The Department of Biological Sciences has an expanding research base, which, in addition to providing leading researchers of national and international standing in these areas, most importantly underpins the delivery of teaching. Research in Biological Sciences at Chester can be divided into three broad groups of expertise, namely Animal Behaviour and Conservation, Food Nutrition and Health, and Stress and Disease.

Recent Submissions

  • Therapeutic potential of salvigenin to combat atrazine induced liver toxicity in rats via regulating Nrf-2/Keap-1 and NF-κB pathway

    Edwards, Henry; Javed, Khadija; Yadev, Kumar; Ara, Chaman; Omer, Al-Mahmoud; University of Melbourne; University of Chester; Ghazi University; Cairo University (Elsevier, 2024-05-24)
    Atrazine (ATR) is the second most extensively used herbicide which adversely affects the body organs including liver. Salvigenin (SGN) is a flavonoid which demonstrates a wide range of biological and pharmacological abilities. This study was planned to assess the protective ability of SGN to avert ATR induced liver damage in rats. Thirty-two rats (Rattus norvegicus) were divided into four groups including control, ATR (5 mg/kg), ATR (5 mg/kg) + SGN (10 mg/kg) and SGN (10 mg/kg) alone supplemented group. ATR exposure reduced the expression of Nrf-2 while instigating an upregulation in Keap-1 expression. Furthermore, the activities of catalase (CAT), glutathione peroxidase (GPx), superoxide dismutase (SOD), heme‑oxygenase-1 (HO-1) and glutathione reductase (GSR) contents were decreased while increasing reactive oxygen species (ROS) and malondialdehyde (MDA) levels after ATR treatment. Moreover, ATR poisoning increased the levels of ALT, AST, and ALP while reducing the levels of total proteins, and albumin in hepatic tissues of rats. Besides, ATR administration escalated the expressions of Bax and Caspase-3 while inducing a downregulation in the expressions of Bcl-2. Similarly, ATR intoxication increased the levels of Interleukin-6 (IL-6), Nuclear factor kappa-B (NF-κB), Interleukin-1β (IL-1β), tumor necrosis factor-α (TNF-α), and the activity of cyclooxygenase-2 (COX-2). Furthermore, ATR disrupted the normal histology of hepatic tissues. However, SGN treatment remarkably protected the liver tissues via regulating antioxidant, anti, inflammatory, anti-apoptotic as well as histology parameters. Therefore, it is concluded that SGN can be used as therapeutic agent to combat ATR-induced hepatotoxicity. [Abstract copyright: Copyright © 2024 Elsevier Inc. All rights reserved.]
  • Carbon dioxide fluxes in Alpine grasslands at the Nivolet Plain, Gran Paradiso National Park, Italy 2017–2023

    Parisi, Angelica; di Valdengo, Francesca Avogadro; Baneschi, Ilaria; Baronetti, Alice; Boiani, Maria V.; Catania, Maurizio; Lenzi, Sara; Magnani, Marta; Mosca, Pietro; Provenzale, Antonello; et al. (Nature Research, 2024-06-21)
    We introduce a georeferenced dataset of Net Ecosystem Exchange (NEE), Ecosystem Respiration (ER) and meteo-climatic variables (air and soil temperature, air relative humidity, soil volumetric water content, pressure, and solar irradiance) collected at the Nivolet Plain in Gran Paradiso National Park (GPNP), western Italian Alps, from 2017 to 2023. NEE and ER are derived by measuring the temporal variation of CO2 concentration obtained by the enclosed chamber method. We used a customised portable non-steady-state dynamic flux chamber, paired with an InfraRed Gas Analyser (IRGA) and a portable weather station, measuring CO2 fluxes at a number of points (around 20 per site and per day) within five different sites during the snow-free season (June to October). Sites are located within the same hydrological basin and have different geological substrates: carbonate rocks (site CARB), gneiss (GNE), glacial deposits (GLA, EC), alluvial sediments (AL). This dataset provides relevant and often missing information on high-altitude mountain ecosystems and enables new comparisons with other similar sites, modelling developments and validation of remote sensing data.
  • Management of intraspecific aggression in two bull giraffes (Giraffa camelopardalis ssp. rothschildi)

