Biology subjects

Schmucki, R.

Publications and source records attributed to Schmucki, R..

10 recordsLinked to original sources

bioRxiv2025

The interplay of climate change, urbanization, and species traits shapes European butterfly population trends

Species populations naturally fluctuate, yet long-term trend analysis can reveal patterns of success, decline, or stability under global change pressures. While responses to climate change are well-documented, its synergy with another major global driver, urbanization, remains understudied. Here, we analyzed long-term monitoring data from over 8,400 populations of 145 butterfly species across Europe, representing a high diversity of species traits, to assess population trends in response to climate change and urbanization. We examined how population responses vary between urban and rural contexts, providing insights into the influence of site-specific conditions. Climate warming was associated with population declines, which were more pronounced in urban areas. The effect of precipitation varied between environments: increases in precipitation generally benefited populations in rural areas but had detrimental effects in urban ones. Aridity consistently drove population declines across environments, with slightly stronger effects in urban areas. Species with colder climatic niches declined the most in response to warming, increased aridity, and reduced precipitation, while trophic specialists were particularly vulnerable to aridity and precipitation changes in urban environments. Although increasing urbanization did not explain overall population trends, its effects became evident when considering species traits, with certain traits being more vulnerable to urbanization. Specifically, species with narrow climatic niches declined the most in response to urbanization in rural areas, while those and larger body sizes decline the most in urban environments. Our findings highlight the complex interplay between environmental change, landscape context, and species traits in shaping biodiversity outcomes. Importantly, our results suggest that urbanization generally amplifies the impact of climate change on insect population trends.

ecology↗

bioRxiv2024

A CRISPR/Cas9 screen reveals proteins at the endosome-Golgi interface that modulate cellular ASO activity

Anti-sense oligonucleotides (ASOs) are modified synthetic single-stranded molecules with enhanced stability, activity, and bioavailability. They associate with RNA through sequence complementarity and can reduce or alter mRNA expression upon binding of splice site positions. To target RNA in the nucleus or cytoplasm, ASOs must cross membranes, a poorly understood process. We have performed an unbiased CRISPR/Cas9 knockout screen with a genetic splice reporter to identify genes that can increase or decrease ASOs activity, resulting in the most comprehensive catalog of ASOs-activity modifier genes. Distinct targets were uncovered, including AP1M1 and TBC1D23, linking ASOs activity to transport of cargo between the Golgi and endosomes. AP1M1 absence strongly increased ASO activity by delaying endosome-to-lysosome transport in vitro and in vivo. Prolonged ASOs residence time in the endosomal system may increase the likelihood of ASOs escape from this organelle before they reach lysosomes. This insight into AP1M1 role in ASOs trafficking suggests a way for enhancing the therapeutic efficacy of ASOs by manipulating the endolysosomal pathways.

cell biology↗

bioRxiv2024

Modelling the spatiotemporal dynamics of multispecies population interactions in the context of climate change

O_LISpecies interactions are fundamental to the stability and productivity of ecosystems. To improve our capacity to predict and understand how climate change shapes the distribution of species and the dynamics of biotic interactions, we need to develop spatially explicit multi-species models that are built upon species-specific responses to changing conditions. C_LIO_LIWe developed a two-dimensional diffusion-advection-reaction predator-prey model that integrates species-specific responses to heterogeneous landscapes, affecting species dispersal, reproduction and survival rates. We derived conditions for the stability and feasibility of the coexistence steady-state and observed how temperature variation stabilises or destabilises the system. C_LIO_LIWe conducted numerical simulations to explore the effect of predicted extreme temperatures on the spatial dynamics of a parasitoid-butterfly system and their interactions. Applied to four different climatic environments, the numerical approximations demonstrate the asymmetric impact of a warming climate on interacting species. The output density distribution maps highlight the capability of our model to produce interpretable multiscale predictions which can be used to identify and evaluate species vulnerability locally and across their range. C_LIO_LIBy building upon a solid mechanistic understanding of species-specific responses to environmental change, our model can be extended to other species and variables, including environments where the availability of empirical data is limited, and explore the dynamics and distribution of interacting species under different scenarios of environmental change. C_LI

ecology↗

bioRxiv2023

splicekit: a comprehensive toolkit for splicing analysis from short-read RNA-seq

MotivationAnalysis of alternative splicing using short-read RNA-seq data is a complex process that involves several steps: alignment of reads to the reference genome, identification of alternatively spliced features, motif discovery, analysis of RNA-protein binding near donor and acceptor splice sites, and exploratory data visualization. ResultsWe introduce splicekit, a python package that provides a comprehensive set of tools for conducting splicing analysis. Availability and implementationhttps://github.com/bedapub/splicekit and over PyPI.

