Biology subjects

Thorn, S.

Publications and source records attributed to Thorn, S..

14 recordsLinked to original sources

bioRxiv2026

Sample coverage standardization ranks species richness of saproxylic beetles across European tree genera

Aims In forest ecosystems, tree species composition and diversity are fundamental drivers of biodiversity and many species are closely associated to specific tree species as hosts. Saproxylic diversity across tree species may be shaped by interactions between ecological and environmental factors, such as resource availability. However, a throughout and unbiased quantification of diversity across tree species is missing. We investigated patterns an drivers of saproxylic beetle diversity across European tree genera while accounting for differences in sampling effort. Location Europe Methods We used a large dataset, of 25 studies, comprising 500,000 deadwood-dependent beetles, representing 1041 saproxylic beetle species, sampled from 29 tree genera. We accounted for sampling effort by estimating diversity using coverage-based standardization across Hill numbers. We than used linear models to identify drivers of saproxylic beetle diversity across tree genera and assessed differences in community composition using Nonmetric Multidimensional Scaling (NMDS). Additionally, the most abundant beetle families were identified for a subset of 14 genera. Results Quercus supported the highest richness of infrequent, frequent, and highly frequent species, while Fagus exhibited the highest observed (unstandardized) species richness. Beetle communities were less differentiated when focusing on infrequent species, whereas tree genera were separated when focusing on frequent and highly frequent species. In addition, we found that resource availability and maximum tree height best predicted infrequent beetle diversity, whereas resource availability was the main driver of frequent species. In contrast, the same analyses for unstandardized data indicated postglacial occurrence as an important factor for infrequent species. Main conclusions Although resource availability supported the species area hypothesis, standardized data revealed higher richness on smaller trees, partly contradicting this pattern. Our results highlight the importance of accounting for sampling bias and promoting tree diversity, particularly oaks, to sustain saproxylic beetle diversity.

ecology↗

bioRxiv2026

Whole genome sequencing of endometrial cancer identifies novel subgroups, drivers, and actionable alterations

Endometrial cancer (EC) is the most common gynaecological malignancy in high income countries, and is increasing in incidence. While molecular stratification has improved its management, precision care is hampered by incomplete characterization of the EC genome. We address this by analysis of whole genome sequencing (WGS) of 665 ECs generated by the UK Genomics England 100,000 Genome Project (100kGP). 5% of cases were associated with germline pathogenic variants in cancer genes, including BRCA1 which we confirmed predisposes to EC. We identified 107 putative coding driver genes, 35% of which had no prior established role in EC. Novel structural variants included gains of MYCN and loss of its negative regulator NEDD4.1 which were significantly mutually exclusive in copy number (CN) high tumours. Immunogenomic analysis confirmed selection for driver alterations of low immunogenicity based on patient HLA haplotype, and pervasive immune escape through multiple mechanisms. Unsupervised clustering of mutational signatures and genomic alterations identified known and novel molecular subgroups, including a CN-high subset with mutational signatures of homologous recombination deficiency (HRD) and favourable outcome. Independent prognostic value of single nucleotide variant (SNV) burden, CN burden and multiple coding drivers, along with the identification of targetable molecular alterations in over one-third of cases, underscores the promise of WGS for precision medicine in EC.