    Stanley, Christina R.; Harley, Jessica L.; Tracey, Roann; Banks, Lindsay; University of Chester; University Centre Reaseheath; Knowsley Safari (Wiley, 2024-05-29)
    Maintaining non-breeding individuals in zoological collections may sometimes necessitate housing bachelor groups. In turn, intact cohabiting males may express increased intraspecific agonistic behaviors and management intervention may be indicated. Where castration is deemed inappropriate (e.g., future breeding, or anesthesia and surgery-related risk), the immune-contraceptive gonadotrophin-releasing hormone (GnRH) is increasingly used as an alternative. When intraspecific aggression (sparring) in two bull giraffes housed as a bachelor pair at Knowsley Safari, UK, escalated in frequency and intensity (despite management interventions), further mediation was warranted to moderate sparring behaviors. The EEP recommendation was for one giraffe, the (slightly) older, outwardly mature (darker, strong musth) individual, to be treated with the GnRH vaccine Improvac® (Zoetis, USA). To gauge the efficacy of vaccination, behavioral observations were conducted during each vaccination Phase to identify changes in the frequency of sparring behaviors. In addition, fecal samples were collected by keepers and sent to Chester Zoo's Endocrine Diagnostic Laboratory for analysis to compare androgen levels between the pre- and post-vaccination Phases. Testicular atrophy was investigated using both visual inspection and photographic images. The GnRH vaccine Improvac® initially appeared to be associated with reduced aggressive behaviors in the two bull giraffes. Sparring behaviors decreased in frequency after each vaccination Phase, although these did not significantly diminish until Phase 4. Physiological markers were inconclusive as testosterone concentrations varied throughout the Phases, although levels remained low after the fourth vaccination Phase. Approximately eight months following the initial vaccination with Improvac®, the unvaccinated bull exhibited heightened aggression, resulting in physical aggression and injury to the vaccinated bull. As a result, both bulls are now on an Improvac® vaccination schedule which has enabled them to remain housed together as a bachelor pair.
  • Environmental factors modulate the distribution of elasmobranchs in southern Mozambique

    Murie, Calum; Oliver, Simon P.; Gavard, Livia; Lebrato, Mario; Brown, James; Lawrence, Andrew; University of Chester; Underwater Africa, Mozambique; The Thresher Shark Research and Conservation Project, Phillipines; Bazaruto Centre for Scientific Studies (BCSS), Mozambique (Frontiers Media, 2024-05-21)
    Investigating the spatiotemporal ecology of elasmobranchs is an important precursor to their effective management. Understanding long-term patterns in the movement and habitat use of threatened species can improve management plans so that they yield increased conservation benefits. We investigated the spatiotemporal and environmental drivers that underpin the abundance and distribution of elasmobranchs around reef habitats in southern Mozambique to highlight reefs that are important (“hotspots”) to the regional elasmobranch community. Visual belt transects (n = 738), supported by video recordings, were completed on 16 reef sites off the coast of southern Mozambique from 2018 to 2022. Nine elasmobranch species were encountered annually (Carcharhinus amblyrhynchos, Triaenodon obesus, Stegostoma tigrinum, Neotrygon caeruleopunctata, Pateobatis jenkinsii, Taeniurops meyeni, Mobula kuhlii, Mobula alfredi, Mobula birostris) and 11 individual environmental and spatiotemporal parameters (horizontal water visibility, tidal range and state, moon illumination, temperature on the reef, cloud cover, time of day, day of the year, transect distance from shore, transect depth, and the region that the transect occurred in) were measured. All species, (bar P. jenkinsii) were significantly more abundant around certain reefs in the sampled region. Total counts for most species were highest in the austral summer however two species’ (M. birostris and S. tigrinum) were most abundant in the winter months. The tidal state, tidal range, and moon illumination correlated significantly with the numbers of each of the nine elasmobranch species. Non-Metric Multidimensional Scaling (NMDS) indicated that species’ responses to the measured parameters grouped taxonomically. Environmental influences resulted in strong seasonal patterns of reef use by large-bodied and pelagic elasmobranch species (e.g. manta rays). The measured environmental parameters also resulted in daily, monthly, and seasonal patterns of abundance of reef-resident stingray and shark species. Banning extraction of elasmobranch species around the reefs where they aggregate and reflecting species distributions within fisheries regulations may significantly benefit the regional elasmobranch community.
  • In Absentia—Can a Lack of Behaviour Be a Useful Welfare Indicator? An Application to the Captive Management of Livingstone’s Fruit Bats, Pteropus livingstonii

