Biology subjects

Schenekar, T.

Publications and source records attributed to Schenekar, T..

6 recordsLinked to original sources

bioRxiv2026

Species ecology, behavior, and substrate type shape eDNA detection of mammals at savanna waterholes

Environmental DNA (eDNA) is increasingly used to monitor terrestrial mammal biodiversity, yet factors that influence detection probability in such systems remain poorly understood. Substrates in and around freshwater drinking areas represent particularly promising eDNA sampling points to capture terrestrial biodiversity, especially in arid and semi-arid landscapes. However, eDNA detection probabilities are expected to depend strongly on the frequency and intensity of animal interaction with the sampled substrate at these watering holes. We combined camera trapping with eDNA metabarcoding to investigate drivers of mammal eDNA detection at savanna waterholes in South Africa (Botsalano Game Reserve) over several weeks during both wet and dry seasons and evaluated the effects of species behavior (interaction intensity with water), species traits, environmental covariates and substrate type (water versus sediment) on eDNA detection probabilities. Camera trapping detected 30 mammal species, whereas eDNA metabarcoding detected 40 species, with 25 species being shared between methods. Body size increased detection probability using camera traps but not using eDNA metabarcoding. eDNA detection was strongly influenced by trophic level, with herbivores exhibiting significantly higher eDNA detection rates than omnivores and carnivores. eDNA detection probability further increased with behavioral water interaction intensity, social group size, visitation frequency, the number of observed individuals, and declined with time elapsed since the last visit of the respective species. A fine-scale spatial analysis within the water bodies revealed that eDNA deposition is highly localized. Substrate type had a pronounced effect, with sediment samples reflecting more long-term mammal activity, whereas water samples reflected more recent interactions and were more sensitive to environmental conditions. Samples collected at wildlife trails exhibited similar patterns, with trophic level and spatial proximity to the trail both increasing detection rates.

ecology↗

bioRxiv2026

Simple soil eDNA sampling reveals terrestrial mammal diversity in the Central Kalahari and highlights waterholes as sampling hotspots

Remote and vast ecosystems present a challenge for biodiversity monitoring. The Central Kalahari Game Reserve in Botswana is one such ecosystem spanning 52,800 km2, a mosaic of fossilized rivers, clay pans, semi-arid sand dunes, scrub, and woodland. It is one of the last remaining untouched wildernesses in the world and hosts unique biodiversity, including populations of threatened mammals. Due to its extreme arid environment, size, and inaccessibility, surveying biodiversity across the reserve is both logistically and technically difficult. Here we demonstrate that a low-effort approach of sampling soil across the reserve is an efficient way to rapidly assess the terrestrial mammal biodiversity using eDNA metabarcoding. We found that eDNA from soil near waterholes performed better at capturing local biodiversity than soil from roads. eDNA metabarcoding detected 38 mammal species, 15 bird species and two amphibians and a simultaneously conducted camera trapping study detected 29 mammal species. eDNA was particularly powerful for detecting small-bodied taxa, including murids, mongooses and bats, which were largely missed by camera traps, while camera trapping was aimed at and performed well for detecting felids. Mammal species that had a higher activity nearby eDNA sampling points (i.e., a higher number of camera trapping recordings nearby) had a higher probability of being detected via eDNA. We propose that simple soil collection for eDNA metabarcoding, particularly close to animal congregation points such as savanna waterholes, offers a practical, scalable and cost-effective strategy for DNA-based biomonitoring in large, remote areas such those in Southern Africa.

ecology↗

bioRxiv2025

MeRIP-seq detects temperature related variation in methylated environmental RNA in fish

Environmental RNA (eRNA) enables non-invasive, near-real-time and potentially functional insight into aquatic communities by capturing RNA molecules released by living organisms. While most eRNA studies focus solely on transcript abundance, this overlooks other regulatory layers that shape how organisms respond to stress. RNA modifications, particularly N6-methyladenosine (m6A), influence RNA stability, processing, and translation and are known to change under temperature challenges. These properties make m6A a compelling target for eRNA-based biomonitoring. We investigated whether m6A marks can be recovered from waterborne eRNA released by an African cichlid fish during elevated temperature exposure. eRNA was collected from tank water under control and thermal treatments, enriched for methylated RNA fragments by immunoprecipitation, and sequenced using immunoprecipitation-based MeRIP-Sequencing. Using this approach, we achieved remarkably high read mapping rates to the target fish species, compared to previous studies focusing solely on mRNA sequencing. Moreover, we detect 412 eRNAs having differing abundances between the elevated temperature and control group. Gene ontology analysis reveals that these are enriched in functional categories related to thermal physiology, suggesting a role in the organisms response to temperature stress. These results indicate an enormous potential of this approach to effectively and non-invasively capture signals of temperature stress response of fish via eRNA. While the current modest replicate depth constrained robust assessment of heat-associated changes in m6A, to our knowledge, this is the first attempt to assess m6A RNA modification in the context of eRNA research and the first evidence indicating that extra-organismal eRNA can retain epitranscriptomic information.