genomics↗

bioRxiv2026

DNA methylation signatures of mismatch repair-deficient colorectal cancer

BackgroundColorectal cancer (CRC) is a molecularly heterogeneous disease shaped by both genetic and epigenetic alterations. Approximately 15% of CRCs display widespread CpG island hypermethylation, known as the CpG Island Methylator Phenotype (CIMP). CIMP-high (CIMP-H) tumours frequently exhibit MLH1 promoter hypermethylation, leading to mismatch repair deficiency (MMRd) and microsatellite instability (MSI). However, DNA methylation patterns associated with MSI, independent of CIMP and MLH1 silencing, and the influence of clinical variables such as anatomical location and patient age on the CRC methylome remain poorly characterised. MethodsWe performed epigenome-wide DNA methylation profiling of 259 primary CRC tissue samples using the Illumina EPICv2 array, comparing differential methylation between MSI and microsatellite stable (MSS) CRC, adjusting for tumour purity, MLH1 promoter methylation, CIMP status, and anatomical location, to account for known confounders. We further evaluated the independent effects of anatomical location and patient age on global methylation patterns. ResultsEpigenome-wide differential methylation between MSS and MSI CRC was dominated by MLH1 promoter hypermethylation. After adjusting for MLH1 hypermethylation and CIMP status, we identified a distinct set of 656 CpG sites associated with MMRd independent of MLH1 silencing. These included hypermethylation at LRP6, GSK3{beta}, and CDK12, implicating altered WNT signalling and transcriptional regulation pathways. Comparison of MSI subgroups revealed the co-occurrence of MLH1 hypermethylation with promoter hypermethylation at TXNRD1. Anatomical location showed a strong independent effect on methylation patterns, while we observed only modest effects of patient age on the CRC methylome after adjustment for confounders. ConclusionsWe identified a distinct methylation profile distinguishing MSS and MSI CRC, including MLH1-independent markers of MMRd, as well as novel differentially methylated loci within MSI subgroups. We further showed that anatomical location has a strong independent impact on the CRC methylome. Together, these findings refine the molecular characterisation of CRC and highlight potential epigenetic markers that could inform patient stratification and precision oncology.

cancer biology↗

bioRxiv2026

Moisture reduces saproxylic bee, wasp, and parasitoid diversity in lying and standing deadwood

Saproxylic insect community assembly is structured by deadwood and forest habitat gradients, as well as biotic interactions such as competition, predation, and parasitism. However, co-variation between abiotic and biotic conditions limits our ability to disentangle their contributions. Furthermore, a focus on beetles in temperate and boreal forests has left important taxonomic and geographic knowledge gaps. Here, we tested how experimentally manipulated tree diversity, deadwood position (lying vs. standing), and biotic interactions with a dominant antagonist (ant exclusion) structure communities of deadwood-cavity-nesting bees, wasps, and their parasitoids in a subtropical forest. Lying deadwood supported less diverse and abundant communities than standing deadwood while retaining approximately twice as much moisture. Moreover, host emergence declined along moisture gradients within each deadwood type. Together, these patterns identify substrate moisture as an important factor limiting bee and wasp communities nesting in deadwood - reflecting reduced brood production, survival, or both - and as a candidate driver for their positive association with standing deadwood in forests. By contrast, neither ant exclusion nor observed ant occurrence was associated with host or parasitoid responses. Because standing deadwood is typically scarce in managed forests, our findings support retaining or creating standing deadwood structures alongside lying deadwood and, more broadly, promoting dry and elevated nesting substrates for cavity-nesting bees and wasps in conservation and restoration measures.

ecology↗

bioRxiv2026

DUCK-Net: Automated deep learning segmentation of Ductular Reaction in murine liver injury captures multicellular niche dynamics from H&E morphology

Ductular Reactions (DRs) are dynamic and complex multicellular responses that occur as a result of various hepatic injuries. Precise identification and quantification of the extent of DRs is a cornerstone of pre-clinical modelling of liver disease, with links to inflammation, fibrosis, regeneration, and disease severity. Here, we apply a deep learning model, Deep Understanding Convolutional Kernel or DUCK-Net, to the automated detection and segmentation of DRs in whole-slide histopathological images of murine models of liver damage. Following annotation of a training dataset by a specialist liver histopathologist, we demonstrate accelerated performance and accurate detection, achieving a mean Dice coefficient (model-expert segmentation overlap) of 85.4% and a specificity of 98%, indicating minimal false positives. Evaluation of model validity and utility was achieved with a histological time course of cholestatic injury and recovery using 3,5-Diethoxycarbonyl-1,4-Dihydrocollidine diet (DDC) in mice. When assessed against a multiple linear regression model incorporating core epithelial and stromal components of the DR as quantified using IHC, DUCK-Net predicted the spatiotemporal response to injury and repair/resolution with a coefficient of determination (R2) of 0.88. Moreover, DUCK-Net kinetics strongly correlated with published spatial transcriptomic (Stereo-seq) analysis of the DDC model, demonstrating that H&E-based segmentation captures molecular DR dynamics comparable to, or exceeding that of individual IHC markers without the need for immunostaining. DUCK-Net provides a novel and accessible platform for rapid, accurate histological quantification of liver injury reflective of the matrix-rich, multicellular regenerative niche observed in DRs.