    Edwards, Morgan J.; Hosie, Charlotte A.; Naidenov, Laura; Price, Eluned; Smith, Tessa E.; Wormell, Dominic; Stanley, Christina R.; University of Chester; Chester Zoo; Durrell Wildlife Conservation Trust (MDPI, 2024-05-23)
    Non-invasive behavioural indicators of welfare can be particularly useful for managing captive breeding populations of endangered species; these allow individual welfare to be monitored and reproductive success maximised without the need for capture and restraint methods. However, most studies focus on the behaviours whose presence or frequency can predict welfare issues; the absence of a behaviour is less frequently considered an indicator of welfare. Here, we investigate potential behavioural correlates with welfare-related health states in captive Livingstone’s fruit bats (Pteropus livingstonii), a critically endangered species that can become obese due to restricted space and reduced activity rates compared with wild populations. In this study, behavioural data were collected on males (which are particularly prone to obesity). Hurdle models were used to separately determine the factors predicting the presence or absence of behaviour and the frequency of observed behaviours. Whilst significantly lower levels of vigilance were observed in males with a larger body mass, those with diagnosed health issues were significantly more likely to show an absence of locomotion and foraging behaviour. Males with a lower body mass were also more likely to show an absence of foraging behaviour. Our study demonstrates how the absence of a behaviour can be informative as to an individual’s welfare state. This study has identified behavioural profiles that can be used to flag at-risk individuals, reducing the need for potentially stressful handling and improving our ability to safeguard the welfare of individuals within a large captive group.
  • Correction: Wiśniewska et al. Heterospecific Fear and Avoidance Behaviour in Domestic Horses (Equus caballus). Animals 2021, 11, 3081

    Wiśniewska, Anna; Janczarek, Iwona; Wilk, Izabela; Tkaczyk, Ewelina; Mierzicka, Martyna; Stanley, Christina R.; Górecka‐Bruzda, Aleksandra; University of Life Sciences in Lublin; University of Chester; Polish Academy of Sciences (MDPI, 2022-08-10)
    Correction to original article
  • ISRA9PHL0474 Monad & Kimud Shoals Factsheet

    Oliver, Simon P.; Cases, Gary; Brown, James; Gokoz, Alp; Faringstam, Isabelle; Gonzalez-Pestana, Adrianna; The University of Chester; IUCN Shark Group; The Thresher Shark Research and Conservation Project; Project Sharklink
    Monad & Kimud Shoals are located southeast of Malapascua Island in the Central Visayan Sea, central Philippines. The Visayan Sea is a relatively shallow area with frequent wind- driven vertical mixing due to its shallow nature, and land-based nutrient run-off which play an important role in supplementing the overall primary production. Monad & Kimud Shoals are shallow seamounts, 7 km apart. The top of the seamounts forms a plateau at 15 to 25 m depth. This area overlaps with the Sulu-Sulawesi Marine Ecoregion an Ecologically and Biologically Significant Marine Area (EBSA), and two marine protected areas. Within this area there are: threatened species and distinctive attributes (Pelagic Thresher Alopias pelagicus).
  • Pain in Sheep

    McLennan, Krista M.; University of Chester (CABI Publishing, 2024-01-19)
    Pain in sheep can occur for a variety of reasons, including disease, injury, and naturally through parturition. Sheep, as a prey species, do not overtly express pain making it challenging for owners and veterinarians to recognise and thus effectively treat pain. By observing facial expressions, it is possible to recognise and quantify the pain a sheep may be experiencing. This enables the provision of treatment and the prevention of any further suffering. Information © The Author 2024
  • Automatic detection of indris songs using convolutional neural networks

    Valente, Daria; Ravaglia, Davide; Ferrario, Valeria; De Gregorio, Chiara; Carugati, Filippo; Raimondi, Teresa; Cristiano, Walter; Torti, Valeria; von Hardenberg, Achaz; Ratsimbazafy, Jonah; et al. (European Acoustics Association, 2024-01-17)
  • How Useful Are Existing Protocols in the Quick Assessment of the Welfare of Semi-Feral Horses? Pilot Study on Konik Polski Horses Living in the Forest Sanctuary

