Biology subjects

Steindl, S.

Publications and source records attributed to Steindl, S..

6 recordsLinked to original sources

bioRxiv2025

How to catch flies in the city (fast): Citizen Science on Drosophila ecology helps to raise awareness for biodiversity in urban environments

To efficiently mitigate biodiversity loss both robust ecological data and broader societal engagement are needed. Citizen science offers a pathway to address these dual challenges by combining data collection with public involvement. Here, we introduce the citizen science project Vienna City Fly, conducted at the Natural History Museum Vienna (NHMW), which used fruit flies (Drosophila) as a model organism group for urban biodiversity research and public engagement. Participants deployed standardized traps across Vienna, enabling systematic sampling and active participation in research, which resulted in hundreds of fly collections, thousands of sampled fly specimens and new insights into the biodiversity and ecology of the collected fly species, demonstrating the feasibility of large-scale ecological research through public collaboration. To assess motivational drivers and perceived impacts of participation, we conducted an online survey (N=59) using the validated psychometric MORFEN-CS scale. Survey results revealed that nature conservation values and the intention to contribute to biodiversity conservation emerged as the strongest drivers of engagement, complemented by sociopolitical responsibility and citizen science-based motivations. Reported outcomes include knowledge gain (61%), more positive attitude toward study organisms (50%), and increased awareness of biodiversity (30%). Satisfaction was very high, with 85% rating their experience at the top of the scale and all participants expressing willingness to join future citizen science projects. Recruitment occurred mainly via social networks, and the sample of participants was highly educated, indicating limits to inclusivity and reach. Our findings demonstrate that citizen science can contribute to robust ecological data collection while gaining knowledge and awareness. Natural history museums, as trusted institutions, play a key role in facilitating such initiatives. Overall, Drosophila research proves to be a suitable field for citizen science, combining accessibility with strong potential for advancing ecological and biodiversity research as well as public engagement in urban biodiversity research.

scientific communication and education↗

bioRxiv2025

Ecology and temporal dynamics of urban Drosophila species communities as potential indicators of biodiversity decline

Understanding the impact of ecological factors on biodiversity is central in the context of accelerating climate change and biodiversity loss. Urban areas, as landscapes under particularly strong anthropogenic influence, are undergoing rapid ecological change, yet the consequences for urban biodiversity and ecosystem functioning remain poorly understood. In this study, we focused on fruit flies of the genus Drosophila - a diverse group of dipterans with variable ecological niches and degrees of synanthropy - to investigate species composition and community ecology in the metropolitan area of Vienna, Austria. With the help of numerous citizen scientists, we have collected approximately 18,000 specimens through dense spatio-temporal sampling both indoors and outdoors of human dwellings. A total of 13 Drosophila species were identified, with communities dominated by widespread cosmopolitan synanthropic species. Among these, D. mercatorum and D. virilis represent novel records for Austria. Comparisons to a previous study from more than 30 years ago revealed that the species richness in Vienna was more than 50% lower than before and showed that formerly common species were potentially replaced by neobiots. We further assessed ecological niches by intersecting species abundance data with high-dimensional, high-resolution earth observation datasets, which revealed distinct ecological preferences among species. In particular, the neozoan D. mercatorum emerged as a highly synanthropic species, tightly confined to urban areas with high levels of imperviousness. In summary, our study underpins the versatility of the Drosophila system as indicators of biodiversity loss in a rapidly changing world.

