Biology subjects

Waldvogel, A.-M.

Publications and source records attributed to Waldvogel, A.-M..

17 recordsLinked to original sources

bioRxiv2026

Plasmid-encoded anatoxin biosynthesis in benthic cyanobacteria

Anatoxin-producing cyanobacteria pose growing ecological and public health risks, yet the genomic organization of anatoxin biosynthesis remains poorly resolved. Using complete genome assembly of a benthic cyanobacterium of the genus Microcoleus, we show that the entire anatoxin biosynthetic gene cluster is encoded on a small circular plasmid rather than the chromosome. This unexpected localization suggests enhanced mobility of anatoxin biosynthesis and has implications for toxin evolution, release, and environmental surveillance.

microbiology↗

bioRxiv2026

Panagrolaimus einhardi sp. nov. and two sisters of fortune

Identifying nematodes to the species level is known to be complicated due to their morphological plasticity and limited number of taxonomically important characters. This is especially apparent in the genus Panagrolaimus, which comprises many cryptic species that are morphologically difficult to distinguish but differ genetically. These roundworms are particularly notable for their adaptation to extreme environments that are inhospitable to many other forms of life. Traditional morphological identification methods often fail at distinguishing genetically divergent populations due to high morphological plasticity in Panagrolaimus, limiting the efficacy of species discovery. High-quality genome assemblies overcome these challenges, offering a comprehensive blueprint of an organisms genetic structure that can be used for species identification. The analysis of ultra-conserved elements across multiple loci harvested from genome assemblies provides robust phylogenetic resolution. In this study, we integrate genome sequencing, ultra-conserved element analysis, and morphological assessment to identify and describe three novel species: Panagrolaimus einhardi sp. nov., formerly Panagrolaimus sp. ES5 from Germany; Panagrolaimus shuimeiren sp. nov. from the Namib Desert; and Panagrolaimus nebliphilus sp. nov. from the Atacama Desert. P. einhardi sp. nov. is named after Prof. Einhard Schierenberg, a renowned expert in roundworm development and cherished member of the nematode community, who isolated this species himself. All three species originate from different geographical locations, and their respective identification are supported by high-quality genome assemblies from either PacBio HiFi or Oxford Nanopore long-read data. The P. einhardi sp. nov. genome was scaffolded using Hi-C technology, which resulted in a 116 Mb collapsed assembly composed of 44 scaffolds (N50: 28 Mb). P. shuimeiren sp. nov. has an assembly size of 69 Mb with 49 scaffolds and a N50 of 13 Mb. P. nebliphilus sp. nov. assembly is 70 Mb with 24 scaffolds (N50: 13 Mb). The capacity of Panagrolaimus to adapt to extreme environments is driving research into their survival mechanisms, requiring comprehensive genomic resources. By combining morphology and genomics, we can gain a more comprehensive understanding of the rich biological diversity in lineages with numerous cryptic species, such as the Panagrolaimidae, thereby clarifying relationships where morphological data alone are ambiguous or confounded.

zoology↗

bioRxiv2025

Influence of geography, seasonality and experimental selection on Chironomus riparius recombination rates

BackgroundUnderstanding recombination rates is crucial in evolutionary biology, as recombination shapes genetic diversity, natural selection, and adaptation. We investigated recombination rate variation in Chironomus riparius across different latitudes, seasons, and experimental treatments using Pool-seq data from five studies and the ReLERNN neural network-based method. We examined its relationship with genetic diversity, GC content, and FST, assessing causality through structural equation modeling. ResultsIn natural populations, recombination rates showed no clear latitudinal pattern, likely due to interactions between climate-driven selection and regional environmental heterogeneity. However, seasonal variation was evident, with higher recombination rates in autumn than winter, possibly due to temperature-induced plasticity or seasonal bottlenecks. A cold snap in March 2018 triggered a sharp recombination increase, potentially suggesting a stress-induced adaptive response. In experimental populations, thermal regimes had no direct effect on recombination, but adaptation to lab conditions was significant. Environmental stressors produced distinct responses: microplastic exposure reduced recombination genome-wide, likely due to stress-induced DNA repair prioritizing genome integrity, while cadmium exposure generally suppressed recombination. ConclusionsOur findings reveal recombination as a highly dynamic process influenced by environment, selection, and genetic background, underscoring the importance of the context in shaping genomic architecture under both natural and experimental conditions.