bioinformatics↗

bioRxiv2020

Combined effect of crop rotation and carabid beetles on weed dynamics in arable fields

Weed management is a resource-intensive practice in arable agriculture, with direct and long-term impacts on both productivity and biodiversity (e.g. plant, pollinators and farmland wildlife). In conventional systems, weed control relies on crop management and herbicide inputs, but for more sustainable production systems, use of herbicides needs to be reduced. This requires a good understanding of the processes that regulate arable weed dynamics in arable fields. We adopted a systems framework to understand and model interacting components that drive the weed dynamics in 168 arable fields. Within this framework, we built a structural equation model (SEM) to quantify the direct and indirect effects of crop rotation (i.e. crops in the previous three years and the current year) and carabid beetles (Coleoptera: Carabidae) on weed density, seed abundance and accumulation in the seedbank. We included results from a mechanistic approach to infer interactions between seed-feeding carabid beetles and seeds to estimate predation pressure in each field. Our results show that weeds in arable fields are regulated by crop type, sowing season, and activity density of carabid beetles. We found a direct effect of crop rotation, including both past and current field management practice, on weed abundance in the field and its seedbank. There was also an indirect effect of crops on weed seed accumulation in the seedbank via the effect of seed-eating carabid beetles. The efficiency of weed control by carabid beetles depended on the cumulative predation pressure, which indicates the importance of functional diversity as well as abundance. Farmers and agronomists can capitalise on the ecosystem services provided by carabid beetles by adapting agronomic practices and crop rotation to maintain a rich fauna of seed-eating carabids in fields and potentially across the agricultural landscapes. When integrated with rotational management practices, this ecosystem services can improve the efficiency of weed management and contribute to the sustainability of cropping systems.

ecology↗

bioRxiv2020

Inferring species interactions from ecological survey data: a mechanistic approach to predict quantitative food webs of seed-feeding by carabid beetles

O_LIEcological networks are valuable for ecosystem analysis but their use is often limited by a lack of data because many types of ecological interaction, e.g. predation, are short-lived and difficult to observe or detect. There are different methods for inferring the presence of interactions, which we lack methods to predict interaction strengths and so use weighted network analysis. C_LIO_LIHere, we develop a trait-based approach suitable for creating quantitative networks, i.e. with varying interaction strengths. We developed the method for seed-feeding carabid ground beetles (Coleoptera: Carabidae) although the principles can be applied to other interactions. C_LIO_LIWe used existing literature data from experimental seed-feeding trials to predict a per-individual interaction cost index based on carabid and seed size with frequency-dependent prey selection and assuming bottom up control. This was scaled up to the population level to create predicted inferred weighted networks using the abundance of carabids and seeds in samples from arable fields and energetic intake rates of carabids from the literature. From these weighted networks, we also calculated a novel measure of predation pressure. C_LIO_LIWe applied it to existing ecological survey data from 255 arable fields with carabid data from pitfall traps and plant seeds from seed rain traps. Analysis of these inferred networks led to testable hypotheses about how networks and predation pressure varied amongst fields. C_LIO_LIInferred networks are valuable because (i) they provide null models for the structuring of food webs to test against empirical species interaction data, e.g. DNA analysis of carabid gut regurgitates, and (ii) they allow weighted inferred networks to be constructed whenever we can estimate interactions between species and have ecological census data available. This would permit network analysis even at times and in places when interactions were not directly assessed. C_LI

ecology↗

bioRxiv2020

Besca, a single-cell transcriptomics analysis toolkit to accelerate translational research

Single-cell RNA sequencing (scRNA-seq) revolutionised our understanding of disease biology and presented the promise of transforming translational research. We developed Besca, a toolkit that streamlines scRNA-seq analyses according to current best practices. A standard workflow covers quality control, filtering, and clustering. Two complementary Besca modules, utilizing hierarchical cell signatures or supervised machine learning, automate cell annotation and provide harmonised nomenclatures across studies. Subsequently, Besca enables estimation of cell type proportions in bulk transcriptomics studies. Using multiple heterogeneous scRNA-seq datasets we show how Besca aids acceleration, interoperability, reusability, and interpretability of scRNA-seq data analysis, crucial aspects in translational research and beyond.

bioinformatics↗

bioRxiv2020

Ecology and population genetics of the parasitoid Phobocampe confusa (Hymenoptera: Ichneumonidae) in relation to its hosts, Aglais species (Lepidoptera: Numphalidae).

