Biology subjects

Creer, S.

Publications and source records attributed to Creer, S..

13 recordsLinked to original sources

bioRxiv2025

Misalignment between perceived and actual ability on a balance beam walking task

Effective dynamic balance control is necessary to maintain stability, but it is an individuals self-perceived ability that ultimately determines movement selection. Accurate self-estimation of balance ability is therefore essential to ensure that movement choices align with true capability. This study examined individuals perception of their ability on a clinically standardized Narrowing Beam Walking Task (NBWT) to examine 1) the initial perception of balance ability before attempting the task, and 2) how experience completing the task improves the accuracy of self-perceived balance. Collegiate athletes provided self-estimates of performance at baseline (before any trials with the task), early-training (after completing two trials), and post-training (after a further 8 trials). Actual task performance was quantified using the final 8 trials. At baseline, athletes poorly estimated their ability: individuals with poorer task performance tended to overestimate their ability while higher-performing individuals tended to underestimate their ability. With practice, absolute estimation error significantly decreased, indicating that task-specific exposure facilitated recalibration to bring self-estimates of performance in closer alignment to actual performance. These effects were consistent across all tested sporting disciplines. These findings show that effective balance control and frequent engagement in similar, but unrelated balance tasks, does not facilitate accurate self-perception of performance on the NBWT. Instead, brief task-specific exposure was required to refine balance estimates. These findings have implications for balance testing and rehabilitation that seeks to improve mobility in populations whose misjudgments of balance ability are often associated with negative outcomes, such as falls.

physiology↗

bioRxiv2024

Metacommunity theory and metabarcoding reveal the environmental, spatial, and biotic drivers of meiofaunal communities in sandy beaches

Sandy beaches are important ecosystems providing coastal protection and recreation, but they face significant threats from human activities and sea level rise. They are inhabited by meiofauna, small benthic invertebrates that are highly abundant and diverse, but are commonly understudied biotic components of beach ecosystems. Here, we investigate the factors shaping meiofaunal metacommunities by employing Generalised Dissimilarity Modelling (GDM) and Joint Species Distribution Modelling (JSDM) to study community turnover and assembly processes. We analysed over 550 meiofauna samples from a >650 km stretch of the southern North Sea coastline using a metabarcoding approach. Our findings reveal that environmental factors, especially Distance from Low Tide and Sediment Grain Size, are important drivers of meiofauna community turnover. This highlights the influence of the gradient from marine to terrestrial habitats and sediment conditions. Spatial factors, which indicate dispersal limitations, also significantly impact community composition, challenging the view that marine meiofauna have broad geographic distributions. The JSDM results show that species sorting by environmental conditions is the dominant process in community assembly with increasing environmental differences between sampling sites, but that biotic associations, or similar environmental preferences, are a major driver of community assembly at sites with similar environmental conditions. Further, we find that spatial factors also significantly influence community assembly across the study region. By facilitating the inference of ecological niches for a high number of meiofaunal taxa, JSDM provides a powerful framework for understanding the ecology of these animals. Our results highlight the importance of considering environmental gradients and dispersal limitations in meiofauna and beach ecosystem research, and future research should aim at adding information on functional traits and biotic interactions under varying environmental conditions to understand meiofauna community dynamics and resilience.

ecology↗

bioRxiv2024

Plastic responses to past environments shape adaptation to novel selection pressures