evolutionary biology↗

bioRxiv2025

Ultraconserved elements coupled with machine learning approaches resolve the systematics in model nematode species

Nematodes are among the most diverse animals, yet only around 28,000 of an estimated one million species have been morphologically described. Their small size, morphological simplicity, and cryptic diversity complicate phylogenetic analyses. Traditional morphological and single-locus molecular approaches often lack resolution for both recent and ancient divergences. To address these limitations, we developed the first ultraconserved elements (UCEs) probe sets for two nematode families: Panagrolaimidae, a group of non-model organisms with limited genomic resources when compared to model taxa, and Rhabditidae, which includes the model species Caenorhabditis elegans. Our probe sets targeted 1,612 loci for Panagrolaimidae and 100,397 for Rhabditidae. In vitro testing recovered up to 1,457 loci in Panagrolaimidae, supporting robust phylogenetic reconstruction. Results were largely consistent with previous analyses, except for one strain reclassified as Neocephalobus halophilus BSS8. Using machine learning, we determined the minimum number of loci needed for accurate genus-level classification. For Rhabditidae, XGBoost achieved high accuracy with just 46 loci. For Panagrolaimidae, 39 loci were most informative. Our UCE-based approach offers a scalable and cost-effective framework for phylogenomics, enhancing taxonomic resolution and evolutionary inference in nematodes. It is well suited for biodiversity assessments and shallow, field-based sequencing, expanding research possibilities across this ecologically important phylum.

evolutionary biology↗

bioRxiv2024

Soil biodiversity in the Atacama Desert shows distinct patterns at different diversity levels

Species diversity and distribution, in relation to how they interact with their environment is a major focus of ecological research. Particularly for soil ecosystems, information about geographical patterns of biota is scarce despite the pivotal role of soils as ecosystem service providers. The Atacama is the driest non-polar desert on earth: water is scarce, high salinity patches are frequent and water bodies have high concentrations of metals. It is believed that only specialized taxa can survive in this Desert. Accordingly, only some microbial life-forms and few plants, and vertebrates are present. Above ground invertebrates have been reported in the desert but its soils have not been comprehensively analyzed. By studying different areas in the Atacama, we aim to better understand resilience of soil organisms in times of global aridification. Nematodes are one of the most important groups of soil organisms in abundance and biodiversity. Here, we investigated diversity of soil nematodes at the genetic, taxonomic, community and life-cycle levels. We find distinct patterns and assemblages along the different habitats in the desert: dune systems, high altitude mountains, saline lakes, river valleys and fog oases. We also find that distribution of asexual taxa is more likely to occur at higher altitudes, and that the distribution of genera richness in the Atacama follows a latitudinal diversity gradient, as well as an increase with increasing precipitation. Our work shows that even under extreme environmental conditions stable, healthy soil communities can persist, but we see indicators of poor soil food webs.

ecology↗

bioRxiv2024

De Novo Genome assembly of the Caucasian dwarf goby Knipowitschia cf. caucasica, a new alien Gobiidae invadingthe River Rhine

The Caucasian dwarf goby Knipowitschia cf. caucasica is a new invasive alien Gobiidae spreading in the Lower Rhine since 2019. Little is known about the invasion biology of the species and further investigations to reconstruct the invasion history are lacking genomic resources. We assembled a high-quality chromosome-scale reference genome of Knipowitschia cf. caucasica by combining PacBio, Omni-C and Illumina technologies. The size of the assembled genome is 956.58 Mb with a N50 scaffold length of 43 Mb, which includes 92.3 % complete Actinopterygii Benchmarking Universal Single-Copy Orthologs. 98.96 % of the assembly sequence was assigned to 23 chromosome-level scaffolds, with a GC-content of 42.83 %. Repetitive elements account for 53.08 % of the genome. The chromosome-level genome contained 26,404 transcripts with 23,210 multi-exons, of which 26,260 genes were functionally annotated. In summary, the high-quality genome assembly provides a fundamental basis to understand the adaptive advantage of the species.

genomics↗

bioRxiv2024

The interplay of recombination landscape, a transposable element and population history in European populations of Chironomus riparius