    Górecka-Bruzda, Aleksandra; Siemieniuch, Marta; Lansade, Léa; Stanley, Christina R.; Polish Academy of Sciences; Institut Français du Cheval et d’Equitation; University of Chester (MDPI, 2023-12-19)
    Scientifically validated and standardised methods for the evaluation of the welfare of free-living horses are urgently needed by both the owners and managers of these populations and those responsible for implementing national welfare legislation. The aim of the study was to test the feasibility and usefulness of two welfare protocols that could be applied to semi-feral populations: a prototype of welfare assessment template (WAT) for Carneddau semi-feral ponies and the IFCE/INRAE Horse Welfare Protocol. Additionally, the body condition scale designed by Henneke (BCS-H) was employed. The study took place in July/August 2022 and April 2023 to evaluate the welfare of a pilot population of nineteen semi-feral Konik polski horses. The horses scored high or satisfactory under indicators across both protocols; only body condition scores were significantly lower in early spring (BCS-WAT: 1.11 ± 0.57; BCS-H: 3.84 ± 1.17) than in the summer (BCS-WAT: 1.58 ± 0.61; BCS-H: 5.63 ± 1.01). Our study confirmed the feasibility of utilising most of the WAT and IFCE/INRAE welfare indicators in semi-feral horses. Some adaptations, such as considering validation of scales, positive welfare indicators and animals’ free-choice of conditions, have been suggested for future in-field application.
  • Coupled information networks drive honeybee (Apis mellifera) collective foraging

    Hasenjager, Matthew; Hoppitt, William; Cunningham‐Eurich, Iona; Franks, Victoria; Leadbeater, Ellouise; University of Tennessee; University of London; Natural History Museum, London; University College London; University of Chester (Wiley, 2023-11-27)
    Collective behaviour by eusocial insect colonies is typically achieved through multiple communication networks that produce complex behaviour at the group level but often appear to provide redundant or even competing information. A classic example occurs in honeybee (Apis mellifera) colonies, where both the dance communication system and robust scent‐based mechanisms contribute to the allocation of a colony's workforce by regulating the flow of experienced foragers among known food sources. Here we analysed social connectivity patterns during the reactivation of experienced foragers to familiar feeding sites to show that these social information pathways are not simply multiple means to achieve the same end but intersect to play complementary roles in guiding forager behaviour. Using artificial feeding stations, we mimicked a natural scenario in which two forager groups were simultaneously collecting from distinct patches containing different flowering species. We then observed the reactivation of these groups at their familiar feeding sites after interrupting their foraging. Social network analysis revealed that temporarily unemployed individuals interacted more often and for longer with foragers that advertised a familiar versus unfamiliar foraging site. Due to such resource‐based assortative mixing, network‐based diffusion analysis estimated that reactivation events primarily resulted from interactions among bees that had been trained to the same feeding station and less so from different‐feeder interactions. Both scent‐ and dance‐based interactions strongly contributed to reactivation decisions. However, each bout of dance‐following had an especially strong effect on a follower's likelihood of reactivation, particularly when dances indicated locations familiar to followers. Our findings illustrate how honeybee foragers can alter their social connectivity in ways that are likely to enhance collective outcomes by enabling foragers to rapidly access up‐to‐date information about familiar foraging sites. In addition, our results highlight how reliance on multiple communication mechanisms enables social insect workers to utilise flexible information‐use strategies that are robust to variation in the availability of social information.
  • Non‐invasive sampling reveals low mitochondrial genetic diversity for an island endemic species: The critically endangered Grenada Dove Leptotila wellsi

    Peters, Catherine; Geary, Matthew; Hosie, Charlotte; Nelson, Howard; Rusk, Bonnie; Muir, Anna; University of Chester; University of Cambridge; Grenada Dove Conservation Programme (Wiley Open Access, 2023-11-23)
    As an island endemic with a decreasing population, the critically endangered Grenada Dove Leptotila wellsi is threatened by accelerated loss of genetic diversity resulting from ongoing habitat fragmentation. Small, threatened populations are difficult to sample directly but advances in molecular methods mean that non‐invasive samples can be used. We performed the first assessment of genetic diversity of populations of Grenada Dove by (a) assessing mtDNA genetic diversity in the only two areas of occupancy on Grenada, (b) defining the number of haplotypes present at each site and (c) evaluating evidence of isolation between sites. We used non‐invasively collected samples from two locations: Mt Hartman (n = 18) and Perseverance (n = 12). DNA extraction and PCR were used to amplify 1751 bps of mtDNA from two mitochondrial markers: NADH dehydrogenase 2 (ND2) and Cytochrome b (Cyt b). Haplotype diversity (h) of 0.4, a nucleotide diversity (π) of 0.00023 and two unique haplotypes were identified within the ND2 sequences; a single haplotype was identified within the Cyt b sequences. Of the two haplotypes identified, the most common haplotype (haplotype A = 73.9%) was observed at both sites and the other (haplotype B = 26.1%) was unique to Perseverance. Our results show low mitochondrial genetic diversity and clear evidence for genetically isolated populations. The Grenada Dove needs urgent conservation action, including habitat protection and potentially augmentation of gene flow by translocation in order to increase genetic resilience and diversity with the ultimate aim of securing the long‐term survival of this critically endangered species.
  • Monitoring wildlife population trends with sample counts: a case study on the Alpine ibex (Capra ibex)