Phenotypic plasticity may pave the way for rapid adaptation to newly encountered environments. Although it is often contested, there is growing evidence that initial plastic responses of ancestral populations to new environmental cues may promote subsequent adaptation. However, we do not know whether plasticity to cues present in the ancestral habitat (past-cue plasticity) can facilitate adaptation to novel cues. Conceivably, this could occur if plastic responses are coincidentally optimal to both past and novel cues (i.e., are pre-adaptive) or if they are transferred to novel cues during adaptation. Past plastic phenotype values could also become fixed and genetically co-opted during adaptation to the new environment. To uncover the role of past-cue plasticity in adaptation, we tested gene expression plasticity responses of two parallel mine-waste adapted Silene uniflora populations and their closest coastal relatives. Plants were exposed to the past and novel-cues of salt and zinc, which revealed that during adaptation to mine-waste plasticity to salt diminishes. Despite this, our results show that ancestral plasticity to salt has a substantial impact on subsequent adaptation to zinc. For a third of genes that have evolved zinc plasticity in mine populations, salt plasticity has been transferred to the zinc response. Furthermore, a quarter of fixed expression differences between mine and coastal populations were similar to ancestral salt responses. Alongside evidence that ancestral plasticity to novel cues can facilitate adaptation, our results provide a clear indication that ancestral past-cue plasticity can also play a key role in rapid, parallel adaptation to novel habitats. Significance StatementThe role of phenotypic plasticity in promoting adaptation is hotly debated, with conflicting evidence for the benefits of ancestral plasticity in newly encountered environments. Here, we present an alternative mode by which ancestral plasticity can promote adaptation. We investigated whether phenotypic plasticity towards environmental cues that are experienced only in ancestral habitats (past-cue plasticity) can significantly contribute towards rapid adaptation to completely distinct cues. We show that, in the maritime plant species, Silene uniflora, past-cue plasticity to salt has made a substantial contribution to rapid adaptation to heavy-metal pollution in newly encountered habitats. This phenomenon has broad implications for the capacity and predictability of species to persist in the face of anthropogenic environmental change.

evolutionary biology↗

bioRxiv2023

Comparative population genomics of manta rays has global implications for management

Understanding population connectivity and genetic diversity is of fundamental importance to conservation. However, in globally threatened marine megafauna, challenges remain due to their elusive nature and wide-ranging distributions. As overexploitation continues to threaten biodiversity across the globe, such knowledge gaps compromise both the suitability and effectiveness of management actions. Here, we use a comparative framework to investigate genetic differentiation and diversity of manta rays, one of the most iconic yet vulnerable groups of elasmobranchs on the planet. Despite their recent divergence, we show how oceanic manta rays (Mobula birostris) display significantly higher heterozygosity than reef manta rays (Mobula alfredi) and that M. birostris populations display higher connectivity worldwide. Through inferring modes of colonisation, we reveal how both contemporary and historical forces have likely influenced these patterns, with important implications for population management. Our findings highlight the potential for fisheries to disrupt population dynamics at both local and global scales and therefore have direct relevance for international conservation of marine species.

evolutionary biology↗

bioRxiv2023

A diversity of diversities: evaluating the relationships between below and aboveground biodiversity

O_LITo predict how biodiversity will respond to global change, it is crucial to understand the relative roles of abiotic drivers and biotic interactions in driving associations between the biodiversity of disparate taxa. It is particularly challenging to understand diversity-diversity links across domains and habitats, because data are rarely available for multiple above- and below-ground taxa across multiple sites. C_LIO_LIHere we analyse data from a unique biodiversity dataset gathered across a variety of oceanic temperate terrestrial habitats in Wales, comprising 300 sites with co-located soil microbial, plant, bird, and pollinator surveys along with climate and soil physicochemical information. Soil groups are analysed using metabarcoding of the 16S, ITS1 and 18S DNA regions, allowing in depth characterisation of microbial and soil animal biodiversity. C_LIO_LIWe explore biodiversity relationships along three aspects of community composition: First, we assess correlation between the alpha diversity of different groups. Second, we assess whether biotic turnover between sites is correlated across different groups. Finally, we investigate the co-occurrence of individual taxa across sites. In each analysis, we assess the contribution of linear or non-linear environmental effects. C_LIO_LIWe find that a positive correlation between alpha diversity of plants, soil bacteria, soil fungi, soil heterotrophic protists, bees and butterflies is in fact driven by complex non-linear responses to abiotic drivers. In contrast, environmental variation did not account for positive associations between the diversity of plants and both birds and AM fungi, suggesting a role for biotic interactions. C_LIO_LIBoth the diversity and taxon-level associations between the differing soil groups remained even after accounting for non-linear environmental gradients. Aboveground, spatial factors played larger roles in driving biotic communities, while linear environmental gradients were sufficient to explain many group- and taxon-level relationships. C_LIO_LISynthesis. Our results show how non-linear responses to environmental gradients drive many of the relationships between plant biodiversity and the biodiversity of above- and belowground biological communities. Our work shows how different aspects of biodiversity might respond non-linearly to changing environments and identifies cases where management-induced changes in one community could either influence other taxa or lead to loss of apparent biological associations. C_LI

