Biology subjects

Adams, C. E.

Publications and source records attributed to Adams, C. E..

8 recordsLinked to original sources

bioRxiv2026

The PSInet Plant Water Potential Database: advancing new perspectives on plant water status, traits, and hydraulic processes

Water potential gradients drive water flow within and between soils and plants, and the internal plant water potential controls a wide range of physiological processes including photosynthesis, growth, and mortality. Notwithstanding this clear relevance for many critical aspects of ecosystem function, water potential data have historically been relatively inaccessible and unnetworked. The absence of a centralized repository for plant water potential time series limits our ability to integrate a wealth of ecophysiological information from other networks and from remote sensing. Closing this gap is necessary to address unresolved questions about plant responses to drought and heat stress, and to make confident predictions about plant and ecosystem function in a warming world. Here, we introduce the PSInet database -- a global collection of plant water potential time series from 285 datasets representing 523 species. We present the workflow that guided database development and evaluate its key features. Through a series of preliminary analyses, we then highlight the potential of the PSInet database for applications including: a) advancing plant water use strategy frameworks; b) disentangling the impacts of soil versus atmospheric drought stress; c) assessing the long-held assumption of pre-dawn equilibration of ecosystem water potential; d) understanding the risk of drought-driven mortality; and e) benchmarking remote-sensing data products and land-surface models.

plant biology↗

bioRxiv2025

Scale dependent temporal and spatial patterns of population change in anadromous sea trout (Salmo trutta) in Scotland over seven decades

The spatial scale at which temporal change in a population is measured has the potential to skew the inferences drawn on patterns of change from monitoring data. This study analysed data from rod catches of anadromous sea trout (Salmo trutta) in Scotland over a period of 72 years and over three spatial scales (National, Regional and District). The pattern of temporal change evident at the national scale mostly did not clearly manifest at Regional or at District spatial scales; which were also generally decoupled (67% of Regions and 80% of Districts exhibited a different pattern from the National pattern). At the National level, very clear and substantive declines over the study period were evident. At Regional levels (N=9) change in rod catches was more nuanced with some Regions showing no change, one Region showing an increase in sea trout caught and 6 (67%) exhibited a different pattern from the National one. At the District levels (N=64) opposing patterns of change were observed over the study period, even in adjacent Districts with 80% of Districts exhibiting a different pattern from the National one. A conclusion of this study is that, as a national resource, sea trout numbers have declined substantively over the last seven decades (by around 50%). However, this general picture is not applicable across all geographic Regions nor all Districts. Two logical inferences derive from these results. Firstly, for best effect, the application of limited resources for management should be focused at smaller scales than at countrywide. Secondly, that monitoring population change at small spatial scales, for example in several index rivers, is unlikely to capture the highly nuanced patterns of change in species with high levels of intra-specific structuring as is commonly exhibited by the Salmonidae.

ecology↗

bioRxiv2025

The historical patterns that have shaped contemporary genetic differentiation across populations of Arctic charr in Scotland

Glacial history is an important contributor to contemporary biogeographic patterns because it caused population fragmentation and consequently diversification. The Arctic charr (Salvelinus alpinus) is a highly diverse non-anadromous salmonid fish species in Britain and Ireland, which likely was anadromous when it colonised around the end of the last ice age. Colonisation history of the species remains largely unexplored and so the potential impact on contemporary patterns of genetic differentiation remains unclear. To address this, we conducted a national-scale genetic study of Arctic charr using a genome-wide dataset of SNPs (24,878 SNPs and 410 individuals) and mitochondrial ND1 sequences (238 sequences). We found several mitochondrial haplotypes were shared across Britain, Ireland, and the wider Holarctic suggesting colonisation by multiple sub-lineages of the Atlantic lineage of the species. Genetic differentiation was not correlated with geographic distance among river catchments, highlighting the effect of spatial isolation and genetic drift. Several populations across different river catchments showed atypical ancestries and evidence for genetic mixing, which we speculate are due to asynchronous ice coverage and the presence of ice-dammed lakes. Our results highlight how glacial history can impact colonisation history and subsequently contemporary patterns of genetic differentiation in this widespread species.

genetics↗

bioRxiv2025

Tissue resident colonic macrophages persist through acute inflammation and adapt to aid tissue repair

Macrophages are crucial for the maintenance of intestinal homeostasis, are considered key proinflammatory effector cells during intestinal inflammation and are implicated in tissue repair following injury or inflammation. Whether these roles are attributed to distinct subsets of macrophages or if macrophages retain a degree of plasticity in the intestine remains poorly understood. Here, through a combination of single cell RNA sequencing, lineage-tracing and immunofluorescence imaging, we define three major subpopulations of murine, colonic macrophages on the basis of CD11c and CD163 expression. These macrophages occupy discrete anatomical niches and display distinct replenishment kinetics. They all accumulate during acute colitis and Cx3cr1-based fate mapping shows that they persist through to inflammation resolution. Moreover, marked transcriptional differences exist between the macrophages present in health and their counterparts in the post-inflammation environment, demonstrating that inflammation leads to transcriptional rewiring of the resident macrophages in a subset-specific manner. Intriguingly, there were minimal transcriptional changes between long-lived macrophages and their recently differentiated counterparts, indicating the environment exerted a greater influence than ontogeny or the time of residency on their functional states in resolution.

immunology↗

bioRxiv2025

Loss of HMGCS2-mediated intestinal stem cell ketogenesis is a metabolic barrier to mucosal healing in Ulcerative colitis