Genome resolution is often constrained for non-model species. This can be challenging for population genomic studies as estimations are highly dependent on the quality of the reference genome. This is the case for population history inferences where accuracy relies on the correct detection of single-nucleotide polymorphisms (SNPs) and accurate recombination rates. Here, we utilize a novel long-read genome assembly of Chironomus riparius with high resolution at a chromosome-scale and reanalyse Illumina resequencing data of five European populations. With the model MSMC2, new population demographies were inferred and compared to an older study based on a fragmented genome. Assembly contiguity and completeness led to an increase in accuracy of past demography, suggesting the onset of divergence of an ancestral population between late Pleistocene and early Holocene. These estimates are additionally supported by paleotemperature data, which reveal significant climate shifts in Central Europe during these times. Recombination severely influences population history estimates. With the new reference genome, it was possible to resolve the recombination landscape on the genome-wide scale across different populations using the tool iSMC. Recombination and the dispersal of transposable elements (TEs) in the genome are suspected to influence each other. One TE, known as Cla-element, is suspected to be involved in the divergence of the different C. riparius populations. As it seems to be highly dynamic in the genome, its potential impact on the recombination landscape was explored. No global pattern could be detected which demonstrated a higher resistance of the recombination landscape to the impact of repetitive elements on genome integrity.

genomics↗

bioRxiv2024

The dilemma of underestimating freshwater biodiversity: morphological and molecular approaches

BackgroundThe Lower Rhine ecosystem has been extensively shaped by human activities, destroying, modifying, and even creating novel water bodies as habitats. Freshwater systems are hotspots of biodiversity and highly complex ecosystems. However, knowledge and description of its biodiversity across all trophic levels is still incomplete and the complexity of interactions remains unresolved, especially below the micro scale. This is even true for important international inland waterways such as the River Rhine. We here document the biodiversity of the Lower Rhine and associated water bodies, spanning from the level of protists up to the level of larger invertebrate predators and herbivores organized in faunal size classes (nano-, micro, meio- and macrofauna). This study is part of a long-term ecological research project (LTER-D REES). Our study includes two riprap sections of the rivers main channel, two oxbows and two gravel-pit lakes in the rivers flood plain. Diversity was assessed through morphotype richness and metabarcoding, as well as accounting for sediment composition. ResultsWe found high discrepancies between amplicon sequencing variants (ASVs) and morphotype richness in all size classes, as well as a problematic limitation of reference sequences from freshwater organisms in public databases. Irrespective of the size class, we observed habitat specific zoobenthos communities in each of the three investigated habitat types, with few taxa or taxonomic groups overlapping. ConclusionsOur results demonstrate the importance to integrate different methodologies and extend freshwater sequencing efforts for the assessment of biodiversity across all trophic levels, as particularly relevant for long term projects.

ecology↗

bioRxiv2023

Reference genome of the ant Lasius platythorax

Ants are a highly diversified insect family of the order Hymenoptera, with many fascinating characteristics such as eusociality, chemical communication, farming, or social parasitism. Moreover, ants frequent a wide variety of habitats from dry deserts, grasslands, and savannas to cold temperate forests. The ability of ants to inhabit such diverse habitat ranges demonstrates their adaptability and ecological resilience. However, little is known about the genetic underpinnings of this vast array of traits and their adaptive potential. Here, we generated a high-quality genome assembly for the ant species Lasius platythorax using long-read PacBio HiFi in combination with chromatin conformation capture (Hi-C) sequencing. We successfully assembled the genome into 15 chromosome-level scaffolds ranging from 7.9 to 19.2 Mb and encompassing 204.6 Mb out of 235.3 Mb (total assembly), and a BUSCO score of 86% (Hymenoptera_odb10). Comparative genomics between the two sister species will provide insights into the genomic basis of trait differentiation.

genomics↗

bioRxiv2023

High germline mutation rates but not extreme population size outbreaks influence genetic diversity in crown-of-thorns sea stars