ecology↗

bioRxiv2023

100 years of anthropogenic impact causes changes in freshwater functional biodiversity

Despite efforts from scientists and regulators, biodiversity is declining at an alarming rate. Unless we find transformative solutions to preserve biodiversity, future generations may not be able to enjoy natures services. We have developed a conceptual framework that establishes the links between biodiversity dynamics and abiotic change through time and space using artificial intelligence. Here, we apply this framework to a freshwater ecosystem with a known history of human impact and study 100 years of community-level biodiversity, climate change and chemical pollution trends. We apply explainable network models with multimodal learning to community-level functional biodiversity measured with multilocus metabarcoding, to establish correlations with biocides and climate change records. We observed that the freshwater community assemblage and functionality changed over time without returning to its original state, even if the lake partially recovered in recent times. Insecticides and fungicides, combined with extreme temperature events and precipitation, explained up to 90% of the functional biodiversity changes. The community-level biodiversity approach used here reliably explained freshwater ecosystem shifts. These shifts were not observed when using traditional quality indices (e.g. Trophic Diatom Index). Our study advocates the use of high throughput systemic approaches on long-term trends over species-focused ecological surveys to identify the environmental factors that cause loss of biodiversity and disrupt ecosystem functions.

ecology↗

bioRxiv2021

Managing human mediated range shifts: understanding spatial, temporal and genetic variation in marine non- native species

The use of molecular methods to manage natural resources is increasingly common. However, DNA-based methods are seldom used to understand the spatial and temporal dynamics of species range shifts. This is important when managing range-shifting species such as non-native species (NNS), which can have negative impacts on biotic communities. Here we investigated the range-shifting NNS Ciona robusta, Clavelina lepadiformis, Microcosmus squamiger and Styela plicata using a combined methodological approach. We first conducted non-molecular biodiversity surveys for these NSS along the South African coastline, and compared the results with historical surveys. We detected no consistent change in range size across species, with some displaying range stability and others showing range shifts. We then sequenced a section of cytochrome c oxidase subunit I (COI) from tissue samples and found genetic differences along the coastline but no change over recent times. Finally, we found that environmental DNA metabarcoding data showed broad congruence with both the non-molecular biodiversity and the COI datasets, but failed to capture complete incidence of all NSS. Overall, we demonstrated how a combined methodological approach can effectively detect spatial and temporal variation in genetic composition and range size, which is key for managing biodiversity changes of both threatened and NSS.

ecology↗

bioRxiv2021

Fauxcurrence: simulating multi-species occurrences for null models in species distribution modelling and biogeography

Defining appropriate null expectations for species distribution hypotheses is important because sampling bias and spatial autocorrelation can produce realistic, but ecologically meaningless, geographic patterns. Generating null species occurrences with similar spatial structure to observed data can help overcome these problems, but existing methods focus on single or pairs of species and do not incorporate between-species spatial structure that may occlude comparative biogeographic analyses. Here, we describe an algorithm for generating randomised species occurrence points that mimic the within- and between-species spatial structure of real datasets and implement it in a new R package - fauxcurrence. The algorithm can be implemented on any geographic domain for any number of species, limited only by computing power. To demonstrate its utility, we apply the algorithm to two common analysis-types: testing the fit of species distribution models (SDMs) and evaluating niche-overlap. The method works well on all tested datasets within reasonable timescales. We found that many SDMs, despite a good fit to the data, were not significantly better than null expectations and identified only two cases (out of a possible 32) of significantly higher niche divergence than expected by chance. The package is user-friendly, flexible and has many potential applications beyond those tested here, such as joint SDM evaluation and species co-occurrence analysis, spanning the areas of ecology, evolutionary biology and biogeography.