    Panaccio, Matteo; Brambilla, Alice; Bassano, Bruno; Smith, Tessa; von Hardenberg, Achaz; University of Chester; Alpine Wildlife Research Centre, Gran Paradiso National Park; University of Zurich (Wiley Open Access, 2023-11-06)
    Monitoring population dynamics is of fundamental importance in conservation but assessing trends in abundance can be costly, especially in large and rough areas. Obtaining trend estimations from counts performed in only a portion of the total area (sample counts) can be a cost‐effective method to improve the monitoring and conservation of species difficult to count. We tested the effectiveness of sample counts in monitoring population trends of wild animals, using as a model population the Alpine ibex Capra ibex in the Gran Paradiso National Park (Italy), both with computer simulations and using historical count data collected over the last 65 years. Despite sample counts failed to correctly estimate the true population abundance, sampling half of the target area could reliably monitor the trend of the target population. In case of strong changes in abundance, an even lower proportion of the total area could be sufficient to identify the direction of the population trend. However, when there is a high yearly trend variability, the required number of samples increases and even counting in the entire area can be ineffective to detect population trends. The effect of other parameters, such as which portion of the area is sampled and detectability, was lower, but these should be tested case by case. Sample counts could therefore constitute a viable alternative to assess population trends, allowing for important, cost‐effective improvements in the monitoring of wild animals of conservation interest.
  • Technical validation and a comparison of two methods to quantify individual levels of glucocorticoids in Alpine marmot hair

    Doss, Elina M.; Jouffroy, Mathilde; Rey, Benjamin; Cohas, Aurélie; von Hardenberg, Achaz; Smith, Tessa E.; University of Chester; Université de Lyon (Elsevier, 2023-10-13)
    Quantification of cortisol concentration in hair has become a promising conservation tool for non-invasive monitoring of “stress” in wild populations, yet this method needs to be carefully validated for each species. The goals of the study were: • Immunologically validate two methods (study 1 and 2 respectively) to extract and quantify cortisol in the hair of wild Alpine marmots. • Compare the amount of cortisol extracted from hair samples using two methods i.e. cut into fine pieces (study 1) and hair samples pulverized using a ball mill (study 2). • Determine the extent to which methods in study 2 could provide individual specific hair cortisol (HC) measures when samples were taken from the same body location. Within and between individual variations in HC levels were examined from multiple hair samples from 14 subjects in study 2. We evaluated if inter-individual variations in HC levels could be explained by sex and age. At least twice the amount of cortisol was obtained per g/hair when samples were pulverized in a ball mill prior to extraction compared to when cut into pieces. Our methods demonstrated intra-individual consistency in HC at a given time point: inter-individual variation in HC was three times larger than within individual variance. Sex and age did not impact HC levels.
  • Sample size assessments for thermal physiology studies: An R package and R Shiny application

    van Steenderen, Clarke J. M.; Sutton, Guy F.; Owen, Candice A.; Martin, Grant D.; Coetzee, Julie A.; Rhodes University; University of Chester; University of the Free State (The Royal Entomological Society, 2023-08-17)
    Required sample sizes for a study need to be carefully assessed to account for logistics, cost, ethics and statistical rigour. For example, many studies have shown that methodological variations can impact the critical thermal limits (CTLs) recorded for a species, although studies on the impact of sample size on these measures are lacking. Here, we present ThermalSampleR; an R CRAN package and Shiny application that can assist researchers in determining when adequate sample sizes have been reached for their data. The method is particularly useful because it is not taxon specific. The Shiny application offers a user‐friendly interface equivalent to the package for users not familiar with R programming. ThermalSampleR is accompanied by an in‐built example dataset, which we use to guide the user through the workflow with a fully worked tutorial.
  • Genetic polymorphisms in the serotonin, dopamine and opioid pathways influence social attention in rhesus macaques (Macaca mulatta)