Lewontins paradox, the observation that levels of genetic diversity ({pi}) among animals do not scale linearly with variation in census population sizes (Nc), is an evolutionary conundrum, where the most extreme mismatches between {pi} and Nc are found for highly abundant marine invertebrates. Yet, whether new mutations influence {pi} relative to extrinsic processes remains unknown for most taxa. Here, we provide the first direct germline mutation rate () estimate for a marine invertebrate, using high-coverage (60x) whole-genome sequencing of wild-caught Acanthaster cf. solaris crown-of-thorns sea stars (Echinodermata). We also provide empirical estimates of adult Nc in Australias Great Barrier Reef to jointly examine the determinants of {pi}. Based on direct observations of 63 de novo mutations across 14 parent-offspring trios, the A. cf. solaris mean was 9.13 x 10-09 mutations per-site per-generation (95% CI: 6.51 x 10-09 to 1.18 x 10-08). This value exceeds estimates for other invertebrates, showing greater concordance with reported vertebrate germline mutation rates. Lower-than-expected Ne ([~]70,000-180,000) and low Ne/Nc values (0.0047-0.048) indicated significant genetic drift and weak influences of contemporary population outbreaks on long-term {pi}. Our findings of elevated and low Ne in A. cf. solaris may help explain high mutational loads and extreme polymorphism levels observed in some marine invertebrate taxa and are consistent with evolving in response to Ne (drift-barrier hypothesis). This study advances our understanding of the processes controlling levels of natural genetic variation and provides new data valuable for further testing hypotheses about mutation rate evolution across animal phyla.

evolutionary biology↗

bioRxiv2022

Parthenogenetic Panagrolaimus species evolve at lower mutation rates, but show increased nucleotide diversity

Asexual reproduction is assumed to lead to the accumulation of deleterious mutations, and reduced heterozygosity due to the absence of recombination. Panagrolaimid nematode species display different modes of reproduction. Sexual reproduction with distinct males and females, asexual reproduction through parthenogenesis in the genus Panagrolaimus, and hermaphroditism in Propanagrolaimus. Here, we compared genomic features of free-living nematode populations in populations and species isolated from geographically distant regions to study diversity, and genome-wide differentiation under different modes of reproduction. We firstly estimated genome-wide spontaneous mutation rates in a triploid parthenogenetic Panagrolaimus population, and a diploid hermaphroditic Propanagrolaimus species via long-term mutation-accumulation-lines. Secondly, we calculated population genetic parameters including nucleotide diversity, and fixation index (FST) between populations of asexually and sexually reproducing nematodes. Thirdly, we used phylogenetic network methods on sexually and asexually reproducing Panagrolaimus populations to understand evolutionary relationships between them. The estimated mutation rate was slightly lower for the asexual population, as expected for taxa with this reproductive mode. Natural polyploid asexual populations revealed higher nucleotide diversity. Despite their common ancestor, a gene network revealed a high level of genetic differentiation among asexual populations. The elevated heterozygosity found in the triploid parthenogens could be explained by the third genome copy. Given their tendentially lower mutation rates it can be hypothesized that this is part of the mechanism to evade Mullers ratchet. Our findings in parthenogenetic triploid nematode populations seem to challenge common expectations of evolution under asexuality.

evolutionary biology↗

bioRxiv2022

Genomic profiling of climate adaptation in Aedes aegypti along an altitudinal gradient in Nepal indicates non-gradual expansion of the disease vector

BackgroundDriven by globalization, urbanization and climate change, the distribution range of invasive vector species has expanded to previously colder ecoregions. To reduce health-threatening impacts on humans, insect vectors are extensively studied. Population genomics can reveal the genomic basis of adaptation and help to identify emerging trends of vector expansion. ResultsBy applying whole genome analyses and genotype-environment associations to populations of the main dengue vector Ae. aegypti, sampled along an altitudinal temperature gradient in Nepal (200- 1300m), we identify adaptive traits and describe the species genomic footprint of climate adaptation to colder ecoregions. We found two clusters of differentiation with significantly different allele frequencies in genes associated to climate adaptation between the highland population (1300m) and all other lowland populations ([≤] 800 m). We revealed non-synonymous mutations in 13 of the candidate genes associated to either altitude, precipitation or cold tolerance and identified an isolation-by-environment differentiation pattern. ConclusionOther than the expected gradual differentiation along the altitudinal gradient, our results reveal a distinct genomic differentiation of the highland population. This finding either indicates a differential invasion history to Nepal or local high-altitude adaptation explaining the populations phenotypic cold tolerance. In any case, this highland population can be assumed to carry pre-adapted alleles relevant for the species invasion into colder ecoregions worldwide that way expanding their climate niche.

genomics↗

bioRxiv2022

Selective effects of a short transient environmental fluctuation on a natural population

