Free-ranging Red Deer (Cervus elaphus elaphus) after Chemical and Physical Restraint (2019), Current Science; (Fusi)
Age and sex differences in niche use at molt and its effect on plumage coloration characteristics in a bird (2019), Current zoology; (Pagani-Nunez)
Visitor Perceptions of Captive, Endangered Barbary Macaques (Macaca sylvanus) Used as Photo Props in Jemaa El Fna Square, Marrakech, Morocco (2018), Anthrozoös; (Mackinnon)
Isotopic niche overlap between the invasive leiothrix and potential native competitors (2018), Animal Biodiversity and Conservation; (Pagani-Nunez)
Breath rate of passerines across an urbanization gradient supports the pace-of-life hypothesis and suggests diet mediated responses to handling stress (2018), Ecology and evolution; (Pagani-Nunez)
Evolution of female choice under intralocus sexual conflict and genotype-by-environment interactions (2018), Philosophical Transactions B: Biological Sciences; (Holman)
Onwards and upwards: a response to comments on Holman (2018), Behavioral Ecology; (Holman)
Queen pheromones and reproductive division of labor: a meta-analysis (2018), Behavioral Ecology; (Holman)
Incubation behaviour of a high-altitude species: the Fire-tailed Sunbird Aethopyga ignicauda (2018), Bird Study; (Pagani-Nunez)
Are vocal characteristics related to leadership patterns in mixed species bird flocks? (2018), Journal of Avian Biology; (Pagani-Nunez)
Building a new research framework for social evolution: intralocus caste antagonism (2018), Biological Reviews; (Holman)
The impact of a small-scale riverine obstacle on the upstream migration of Atlantic Salmon (2018), Hydrobiologia; (Dodd)
Citizen Science
Citizen science is an approach that enables public participation and collaboration in scientific research and improves data coverage and knowledge sharing.
Projects
Online Plant Identification Training for Water of Leith Conservation Trust
Publications
Citizen crowds and experts: observer variability in image-based plant phenotyping (2018), Plant Methods; (Giuffrida)
Passive Acoustic Monitoring
Monitoring ecosystems through recording and analysing their sounds is a non-destructive way to gather information about the environment and the species which are present. Many species, from songbirds to fish and crabs, make sound and often use it for communication and finding a good place to live. Acoustic monitoring facilitates information gathering over large spatial and time scales, helping to assess changes in the biological and physical environment.
Projects
Easter Beltie Ecological Restoration Monitoring Research
Publications
Remote Sensing
Remote sensing allows the collection of data form a distance, e.g. using drones or satellites. It is a powerful surveying tool, for example, to assess habitat change.
Projects
Publications
Assessment of the accuracy of counting large ungulate species (red deer Cervus elaphus) with UAV mounted thermal infrared cameras during night flights (2023), Wildlife Biology; (White)
The Graphene Field Effect Transistor Modeling Based on an Optimized Ambipolar Virtual Source Model for DNA Detection (2021), Applied Sciences; (La Spada)
Plant phenotyping on-demand: an integrative web-based framework using drones and participatory sensing in greenhouses (2021), ; (Giuffrida)
The diel activity pattern of mountain hare (Lepus timidus) on managed heather moorland in Scotland (2021), Ecology and Evolution; (Gilchrist)
Towards the Development of Rapid and Low-Cost Pathogen Detection Systems Using Microfluidic Technology and Optical Image Processing (2020), Applied Sciences; (Kerrouche)
Pheno-Deep Counter: a unified and versatile deep learning architecture for leaf counting (2018), The Plant Journal; (Giuffrida)
Citizen crowds and experts: observer variability in image-based plant phenotyping (2018), Plant Methods; (Giuffrida)
Smart Technologies
‘Smart’ in smart technologies stands for ‘Self-Monitoring Analysis and Reporting Technology’. For example, a smart robot is an artificial intelligence system that learns from its surrounding and ‘evolves’ through learning and knowledge. Smart robots can help monitor the environment and animal behaviour.