Human colonic epithelial cells express high levels of 3-Hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2), the crucial mitochondrial enzyme responsible for the production ketone bodies, predominantly beta-hydroxybutyrate ({beta}HB). Ketogenesis is an important metabolic pathway responsible for energy production in states of fasting and in the intestine ketone bodies are also important in regulating intestinal stem cell (ISC) homeostasis and regeneration. Using combined single-cell and spatial transcriptomics, organoids and prospective longitudinal mucosal analysis, we demonstrated a profound loss of ISC HMGCS2-mediated ketogenesis with consequential detrimental effect on Ulcerative colitis (UC), a chronic inflammatory bowel disease that affects [~]4 million individuals worldwide. We show that {beta}HB restores UC ISC metabolic function, reduces cellular stress with further evidence of epigenetic programming key for restoration of ISC function. Furthermore, low colonic HMGCS2 expression is associated with treatment failure of multiple biological immune therapies in UC. Our findings reveal the crucial role for HMGCS2 and loss of ketogenesis as the tipping point for pathogenic epithelial dysfunction and importantly, a promising metabolic therapeutic target for UC.

cell biology↗

bioRxiv2025

Defining conservation units in a highly diverse species: A case on Arctic charr

Defining appropriate conservation units is crucial to the protection and management of biodiversity. These delineations deliver further benefit when they include assessments of population vulnerability to extinction from pressures such as climate change. However, delineations and vulnerability assessments are particularly difficult within highly diverse species, such as the salmonid fish Arctic charr (Salvelinus alpinus), that show extensive phenotypic and genetic variation within and across locations, variable and complex life histories, and broad geographic distributions. As yet, the nature and scope of Arctic charr diversity has not been characterised at the scale needed to delineate key conservation units in Scotland. To identify evolutionarily significant and vulnerable populations to prioritise for conservation, we conducted a genomic study of Arctic charr populations across Britain and Ireland with a focus on Scottish populations (N=64 populations; 24,878 SNPs; 410 individuals). We found that most lake populations represented distinct genetic clusters, with limited gene flow between them and resulting in substantial genetic differentiation. Higher level groupings of genetic similarity across catchments likely reflect historic anadromy and migration, with populations primarily grouping east or west of the central watershed divide in Scotland. Analysing genetic offset, also known as genomic vulnerability, we identified strong inverse correlations between genetic vulnerability with latitude and distance to the sea suggesting that more southern and more inland populations are more vulnerable to loss due to climate change. Additionally, patterns of vulnerability across several additional metrics identified further populations that may be at high vulnerability to loss. We further used our genetic data, along with phenotypic and geographic information, to identify populations of greatest evolutionary significance. This highlighted the most important ones to protect are those in locations with multiple ecotypes, a key facet of functional Arctic charr biodiversity, and populations that are the only ones in their Hydrometric Area.

genomics↗

bioRxiv2023

Individual genotype but not phenotype predicts river migration success in Atlantic salmon

Migratory species typically undertake demanding long-distance journeys, across different habitat types during which they are exposed to multiple natural and anthropogenic stressors. Mortality during migration is typically high, and may be exacerbated by human-induced pressures. Understanding individual responses to these selection pressures is rarely attempted, because of the challenges of relating individual phenotypic and genetic data to migration success. Here we show distinct Single Nucleotide Polymorphism (SNP) sets significantly differentiated between Atlantic salmon smolts making successful migrations to sea and those that failed to migrate, in two different rivers. In contrast, morphological variation was not diagnostic of migration success. Populations from each river were genetically distinct, and while different genes were possibly implicated in migration success in each river, they related to common biological processes (for example osmoregulation and immune and stress response). Given that migration failure should quickly purge polymorphism at selected SNPs from a population, the question of how genetic diversity in these populations is maintained is an important one. Standing genetic variation could be maintained by different life history strategies and/or environmentally driven balancing selection. Our work highlights the importance of preserving genetic diversity to ensure evolutionary resilience at the population level, and has practical implications for management.

evolutionary biology↗

bioRxiv2022

Is shape in the eye of the beholder? The reproducibility of geometric morphometric analyses on live animals

Geometric morphometrics is widely used to quantify morphological variation between biological specimens, but the fundamental influence of operator bias on data reproducibility is rarely considered, particularly in studies using photographs of live animals taken under field conditions. We examined this using four independent operators that applied an identical landmarking scheme to replicate photographs of 291 live Atlantic salmon (Salmo salar L.) from two rivers. Using repeated measures tests, we found significant inter-operator differences in mean body shape, suggesting that the operators introduced a systematic error despite following the same landmarking scheme. No significant differences were detected when the landmarking process was repeated by the same operator on a random subset of photographs. Importantly, in spite of significant operator bias, small but statistically significant morphological differences between fish from the two rivers were found consistently by all operators. Pairwise tests of angles of vectors of shape change showed that these between-river differences in body shape were analogous across operator datasets, suggesting a general reproducibility of findings obtained by geometric morphometric studies. In contrast, merging landmark data when fish from each river are digitised by different operators had a significant impact on downstream analyses, highlighting an intrinsic risk of bias. Overall, we show that, even when significant inter-operator error is introduced during digitisation, following an identical landmarking scheme can identify morphological differences between populations. This study indicates that operators digitising at least a sub-set of all data groups of interest may be an effective way of mitigating inter-operator error and potentially enabling data sharing.

zoology↗