ecology↗

bioRxiv2020

Consistent marine biogeographic boundaries across the tree of life despite centuries of human impacts

Over millennia, ecological and evolutionary mechanisms have shaped macroecological distributions across the tree of life. Research describing patterns of regional and global biogeography has traditionally focussed on the study of conspicuous species. Consequently, there is limited understanding of cross-phyla biogeographic structuring, and an escalating need to understand the macroecology of both microscopic and macroscopic organisms. Here we used environmental DNA (eDNA) metabarcoding to explore the biodiversity of marine metazoans, micro-eukaryotes and prokaryotes along an extensive and highly heterogeneous coastline. Our results showed remarkably consistent biogeographic structure across the kingdoms of life, which were underpinned by environmental and anthropogenic influence. Additionally, metazoan communities displayed biographic patterns that suggest regional biotic homogenisation of conspicuous species. Against the backdrop of global pervasive anthropogenic environmental change, our work highlights the importance of considering multiple domains of life to understand the maintenance and drivers of marine biodiversity across broad taxonomic, ecological and geographical scales.

ecology↗

bioRxiv2020

Mutational, transcriptional and viral shedding dynamics of the marine turtle fibropapillomatosis tumor epizootic

Sea turtle populations are directly and indirectly under threat from a range of anthropogenic processes. Perhaps the most visibly apparent of these is the disfiguring tumor disease epizootic (animal epidemic) known as fibropapillomatosis. Fibropapillomatosis continues to spread geographically, with prevalence of the disease also growing at a number of affected sites globally. Environmental exposures seem key to inducing tumor development, possibly through weakening host immune systems to the point of enabling pathogen-induced tumor formation. However, we do not yet understand the precise molecular and mutational events driving fibropapillomatosis tumor formation and progression. Similarly, many open questions remain about the role of the herpesvirus (chelonid herpesvirus 5, ChHV5) associated with the disease as a potential co-trigger, and whether its occurrence within tumors is causative or opportunistic. Without improved understanding of the basic biology of this disease epizootic, treatment, containment and mitigation options are severely hampered. To address fundamental questions relating to the oncogenic signaling, mutational spectrum, viral load, viral transcriptional status (lytic or latent) and spread, we employed transcriptomic profiling, whole genome sequencing, immunohistochemistry and environmental (e)DNA-based monitoring of viral shedding. In particular we focused on the mutational landscape of tumors and assessing the transcriptional similarity of external (skin) and internal (visceral organs) tumors, and the oncogenic signaling events driving early stage tumor growth and post-surgical tumor regrowth. These analyses revealed that internal fibropapillomatosis tumors are molecularly distinct from the more common external tumors. However, our molecular analyses also revealed that there are a small number of conserved potentially therapeutically targetable molecular vulnerabilities in common between internal and external tumors, such as the MAPK, Wnt, TGF{beta} and TNF oncogenic signaling pathways. We also determined that the tumor genomes can harbor copy number gains, indicating potentially viral-independent oncogenic processes. Genes within such mutated genomic regions have known roles in human skin cancer, including MAPK-associated genes. Turtles attempt to mount an immune response, but in some animals this appears to be insufficient to prevent tumor development and growth. ChHV5 was transcriptionally latent in all tumor stages sequenced, including early stage and recurrent tumors. We also revealed that the tumors themselves are the primary source of viral shedding into the marine environment and, if they are surgically removed, the level of ChHV5 in the water column drops. Together, these results offer an improved understanding of fibropapillomatosis tumorigenesis and provide insights into the origins, therapeutic treatment, and appropriate quarantine responses for this wildlife epizootic. Furthermore, they provide insights into human pathogen-induced cancers, particularly mechanisms which are difficult to study in the human and terrestrial context, such as time-course quantification-based monitoring of viral shedding.