Projects
Subjective orientation in VR audio
Long-Term Monitoring for Environmental Conservation and Restoration Using Adaptable Robots: Identification and Collation of End User Needs
Towards Guided Self-Organisation in Artificial Complex Systems: A Swarm Robotics Case Study
Autonomous Robot Evolution: Cradle to Grave
Publications
A Quality-Diversity Approach to Evolving a Repertoire of Diverse Behaviour-Trees in Robot Swarms (2023), ; (Hart)
Assessment of the accuracy of counting large ungulate species (red deer Cervus elaphus) with UAV mounted thermal infrared cameras during night flights (2023), Wildlife Biology; (White)
Augmenting Novelty Search with a Surrogate Model to Engineer Meta-Diversity in Ensembles of Classifiers (2022), Applications of Evolutionary Computation: EvoApplications; (Hart)
Lifelong Learning Machines: Towards Developing Optimisation Systems That Continually Learn (2022), ; (Hart)
Artificial evolution of robot bodies and control: on the interaction between evolution, individual and cultural learning (2022), Philosophical Transactions of the Royal Society B: Biological Sciences; (Hart, Le Goff)
Morpho-evolution with learning using a controller archive as an inheritance mechanism (2022), IEEE Transactions on Cognitive and Developmental Systems; (Le Goff, Hart)
Towards Autonomous Robot Evolution (2021), ; (Hart)
Evolution of Diverse, Manufacturable Robot Body Plans (2020), ; (Hart, Le Goff)
Bootstrapping artificial evolution to design robots for autonomous fabrication (2020), Robotics; (Le Goff, Hart)
On Pros and Cons of Evolving Topologies with Novelty Search (2020), ; (Hart, Le Goff)
Sample and time efficient policy learning with CMA-ES and Bayesian Optimisation (2020), ; (Hart, Le Goff)
Comparing encodings for performance and phenotypic exploration in evolving modular robots (2019), ; (Hart)
The ARE Robot Fabricator: How to (Re)produce Robots that Can Evolve in the Real World (2019), ; (Hart)
Evolution of a Functionally Diverse Swarm via a Novel Decentralised Quality-Diversity Algorithm (2018), ; (Hart)
On the performance of the hybridisation between migrating birds optimisation variants and differential evolution for large scale continuous problems (2018), Expert Systems with Applications; (Hart)
Leveraging multiple datasets for deep leaf counting (2018), ; (Giuffrida)
Environmental Informatics
Environmental informatics is the field of research and system development focusing on the collection, processing, management and sharing of environmental data and information (using e.g., artificial intelligence, machine learning, big data, statistical codes etc).
Projects
Optimisation of moorland bird surveys project
Easter Beltie Ecological Restoration Monitoring Research
Improving AI-based Image Analysis for High-Throughput Plant Phenotyping
Statistical mechanism of particle breakage, fragmentation and shape evolution during shearing of granular materials
Publications
Semi-Supervised Domain Adaptation for Holistic Counting under Label Gap (2021), Journal of Imaging; (Giuffrida)
A Neural Approach to Generation of Constructive Heuristics (2021), ; (Hart)
On the challenges of jointly optimising robot morphology and control using a hierarchical optimisation scheme (2021), ; (Le Goff, Hart)
Using novelty search to explicitly create diversity in ensembles of classifiers (2021), ; (Hart)
Same data, different conclusions: Radical dispersion in empirical results when independent analysts operationalize and test the same hypothesis (2021), Organizational Behavior and Human Decision Processes; (Briers)
From theory to practice in pattern-oriented modelling: identifying and using empirical patterns in predictive models (2021), Biological Reviews; (White)
WILDA: Wide Learning of Diverse Architectures for Classification of Large Datasets (2021), ; (Hart)
Understanding Deep Neural Networks For Regression In Leaf Counting (2020), ; (Giuffrida)
Doing More With Less: A Multitask Deep Learning Approach in Plant Phenotyping (2020), Frontiers in Plant Science; (Giuffrida)
Use of machine learning techniques to model wind damage to forests (2019), Agricultural and Forest Meteorology; (Hart)
Algorithm selection using deep learning without feature extraction (2019), ; (Hart)
An Illumination Algorithm Approach to Solving the Micro-Depot Routing Problem (2019), ; (Hart)
A novel similarity-based mutant vector generation strategy for differential evolution (2018), Proceedings of the Genetic and Evolutionary Computation Conference; (Hart)