    Howarth, Emmeline; Szott, Isabelle D.; Witham, Claire L.; Wilding, Craig S.; Bethell, Emily J.; Liverpool John Moores University; University of Chester; Centre for Macaques, Harwell Institute, Medical Research Council, Salisbury; (Public Library of Science, 2023-08-02)
    Behaviour has a significant heritable component; however, unpicking the variants of interest in the neural circuits and molecular pathways that underpin these has proven difficult. Here, we present a comprehensive analysis of the relationship between known and new candidate genes from identified pathways and key behaviours for survival in 109 adult rhesus macaques (Macaca mulatta). Eight genes involved in emotion were analysed for variation at a total of nine loci. Genetic data were then correlated with cognitive and observational measures of behaviour associated with wellbeing and survival using MCMC-based Bayesian GLMM in R, to account for relatedness within the macaque population. For four loci the variants genotyped were length polymorphisms (SLC6A4 5-hydroxytryptamine transporter length-polymorphic repeat (5-HTTLPR), SLC6A4 STin polymorphism, Tryptophan 5-hydroxylase 2 (TPH2) and Monoamine oxidase A (MAOA)) whilst for the other five (5-hydroxytryptamine receptor 2A (HTR2A), Dopamine Receptor D4 (DRD4), Oxytocin receptor (OXTR), Arginine vasopressin receptor 1A (AVPR1a), Opioid receptor mu(μ) 1 (OPRM1)) SNPs were analysed. STin genotype, DRD4 haplotype and OXTR haplotype were significantly associated with the cognitive and observational measures of behaviour associated with wellbeing and survival. Genotype for 5-HTTLPR, STin and AVPR1a, and haplotype for HTR2A, DRD4 and OXTR were significantly associated with the duration of behaviours including fear and anxiety. Understanding the biological underpinnings of individual variation in negative emotion (e.g., fear and anxiety), together with their impact on social behaviour (e.g., social attention including vigilance for threat) has application for managing primate populations in the wild and captivity, as well as potential translational application for understanding of the genetic basis of emotions in humans.
  • Parental breeding decisions and genetic quality predict social structure of independent offspring

    Franks, Victoria; Thorogood, Rose; Brekke, Patricia; University of Chester; University of Helsinki; Zoological Society of London (Wiley, 2023-07-03)
    Across the animal kingdom, newly-independent juveniles form social associations that influence later fitness, mate choice, and gene flow, but little is known about the ontogeny of social environments, particularly in wild populations. Here we test whether associations among young animals form randomly, or are influenced by environmental or genetic conditions established by parents. Parents’ decisions determine natal birth sites, which could affect who independent young initially encounter; secondly, mate choice determines genetic condition (e.g. inbreeding) of young and the parental care they receive, which can affect sociability. However, genetic and environmental factors are confounded unless related offspring experience different natal environments. Therefore, we used a long-term genetic pedigree, breeding records, and social network data from three cohorts of a songbird with high extra-pair paternity (hihi, Notiomystis cincta) to disentangle (1) how nest location and relatedness contribute to association structure once juveniles disperse away from birth sites, and (2) if juvenile and/or parental inbreeding predicts individual sociability. We detected positive spatial autocorrelation: hihi that fledged closer by were more likely to associate even after dispersing, irrespective of genetic relatedness. Juvenile inbreeding did not predict sociability, but those raised by more inbred fathers formed more, stronger, associations, which did not depend on whether that male was the genetic parent or not. These results suggest that the natal environment created by parents, rather than focal genetic condition, establishes the foundation for social associations. Overall, we highlight how social inheritance may play an important role in population dynamics and evolutionary potential in wild animals.
  • Machine Learning for collagen peptide biomarker determination in the taxonomic identification of archaeological fish remains