cancer biology↗

bioRxiv2018

Phylogenomics and species delimitation of mobulid rays reveals cryptic diversity and a new species of manta ray

Practical biodiversity conservation relies on delineation of biologically meaningful units, particularly with respect to global conventions and regulatory frameworks. Traditional approaches have typically relied on morphological observation, resulting in artificially broad delineations and non-optimal species units for conservation. More recently, species delimitation methods have been revolutionised with High-Throughput Sequencing approaches, allowing study of diversity within species radiations using genome-wide data. The highly mobile elasmobranchs, manta and devil rays (Mobula spp.), are threatened globally by targeted and bycatch fishing pressures resulting in recent protection under several global conventions. However, a lack of global data, morphological similarities, a succession of recent taxonomic changes and ineffectual traceability measures combine to impede development and implementation of a coherent and enforceable conservation strategy. Here, we generate genome-wide Single Nucleotide Polymorphism (SNP) data from among the most globally and taxonomically representative set of mobulid tissues. The resulting phylogeny and delimitation of species units represents the most comprehensive assessment of mobulid diversity with molecular data to date. We find a mismatch between current species classifications, and optimal species units for effective conservation. Specifically, we find robust evidence for an undescribed species of manta ray in the Gulf of Mexico and show that species recently synonymised are reproductively isolated. Further resolution is achieved at the population level, where cryptic diversity is detected in geographically distinct populations, and indicates potential for future traceability work determining regional location of catch. We estimate the optimal species tree and uncover substantial incomplete lineage sorting, where standing variation in extinct ancestral populations is identified as a driver of phylogenetic uncertainty, with further conservation implications. Our study provides a framework for molecular genetic species delimitation that is relevant to wide-ranging taxa of conservation concern, and highlights the potential for genomic data to support effective management, conservation and law enforcement strategies.

genomics↗

bioRxiv2018

The detection of novel and resident marine non-indigenous species using environmental DNA metabarcoding of seawater and sediment

Environmental DNA (eDNA) surveys are increasingly being used for biodiversity monitoring, principally because they are sensitive and can provide high resolution community composition data. Despite considerable progress in recent years, eDNA studies examining how different environmental sample types can affect species detectability remain rare. Comparisons of environmental samples are especially important for providing best practice guidance on early detection and subsequent mitigation of non-indigenous species. Here we used eDNA metabarcoding of COI (cytochrome c oxidase subunit I) and 18S (nuclear small subunit ribosomal DNA) genes to compare community composition between sediment and water samples in artificial coastal sites across the United Kingdom. We first detected markedly different communities and a consistently greater number of distinct operational taxonomic units in sediment compared to water. We then compared our eDNA datasets with previously published rapid assessment biodiversity surveys and found excellent concordance among the different survey techniques. Finally, our eDNA surveys detected many non-indigenous species, including several newly introduced species, highlighting the utility of eDNA metabarcoding for both early detection and temporal / spatial monitoring of non-indigenous species. We conclude that careful consideration on environmental sample type is needed when conducting eDNA surveys, especially for studies assessing community change.

molecular biology↗

bioRxiv2018

Temperate grass allergy season defined by spatio-temporal shifts in airborne pollen communities

Grass pollen is the worlds most harmful outdoor aeroallergen and sensitivity varies between species. Different species of grass flower at different times, but it is not known how airborne communities of grass pollen change in time and space. Persistence and high mobility of grass pollen could result in increasingly diverse seasonal pollen communities. Conversely, if grass pollen does not persist for an extended time in the air, shifting pollen communities would be predicted throughout the summer months. Here, using targeted high throughput sequencing, we tracked the seasonal progression of airborne Poaceae pollen biodiversity across Britain, throughout the grass allergy season. All grass genera displayed discrete, temporally restricted peaks of pollen incidence which varied with latitude, revealing that the taxonomic composition of grass pollen exposure changes substantially across the allergy season. By developing more refined aeroallergen profiling, we predict that our findings will facilitate the exploration of links between taxon-specific exposure of harmful grass pollen and disease, with concomitant socio-economic benefits.

ecology↗