cell biology↗

bioRxiv2026

Reforestation under climate change - a cross-regional deadwood retention experiment to develop multifunctional forests on disturbed Norway spruce areas

The impact of extreme weather events such as droughts, heatwaves, storms and the associated intensification of bark beetle outbreaks in Norway spruce forests in recent years, has led to a large-scale forest loss in Central Europe. There are various options for post-disturbance management, from complete clearing to no intervention, but their pros and cons - in the context of multifunctional forest management - are not resolved. The "ResEt-Fi" project ("Pioneering reforestation: Regional management for establishing multifunctional forests on post-disturbed Norway spruce areas") consortium implemented a cross-regional field trial to test how specific practices of deadwood retention affect the ecological conditions and subsequent reforestation dynamics of natural regeneration and planted trees. It aims at generating climate-stable mixed forests within an ecological valuable transition, balancing ecosystem functioning and socio-economic benefits. As an outcome for stakeholders and forest practitioners, guidelines and showcase scenarios for facilitating the selection of management procedures will be created. In this article, we provide insight into (i) the applied post-disturbance deadwood management practices and the rationale for their selection, (ii) the experimental setup of our cross-regional field trial, (iii) the initial post-disturbance status and perspective with respect to regional site conditions and deadwood treatment. While the setup and site conditions will primarily serve as a reference for subsequent studies in our joint project, this is the first systematic, cross-regional study on the effects of the management options standing deadwood, high stumps and clearing on microclimate, biodiversity, and tree regeneration in the critical early stages of forest regeneration after disturbance.

ecology↗

bioRxiv2025

From forest decline to salvage logging: cascading impacts on saproxylic beetle diversity

Understanding the cascading effects of forest decline on saproxylic communities is fundamental for optimizing the management of disturbed forests toward biodiversity conservation objectives. We postulated that the nature and intensity of cascading pathways would vary along decline gradients, encompassing stages from stand decline to mortality and subsequent salvage logging, as mediated by shifts in habitat conditions and resource availability. This study was conducted across three representative European forest contexts: fir forests in the French Pyrenees, spruce forests in the Bavarian Alps, and oak forests in the lowlands of the Loire Valley. Within these systems, we assessed how the taxonomic and functional -diversity of saproxylic beetles responded to variations in both the diversity and density of deadwood and tree-related microhabitats (TreMs). Our analyses identified key cascading effects of stand decline and mortality that were shaped by the considered beetle guild and by the forest type, reflecting tree species-specific disturbance legacies. Stand decline and mortality produced distinct responses within saproxylic beetle assemblages, as different successional guilds preferentially utilized either dying or dead trees. The overall influence of decline processes was positive in conifer-dominated forests. TreMs played a central role in mediating cascading processes structuring saproxylic beetle communities throughout the forest decline continuum. The increase in TreM heterogeneity associated with stand decline or mortality enhanced saproxylic diversity, with exposed wood and trunk injuries identified as particularly influential microhabitats. Snags and large deadwood elements, especially in spruce forests, and deadwood diversity further contributed to sustaining high levels of beetle diversity. Conversely, salvage logging exerted detrimental effects on numerous guilds, primarily through reductions in TreM diversity, decreased TreM trait dispersion, and the depletion of saproxylic TreMs. Given the pronounced context dependency of the processes driving these cascading community dynamics, and considering the increasing frequency, severity, and spatial extent of forest disturbances and global forest decline, it is imperative to integrate this complexity into management and conservation frameworks. Addressing these mechanisms with greater precision will be critical for maintaining functional biodiversity within rapidly changing forest ecosystems.

