Biology subjects

Hellemans, B.

Publications and source records attributed to Hellemans, B..

4 recordsLinked to original sources

bioRxiv2025

Fish Show Genetic Evolutionary Responses to River Regulation

Eco-hydraulics traditionally aims at managing riverine systems in a semi-natural state while meeting human demands, assuming aquatic species are static. However, evidence of rapid evolution suggests that ignoring evolutionary dynamics of fish species might limit long-term effectiveness of eco-hydraulics frameworks. It remains unclear how freshwater fish adapt to human perturbation. Why are some fish populations more resilient to human perturbation than others? What are the genetic mechanisms behind it? To answer these questions, we genotyped eleven populations of three-spined stickleback in a regulated river system and collected data on river morphology, connectivity, flow regimes, physico-chemistry and parasite abundance through a combination of field surveys and modelling. Gene-environment association analysis detected strong signals of genetic divergence associated with hydraulic features. Gene ontology analysis revealed evolutionary responses that primarily involve functions in the nervous and sensory systems. These findings demonstrate that fish can evolve in response to river regulation, highlighting the need to transition from eco-hydraulics toward eco-evo-hydraulics.

evolutionary biology↗

bioRxiv2025

Improving eDNA filtration and purification for qPCR detection of Schistosoma mansoni in lakes Albert and Victoria

BackgroundSchistosomiasis, a parasitic disease caused by Schistosoma trematodes, remains a significant public health burden in sub-Saharan Africa, particularly in regions with limited access to clean water, sanitation and hygiene. Effective disease control strategies rely on large-scale surveillance to accurately identify and target high-risk populations. However, traditional methods such as malacological surveys and stool/urine microscopy in humans often lack sensitivity and scalability. Environmental DNA (eDNA) is emerging as a promising tool for non-invasive surveillance of aquatic pathogens, offering enhanced sensitivity and feasibility for large-scale monitoring. MethodsThis study evaluated the efficacy of eDNA-based detection of Schistosoma mansoni in water samples from Lake Albert and Lake Victoria, Uganda. Three eDNA filtration techniques: open membrane, Waterra capsule and Sylphium capsule filters, were compared for DNA yield and detection efficiency. SYBR Green quantitative polymerase chain reaction (qPCR) targeting the mitochondrial cytochrome oxidase subunit I (COI) gene was performed to quantify S. mansoni eDNA, following in silico and in vitro optimisation of primers. Conventional malacological surveys were conducted in parallel to validate eDNA findings, and statistical analyses examined the influence of environmental factors (turbidity and total dissolved solids (TDS)) on eDNA yield and detection rates. ResultsThe SYBR Green S. mansoni qPCR assay had a practical limit of detection (LOD), defined as amplification in >95% of 33 technical replicates, of 100 copies per reaction. The assay amplified in 82% of reactions with 10 DNA copies and 76% with a single copy. The theoretical LOD, determined via amplification probabilities in RStudio, was 83 copies per reaction, which was also the calculated limit of quantification (LOQ). Schistosoma mansoni eDNA was detected in 58.1% (25/43) of filters from Lake Albert and 19.2% (10/52) from Lake Victoria. The Waterra capsule filter yielded the highest eDNA concentrations, while the Sylphium-coupled capsule filter exhibited comparable detection efficiency. Among the DNA purification methods tested, the Sylphium precipitation-based protocol produced significantly higher eDNA yield than column-based kits (DNeasy Blood and Tissue and Zymo Research). Despite significant variation in eDNA recovery across filtration methods, qPCR detection rates were consistent. No significant correlation was observed between turbidity and S. mansoni eDNA detectability. ConclusionOur findings highlight the potential of eDNA as a sensitive, scalable tool for schistosomiasis surveillance. While Waterra filters and Sylphium extraction maximised DNA yield, lower-yield filtration methods still enabled S. mansoni detection in high-transmission settings. These findings support the adaptability of eDNA approaches across varying resource contexts. Future work should prioritise protocol standardisation, ecological validation, and development of field-ready diagnostics such as LAMP to enable broader implementation in endemic regions.

molecular biology↗

bioRxiv2024

First evidence of a causal link between genetic variation and thermal adaptation in a schistosome host snail

Freshwater snails are pivotal in transmitting schistosomiasis, a tropical parasitic disease affecting over 150 million people. The adaptive potential of these snails is a critical factor in determining how climate change and other environmental factors influence disease transmission dynamics, yet it has remained unexplored. Bulinus truncatus is the schistosome intermediate host snail with the widest geographic distribution and therefore plays a pivotal role in determining the maximum range of urogenital schistosomiasis. In this study, we assessed the local adaptation capacity of B. truncatus to temperature through an integrative approach encompassing phenotypic, ecophysiological, and genomic data. Ten snail populations from diverse thermal environments were collected in three countries, with eight populations reared in a common garden. The F2 generation (total N= 2592) was exposed to eight chronic temperature treatments and various life-history traits were recorded for over 14 weeks. Subsequently, ecophysiological analyses were conducted on the ten last surviving snails per population. Genotyping the parental generation collected in the field using a genotyping-by-sequencing (GBS) approach, revealed 12,875 single nucleotide polymorphisms (SNPs), of which 4.91 % were potentially under selection. We observed a significant association between these outlier SNPs, temperature, and precipitation. Thermal adaptations in life-history traits were evident, with lower survival rates at high temperatures of warm- origin snails compensated for by higher reproduction rates. Cold-origin snails, on the other hand, exhibited higher growth rates adapted to a shorter growing season. Ecophysiological adaptations included elevated sugar and haemoglobin contents in cold-adapted snails. In contrast, warm-adapted snails displayed increased protein levels but also more oxidative damage. Furthermore, heightened phenoloxidase levels indicated a more robust immune response in snails from parasite-rich regions. The substantial local adaptation capacity of B. truncatus holds profound implications for its response to climate change, future schistosomiasis risk, and the effectiveness of schistosomiasis control measures. HighlightsO_LILocal adaptation influences species responses to climate change C_LIO_LIThe snail Bulinus truncatus showed a high thermal local adaptation (LA) potential C_LIO_LILA is apparent through variations in life history and ecophysiological traits C_LIO_LIWe identified a significant genetic basis underlying this LA C_LIO_LILA of the hosts could sustain schistosomiasis transmission under global warming C_LI

ecology↗

bioRxiv2021

Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing

Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.

genomics↗