The biology of parasitoids in natural ecosystems remain very poorly studied, while they are key species for their functioning. Here we focused on Phobocampe confusa, a vanessines specialist, responsible for high mortality rates in very emblematic butterfly species in Europe (genus Aglais). We studied its ecology and genetic structure in connection with those of its host butterflies in Sweden. To this aim, we gathered data from 428 P. confusa individuals reared from 6094 butterfly larvae (of A. urticae, A. io and in two occasions of Araschnia levana) collected over two years (2017 and 2018) and 19 sites distributed along a 500 km latitudinal gradient. We found that P. confusa is widely distributed along the latitudinal gradient. Its distribution is constrained over time by the phenology of its hosts. The large variation in climatic conditions between sampling years explains the decrease in phenological overlap between P. confusa and its hosts in 2018 and the 33.5% decrease in the number of butterfly larvae infected. At least in this study, P. confusa seems to favour A. urticae as host: while it parasitized nests of A. urticae and A. io equally, the proportion of larvae is significantly higher for A. urticae. At the landscape scale, P. confusa is almost exclusively found in vegetated open land and near deciduous forests, whereas artificial habitats are negatively correlated with the likelihood of a nest to be parasitized. The genetic analyses on 89 adult P. confusa and 87 adult A. urticae using COI and AFLP markers reveal a low genetic diversity in P. confusa and a lack of population genetic structure in both species, at the scale of our sampling. Further genetic studies using high-resolution genomics tools will be required to better understand the population genetic structure of P. confusa, its biotic interactions with its hosts, and ultimately the stability and the functioning of natural ecosystems.Competing Interest StatementThe authors have declared no competing interest.View Full Text

zoology↗

bioRxiv2020

Altered parasitism of a butterfly assemblage associated with a range-expanding species

AimBiotic interactions are an important factor structuring ecological communities but data scarcity limits our understanding of the impact of their response to climate and land use changes on communities. We studied the impact of a change in species assemblage on biotic interactions in a community of closely-related butterflies. Specifically, we examined the impact of the recent range expansion of Araschnia levana on the resident species, with a particular focus on natural enemies, parasitoids, shared with other butterfly species in the assemblage. LocationSweden. Time periodTwo years (2017-2018). Major taxa studiedNettle-feeding butterflies (Aglais urticae, Aglais io, Araschnia levana, and Vanessa atalanta) and their parasitoids. MethodsWe assessed parasitism in 6777 butterfly larvae sampled in the field from 19 sites distributed along a 500 km latitudinal gradient, and every two weeks throughout species reproductive seasons. We identified the parasitoid complex of each butterfly species and their overlap, and analysed how parasitism rates were affected by species assemblage, variations in abundance, time, and the arrival of A. levana. ResultsParasitoids caused high mortality, with substantial overlap across the four host species. The composition of the host community influenced parasitism rates and this effect was specific to each species. In particular, the rate of parasitism in resident species was comparatively higher at sites where A. levana has been established for longer. Main conclusionsParasitoid pressure is a significant source of mortality in the nettle-feeding butterfly community studied. Variations in butterfly species assemblages are associated with substantial variations in rates of parasitism. This is likely to affect the population dynamics of their butterfly host species, and, potentially, the larger number of species with which they interact.

ecology↗

bioRxiv2017

Draft genome of the Heterotardigrade Milnesium tardigradum sheds light on ecdysozoan evolution

Tardigrades are among the most stress tolerant animals and survived even unassisted exposure to space in low earth orbit. Still, the adaptations leading to these unusual physiological features remain unclear. Even the phylogenetic position of this phylum within the Ecdysozoa is unclear. Complete genome sequences might help to address these questions as genomic adaptations can be revealed and phylogenetic reconstructions can be based on new markers. Here, we present a first draft genome of a species from the family Milnesiidae, namely Milnesium tardigradum. We consistently place M. tardigradum and the two previously sequenced Hypsibiidae species, Hypsibius dujardini and Ramazzottius varieornatus, as sister group of the nematodes with the arthropods as outgroup. Based on this placement, we identify a massive gene loss thus far attributed to the nematodes which predates their split from the tardigrades. We provide a comprehensive catalog of protein domain expansions linked to stress response and show that previously identified tardigrade-unique proteins are erratically distributed across the genome of M. tardigradum. We further suggest alternative pathways to cope with high stress levels that are yet unexplored in tardigrades and further promote the phylum Tardigrada as a rich source of stress protection genes and mechanisms.

evolutionary biology↗