ecology↗

bioRxiv2025

Old growth attributes by chain saw: how between-patch heterogeneity changes the metacommunities of beetles in temperate forests

Metacommunity theory has expanded our understanding of how spatial dynamics and local interactions influence species communities. Different assembly archetypes, reflecting different roles of species differences, habitat differences, and dispersal have been described, but we lack empirical studies specifically in terrestrial habitats testing which archetype is most important. In a replicated design we experimentally enhanced structural between-patch heterogeneity in homogeneous production forests and developed a statistical framework controlling for sample incompleteness to detect different metacommunity processes. Meta-analyses on >100K individuals of >1.3K beetle species showed an increase of [~]60 species in heterogenized forests at {gamma}-level promoted by increasing -diversity consistent with the mass-effect and an increase of {beta}-diversity by [~]10% supporting species-sorting. Additionally, we tested {beta}-deviations from random assembly as a proxy of neutral processes. Findings indicate that enhancing structural heterogeneity can shift forests from patch-dynamics dominance towards mass-effect and species-sorting, offering a promising pathway to restore biodiversity in managed landscapes.

ecology↗

bioRxiv2025

The potential role of volatile organic compounds on the colonisation of deadwood by saproxylic beetles

Volatile organic compounds (VOCs) emitted by deadwood are increasingly recognised as key olfactory cues used by saproxylic beetles to locate suitable substrates. However, how beetle communities respond to these cues during the colonisation of deadwood remains poorly understood. To address this gap, it is essential to quantify both VOC emissions and beetle assemblages, and to experimentally disentangle the main ecological drivers of the deadwood volatilome (i.e., tree species, sun exposure). To explore the potential role of VOCs on saproxylic beetle colonisation, we exposed 1200 freshly cut branches of oak, beech, spruce, and pine across Central Europe. To mimic natural variation in deadwood and disturbance processes, the bundles were experimentally manipulated either by sterilisation (to reduce endogenous fungi), fungal inoculation with a brown rot fungus (Fomitopsis pinicola), a white rot fungus (Fomes fomentarius), or burning. From each deadwood bundle, we sampled 448 substances, 89 of which were identified as VOCs and reared 134 saproxylic beetle species. We observed distinct VOC profiles emitted by broadleaf and conifer species, aligning with the beetles tree-type preferences. In conifers, bark beetles, longhorn beetles, and jewel beetles were associated with different chemical cues, whereas beetle taxonomic separation was not observed in broadleaf species. Although experimental treatments altered VOC composition, they could not explain beetle colonisation patterns. Our study highlights that VOCs emitted during the early decay stage of deadwood are associated with distinct saproxylic beetle assemblages. VOC composition varied across tree species and treatments, suggesting that chemical variation reflects multiple ecological factors. These findings indicate that deadwood diversity, particularly in tree species, contributes to chemical heterogeneity, which is linked to broader beetle assemblages. Forest conservation efforts may therefore need to consider the role of chemical variation in deadwood, as it could influence colonisation patterns of saproxylic beetles and affect the success of biodiversity management strategies.

ecology↗

bioRxiv2025

Higher bat and bird γ-diversity in structurally complex forests is driven by distinct α- and β-diversity responses