ecology↗

bioRxiv2024

AmpliPiper: A versatile amplicon-seq analysis tool for multilocus DNA barcoding

The advent of third generation sequencing technology has revolutionized parallelized sequencing of DNA fragments of varying lengths, such as PCR amplicons, which provides unprecedented new opportunities for large-scale and diverse DNA barcoding projects that, for example, aim to quantify the accelerating biodiversity crisis. However, the broad-scale application of these new technologies for biodiversity research is often hindered by the demand for advanced bioinformatics skills to carry out quantitative analyses. To facilitate the application of multilocus amplicon sequencing (amplicon-seq) data for biodiversity and integrative taxonomic research questions, we present AmpliPiper, an automated and user-friendly software pipeline which carries out bioinformatics analyses of multilocus amplicon-seq data generated with Oxford Nanopore (ONT) sequencing. AmpliPiper combines analysis methods for DNA barcoding data that include demultiplexing of pooled amplicon-seq data, haplotype-specific consensus sequence reconstruction, species identification based on comparison to the BOLD and GenBank databases, phylogenetic analyses and species delimitation. We demonstrate the applicability and workflow of our approach based on a newly generated dataset of 14 hoverfly (Syrphidae) samples that were amplified and sequenced at four marker genes. We further benchmark our approach with Sanger sequencing and simulated amplicon-seq data which show that DNA barcoding with ONT is both accurate and sensitive to detect even subtle genetic variation.

bioinformatics↗

bioRxiv2024

Footprints of worldwide adaptation in structured populations of D. melanogaster through the expanded DEST 2.0 genomic resource

Large scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population genetics of the fruit fly Drosophila melanogaster, we present an expanded release of the community-generated population genomics resource Drosophila Evolution over Space and Time (DEST 2.0; https://dest.bio/). This release includes 530 high-quality pooled libraries from flies collected across six continents over more than a decade (2009-2021), most at multiple time points per year; 211 of these libraries are sequenced and shared here for the first time. We used this enhanced resource to elucidate several aspects of the species demographic history and identify novel signs of adaptation across spatial and temporal dimensions. We showed that patterns of secondary contact, originally characterized in North America, are replicated in South America and Australia. We also found that the spatial genetic structure of populations is stable over time, but that drift due to seasonal contractions of population size causes populations to diverge over time. We identified signals of adaptation that vary between continents in genomic regions associated with xenobiotic resistance, consistent with independent adaptation to common pesticides. Moreover, by analyzing samples collected during spring and fall across Europe, we provide new evidence for seasonal adaptation related to loci associated with pathogen response. Furthermore, we have also released an updated version of the DEST genome browser. This is a useful tool for studying spatio-temporal patterns of genetic variation in this classic model system.

evolutionary biology↗

bioRxiv2022

Automation of tree-ring detection and measurements using deep learning

O_LIWe present an implementable neural network-based automated detection and measurement of tree-ring boundaries from coniferous species. C_LIO_LIWe trained our Mask R-CNN extensively on over 8,000 manually annotated rings. We assessed the performance of the trained model from our core processing pipeline on real world data. C_LIO_LIThe CNN performed well, recognizing over 99% of ring boundaries (precision) and a recall value of 95% when tested on real world data. Additionally, we have implemented automatic measurements based on minimum distance between rings. With minimal editing for missed ring detections, these measurements were a 99% match with human measurements of the same samples. C_LIO_LIOur CNN is readily deployable through a Docker container and requires only basic command line skills. Application outputs include editable annotations which facilitate the efficient generation of ring-width measurements from tree-ring samples, an important source of environmental data. C_LI

ecology↗

bioRxiv2022

Multi-GBS: A massively multiplexed GBS-based protocol optimized for large, repetitive conifer genomes

Reduced representation library approaches are still a valuable tool for breeding and population and ecological genomics, even with impressive increases in sequencing capacity in recent years. Unfortunately, current approaches only allow for multiplexing up to 384 samples. To take advantage of increased sequencing capacity, we present Multi-GBS, a massively multiplexable extension to Genotyping-by-Sequencing that is also optimized for large conifer genomes. In Norway Spruce, a highly repetitive 20Gbp diploid genome with high population genetic variation, we call over a million variants in 32 genotypes from three populations, two natural forest in the Alps and Bohemian Alps, and a managed population from southeastern Austria using the existing TASSEL GBSv2 pipeline. Metric MDS analysis of replicated genotypes shows that technical bias in resulting genotype calling is minimal and that populations cluster in biologically meaningful ways.

genomics↗