molecular biology↗

bioRxiv2025

Unveiling vertebrate biodiversity in arid and semi-arid terrestrial ecosystems through eDNA metabarcoding at savanna waterholes

Applying environmental DNA (eDNA) metabarcoding to samples from waterholes and their surroundings offers a promising approach for monitoring terrestrial vertebrates in semi-arid and arid ecosystems, such as the southern African savannas. However, minimal guidance exists on key sampling design parameters for terrestrial ecosystems, which can significantly influence species detection. This study investigated the effects of sampled substrate, sampling season, and metabarcoding primer pair on species richness and taxonomic group detection in terrestrial vertebrates, with a focus on mammals, using eDNA samples from waterholes in Botsalano Game Reserve, South Africa. A total of 725 eDNA samples were collected from 94 sampling events across wet and dry seasons, detecting 95 species (45 birds, 42 mammals, 4 amphibians, 3 reptiles, and 1 fish). Sediment samples provided more reliable detection of abundant taxa, whereas water samples had higher detection frequencies of rare taxa. A mixed sampling approach yielded the highest species richness. Sampling during the wet season yielded higher species richness overall, while more mammal species were detected from dry season sampling. Overlap in species detection between the two metabarcoding primers tested was low (47%). We formulate recommendations for future eDNA metabarcoding study designs in similar systems, including remote sampling logistics and discuss potential sources of false positives in eDNA metabarcoding, including (1) secondary eDNA input, (2) incomplete genetic reference databases, and (3) the low genetic resolution of metabarcoding markers.

ecology↗

bioRxiv2025

Globally unified analysis of riverine eDNA reveals common associations of fish biodiversity with drainage characteristics

Freshwater biodiversity is declining at a pace that outstrips the capacity of existing monitoring approaches both in temporal and spatial dimensions, highlighting the urgent need for rapid and scalable assessment and attribution of biodiversity states and changes. Here, we present one of the first global assessments and unified analyses of riverine fish biodiversity using environmental DNA (eDNA) collected from 1818 sites across 113 river systems. We quantified species richness, functional redundancy, phylogenetic diversity, and genetic sequence diversity, and related them to drainage characteristics. Our results showed that eDNA effectively captured global patterns of multi-faceted riverine fish biodiversity and disentangled the roles of climate and human activities in shaping biodiversity-area relationships. Catchments in warmer climates consistently enhanced biodiversity accumulation with area, while higher human activity intensity weakened this scaling. Species richness, functional, and genetic sequence diversity exhibited stronger negative responses to human activities in larger catchments. In contrast, phylogenetic diversity showed the strongest negative effects in smaller catchments with these impacts diminishing as catchment area increased, highlighting the facet-dependent nature of biodiversity responses to environmental gradients. Our findings demonstrate the power of eDNA-based datasets for harmonized, multi-faceted biodiversity assessments, offering a scalable approach for detecting and attributing biodiversity change and informing conservation strategies under accelerating global change.

ecology↗

bioRxiv2025

Integrated reanalysis of global riverine fish eDNA datasets shows robustness and congruence of biodiversity conclusions

The analysis of environmental DNA (eDNA) has revolutionized biodiversity assessments in aquatic ecosystems, enabling non-invasive monitoring of fish communities across diverse regions. However, the global comparability of these eDNA datasets remains ambiguous due heterogeneous sampling protocols and bioinformatic workflows across studies, particularly regarding the robustness of their conclusions on biodiversity assessments. Here, we conducted a meta-analysis of 58 riverine fish eDNA metabarcoding datasets, covering 1,818 sampling sites worldwide, to evaluate the robustness of eDNA-derived biodiversity patterns. We found that species richness estimates and metrics of community structure derived under a common bioinformatic workflow were overall consistent with those of original analyses, despite the relatively high variability in bioinformatic analyses in the respective original studies. Contrastingly, congruence of species identity varied more extensively across datasets, mostly reflecting different completeness and regional relevance of reference databases. Restricting taxonomic assignment to basin-specific species pools improved species identification accuracy, while datasets lacking publicly accessible or well-curated reference data were more prone to mismatches. Year of sampling had a positive effect on taxonomic congruence, such that more recent studies showed increased robustness, also reflecting improved reference database coverage and enhanced species-level identification over time and overall method congruence in more recent years. Overall, the suitability and potential of eDNA for global biodiversity monitoring is corroborating overall robust biodiversity estimates, irrespective of the bioinformatic approaches. Our study underlines the effectiveness and need of further harmonization of bioinformatic workflows and strengthened region-specific reference databases for improved taxonomic resolution and comparability across studies.

ecology↗