Effective conservation management and habitat restoration rely on understanding how biodiversity responds to environmental change. Centuries of silviculture have homogenized forests and their species communities globally, reducing biodiversity. To test whether restoring forest structural complexity can promote biodiversity, we conducted a large-scale, spatially explicit landscape experiment. At 11 sites across Germany, we compared bat and bird diversity in forests with experimentally enhanced heterogeneity by increasing deadwood and canopy complexity to homogeneous production forests. Both taxa were investigated by autonomous acoustic recorders and automatic species identification. We quantified within-patch (-), between-patch ({beta}-), and landscape-level ({gamma}-) diversity, emphasizing infrequent to highly frequent species for taxonomic, functional, and phylogenetic diversity. The pairwise comparisons of the sites were synthesized using a newly developed meta-analysis of rarefaction-extrapolation curves. {gamma}-diversity increased significantly in structurally heterogeneous forests for both taxa, albeit through distinct taxon-specific mechanisms. Bat {gamma}-diversity gains were primarily driven by higher {beta}-diversity, indicating greater dissimilarity in species assemblages among patches, while bird {gamma}-diversity increased via higher -diversity within patches. Bat diversity increases were mainly taxonomic, suggesting functional similarity in the communities, whereas birds showed the highest gains in functional diversity, indicating that experimental treatments resulted in greater trait dissimilarity. Our results provide experimental evidence under real-world conditions that {gamma}-diversity can be shaped by different diversity mechanisms. These patterns likely originate from differences in activity ranges, such as the large-scale movements of foraging bats in contrast to the more spatially restricted, territorial behavior of birds. This highlights the need for taxon-specific restoration strategies in homogenized landscapes.

ecology↗

bioRxiv2025

A continuum of information-based temporal stability measures and their decomposition across hierarchical levels

When biodiversity-stability relationships are assessed from temporal patterns of species (or species assemblages) biomass or other key variables, ecological stability is commonly quantified as the inverse of the coefficient of variation (CV) or its square. However, just as biodiversity cannot be fully characterized by a single value, the complexity of temporal stability/invariability cannot be completely captured by one metric, especially since CV is disproportionally sensitive to large data values. Ecologists now recognize that species diversity can be fully characterized by a continuum of Hill-number-based measures parametrized by a diversity order q[≥]0, which determines the sensitivity of the measure to species abundance. Building on the intuitive concept that temporal stability can be quantified by the closeness between the data vector and the ideally maximally stable vector, we propose a continuum of information-based measures of temporal stability/invariability parameterized by an order q>0. This continuous parameter q determines the sensitivity of the measure to the magnitude of biomass or other ecosystem functions. By varying q, researchers can differentially weight small, medium, or large values in a time series, thereby disentangling their respective contributions to stability. Our framework unifies and generalizes classical measures: the case q=1 links to Shannon entropy, reflecting MacArthurs 1955 stability concept; q=2 connects to the conventional CV-based measure. Unlike these traditional metrics, our approach explicitly accounts for the number of data values (i.e., time points), adjusting for time-series-length effects to enable fair and meaningful comparisons across datasets of varying lengths. We extend the framework to hierarchical structures by developing additive and multiplicative decompositions of stability in a metacommunity (or metapopulation) into alpha and beta components. The beta component can be further used to obtain measures that quantify (a)synchrony among communities (or populations). For q=2, the resulting (a)synchrony measure provides a mathematically rigorous, CV-based metric. The proposed measures are illustrated using 22-year biomass time series data from the Jena Experiment in Germany. We developed the R package iSTAY (information-based stability measures) and online tools for computation and visualization. Our measures are adaptable to other functions beyond biomass and are applicable in both temporal and spatial contexts. Open Research StatementThe original biomass data of the Jena Experiment, covering the years 2003 to 2023, can be retrieved from https://jexis.idiv.de/ddm/Data/ShowData/624, while the 2024 data are available at https://jexis.idiv.de/ddm/Data/ShowData/695. These datasets, along with the R code used in this study, are currently accessible on Github at https://github.com/AnneChao/MS_iSTAY for review purposes and will be archived on Zenodo upon journal acceptance.

ecology↗

bioRxiv2022

Whole genome sequencing of 2,023 colorectal cancers reveals mutational landscapes, new driver genes and immune interactions