    Baker, Andrew; Harvey, Virginia L.; Buckley, Michael; University of Chester; University of Manchester (Elsevier, 2023-04-22)
    Species identification of archaeofaunal remains can be informative of changing local and global ecosystems, as well as how we interacted with them in the past. However, with the vast majority of assemblages being dominated by morphologically indeterminate specimens, methods of biomolecular species identification are becoming more popular, such as the protein fingerprint-based identification approach known as ZooMS (Zooarchaeology by Mass Spectrometry). As larger datasets are being produced, Machine Learning techniques such as those using Random Forest algorithms have been considered to expedite the identification process. However, it has proven difficult to extract meaningful biomarkers from these processes alone and so far only tackled for mammals. Here, we introduce a novel approach based on the principles of the ID3 algorithm for biomarker identification from ZooMS spectral databases, focussing on archaeological fish remains from Europe and the Caribbean. We show that the tool is highly effective at generating comprehensible lists of family- and genus-level biomarkers. At family-level identification, the average sensitivity across five families of fish was ∼0.9, where a specificity of 1 would indicate a greatly effective algorithm that outperforms both traditional Random Forest and Naïve Bayes approaches; at the genus level the mean sensitivity reduced to ∼0.8 across the nine genera tested. However, some anomalous matches were produced, with accuracy dropping when distinguishing between genera of the same family, such as Epinephelus and Mycteroperca belonging to the Serranidae. Therefore, while this tool has value in rapidly producing lists of biomarkers and can efficaciously identify new ZooMS fingerprints based on those markers, it indicates that manual intervention remains a requirement at finer taxonomic resolutions.
  • A multidisciplinary approach to estimating wolf population size for long-term conservation

    Marucco, Francesca; Boiani, Maria V.; Dupont, Pierre; Milleret, Cyril; Avanzinelli, Elisa; Pilgrim, Kristine; Schwartz, Michael K.; von Hardenberg, Achaz; Perrone, Domenica S.; Friard, Olivier P.; et al. (Wiley, 2023-06-01)
    The wolf (Canis lupus) is among the most controversial of wildlife species. Abundance estimates are required to inform public debate and policy decisions, but obtaining them at biologically relevant scales is challenging. We developed a system for comprehensive population estimation across the Italian Alpine Region (100,000 km ), involving 1,513 trained operators representing 160 institutions. This extensive network allowed for coordinated genetic sample collection and landscape-level spatial capture-recapture analysis transcending administrative boundaries. We produced the first estimates of key parameters for wolf population status assessment including wolf abundance (952 individuals, 95% CrI: 816-1120), the number of reproductive units (135 packs, 95% CrI: 112-165), and the proportion of mature individuals (33-45%). The results also provided reliable information about the monitoring effort, thereby overcoming an important limitation of citizen-science data. This is an effective approach for promoting wolf-human coexistence based on wolf abundance monitoring, and a tool for endorsing large-scale harmonized conservation practices. This article is protected by copyright. All rights reserved. [Abstract copyright: This article is protected by copyright. All rights reserved.]
  • Human-Wildlife Conflict in Golden Monkeys (Cercopithecus mitis kandti) of the Volcanoes National Park, Rwanda

    Ndayishimiye, Eric; Eckardt, Winnie; Fletcher, Alison W.; University of Chester; Dian Fossey Gorilla Fund (Springer, 2023-05-04)
    Human-wildlife conflict, in particular crop-foraging, challenges conservationists worldwide. Endangered golden monkeys (Cercopithecus mitis kandti) are frequent crop-foragers around Volcanoes National Park (VNP), Rwanda. To evaluate the impact of crop-foraging behaviour on monkeys and farmers, we interviewed 45 farmers near VNP using a structured questionnaire and organised a workshop for local and regional actors to discuss mitigation measures. To investigate differences in monkey behaviour when foraging inside versus outside VNP, and to inform mitigation strategies, we collected ad libitum behavioural data from one habituated golden monkey group for 11 weeks. We tested the feasibility of a taste aversion technique to deter monkeys, by placing chilli-laced potatoes in harvested potato fields adjacent to the study group’s home range, but found that experimental aversion techniques were logistically challenging. Of 38 farmers, 95% experienced potato loss to monkeys and 36% of 44 farmers threw objects at/chased monkeys in the previous farming season. Farmers and workshop participants judged the most effective way to mitigate crop-foraging to be through improvement of existing crop-guarding. Behavioural observations indicated increased vigilance behaviour and decreased social behaviour when in farmland. Monkeys (N=9) that visited the experimental area avoided chilli-laced potatoes but continued to forage on nearby crops. In conclusion, our results indicate that crop-foraging can negatively impact farmers' livelihoods and attitudes and can increase vigilance behaviour of monkeys. Our multi-faceted approach enabled the involvement of a wide range of stakeholders, highlighted the urgent need to improve existing management measures and explored alternatives to facilitate positive coexistence between monkeys and farmers.

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