To characterise the somatic alterations in colorectal cancer (CRC), we conducted whole-genome sequencing analysis of 2,023 tumours. We provide the most detailed high-resolution map to date of somatic mutations in CRC, and demonstrate associations with clinicopathological features, in particular location in the large bowel. We refined the mutational processes and signatures acting in colorectal tumorigenesis. In analyses across the sample set or restricted to molecular subtypes, we identified 185 CRC driver genes, of which 117 were previously unreported. New drivers acted in various molecular pathways, including Wnt (CTNND1, AXIN1, TCF3), TGF-{beta}/BMP (TGFBR1) and MAP kinase (RASGRF1, RASA1, RAF1, and several MAP2K and MAP3K loci). Non-coding drivers included intronic neo-splice site alterations in APC and SMAD4. Whilst there was evidence of an excess of mutations in functionally active regions of the non-coding genome, no specific drivers were called with high confidence. Novel recurrent copy number changes included deletions of PIK3R1 and PWRN1, as well as amplification of CCND3 and NEDD9. Putative driver structural variants included BRD4 and SOX9 regulatory elements, and ACVR2A and ANKRD11 hotspot deletions. The frequencies of many driver mutations, including somatic Wnt and Ras pathway variants, showed a gradient along the colorectum. The Pks-pathogenic E. coli signature and TP53 mutations were primarily associated with rectal cancer. A set of unreported immune escape driver genes was found, primarily in hypermutated CRCs, most of which showed evidence of genetic evasion of the anti-cancer immune response. About 25% of cancers had a potentially actionable mutation for a known therapy. Thirty-three of the new driver genes were predicted to be essential, 17 possessed a druggable structure, and nine had a bioactive compound available. Our findings provide further insight into the genetics and biology of CRC, especially tumour subtypes defined by genomic instability or clinicopathological features.

genomics↗

bioRxiv2021

Performance of genetic imputation across commercial crop species

We show that accurate imputation can be carried out in three commercial plant species (maize, sugar beet and wheat) and that accurate imputation does not require a pedigree, although pedigree information can improve accuracy and speed. Our approach uses a hidden Markov model to build a haplotype library from individuals genotyped at high-density and then uses this library to impute low-density genotyped individuals to high-density. To build the library, we use founders when the pedigree is known, or a sample of progeny when the pedigree is unknown. Without a pedigree, and with 50 individuals genotyped at high-density and 100 low-density markers per chromosome, the median accuracies were 0.97 (maize), 0.96 (sugar beet), and 0.94 (wheat). We obtained similar accuracies with a pedigree. For biparental crosses with 100 markers per chromosome, median accuracies were 0.96 (maize), 0.96 (sugar beet) and 0.94 (wheat). For the imputation scenarios without a pedigree, we compared accuracies with those obtained by running Beagle 5.1. In all but one scenario, our method outperformed Beagle. We believe that plant breeders can effectively apply imputation in many crop species.

genetics↗

bioRxiv2021

Climate-induced forest dieback drives compositional change in insect communities that is concentrated amongst rare species

Marked decline in insect species richness, abundance and biomass have recently been quantified in Europe. We metabarcoded 224 Malaise-trap samples to investigate whether drought-induced forest dieback and subsequent salvage logging have an impact on flying insects (ca. 3000 insect species) in silver fir Pyrenean forests. We found no evidence that climate-induced forest dieback impacted species richness of flying insects but revealed compositional turnover patterns consistent with those seen during natural forest succession, given that the key covariates explaining compositional variation were canopy openness versus microhabitat diversity and deadwood amount at local and landscape scales, respectively. Importantly, most change was driven by rare species. In contrast, observed levels of salvage logging did not explain change in species richness or composition. Hence, although forest dieback appears to cause changes in species assemblages mimicking natural forest succession, it also increases the risk of catastrophic loss of rare species through homogenization of environmental conditions.

ecology↗