Natural populations experience continuous and often transient changes of environmental conditions. These in turn may result in fluctuating selection pressures leading to variable demographic and evolutionary population responses. Rapid adaptation as short-term response to a sudden environmental change has in several cases been attributed to polygenic traits, but the underlying genomic dynamics and architecture are poorly understood. In this study, took advantage of a natural experiment in an insect population by monitoring genome-wide allele frequencies before and after a cold snap event. Whole genome pooled sequencing of time series samples revealed ten selected haplotypes carrying ancient polymorphisms, partially with signatures of balancing selection. By constantly cold exposing genetically variable individuals in the laboratory, we could demonstrate with whole genome resequencing i) among the survivors, the same alleles rose in frequency as in the wild and ii) that the identified variants additively predicted fitness (survival time) of its bearers. Finally, by simultaneously sequencing the genome and the transcriptome of cold exposed individuals we could tentatively link some of the selected SNPs to the cis- and trans-regulation of genes and pathways known to be involved in cold response of insects, like Cytochrome P450 and fatty acid metabolism. Altogether, our results shed light on the strength and speed of selection in natural populations and the genomic architecture of its underlying polygenic trait. Population genomic time series data thus appear as promising tool for measuring the selective tracking of fluctuating selection in natural populations.

evolutionary biology↗

bioRxiv2021

Genome structure of Brachionus asplanchnoidis, a Eukaryote with intrapopulation variation in genome size

Eukaryotic genomes vary greatly in size due to variation in the proportion of non-coding DNA, a pattern that emerges both in comparisons at a larger taxonomic scale and at the level of individuals within a species. The rotifer Brachionus asplanchnoidis represents one of the most extreme cases of intraspecific genome size variation among Eukaryotes, displaying almost 2-fold variation within a geographic population. Here we used a whole-genome sequencing approach to identify the underlying DNA sequence differences by assembling a high-quality reference genome draft for one individual of the population and aligning short-reads of 15 individuals from the same geographic population. We identified large, contiguous copy number variable regions (CNVs), which exhibited significant coverage differences among individuals, and whose coverage overall scaled with genome size. CNVs were mainly composed of tandemly repeated satellite DNA, with only few interspersed genes or other sequences, and were characterized by an elevated GC-content. Judging from their distributions across contigs, some CNVs are fragments of accessory (B-)chromosomes while others resemble large insertions to normal chromosomes. CNV patterns in offspring of two parents with divergent genome size, and CNV patterns in several individuals from an inbred line differing in genome size demonstrated inheritance and accumulation of CNVs across generations. Our study provides unprecedented insights into genome size evolution at microevolutionary time scales and thus paves the way for studying genome size evolution in contemporary populations rather than inferring patterns and processes a posteriori from species comparisons.

evolutionary biology↗

bioRxiv2020

Temperature-dependence of spontaneous mutation rates

Mutation is the source of genetic variation and the fundament of evolution. At the interphase of ecology and evolution, temperature has long been suggested to have a direct impact on realised spontaneous mutation rates. The question is whether mutation rates can be a species-specific constant under variable environmental conditions, such as variation of the ambient temperature. By combining mutation accumulation with whole genome sequencing in a multicellular organism, we provide empirical support to reject this null hypothesis. Instead mutation rates depend on temperature in a U-shaped manner with increasing rates towards both temperature extremes. This relation has important implications for mutation dependent processes in molecular evolution, processes shaping the evolution of mutation rates and even the evolution of biodiversity as such.

evolutionary biology↗

bioRxiv2020

Measuring mutagenicity in ecotoxicology: A case study of Cd exposure in Chironomus riparius

Existing mutagenicity tests for metazoans lack the direct observation of enhanced germline mutation rates after exposure to anthropogenic substances, therefore being inefficient. Cadmium (Cd) is a metal described as a mutagen in mammalian cells and listed as a group 1 carcinogenic and mutagenic substance. But Cd mutagenesis mechanism is not yet clear. Therefore, in the present study, we propose a method coupling short-term mutation accumulation (MA) lines with subsequent whole genome sequencing (WGS) and a dedicated data analysis pipeline to investigate if chronic Cd exposure on Chironomus riparius can alter the rate at which de novo point mutations appear. Results show that Cd exposure did not affect the basal germline mutation rate nor the mutational spectrum in C. riparius, thereby arguing that exposed organisms might experience a range of other toxic effects before any mutagenic effect may occur. We show that it is possible to establish a practical and easily implemented pipeline to rapidly detect germ cell mutagens in a metazoan test organism. Furthermore, our data implicate that it is questionable to transfer mutagenicity assessments based on in vitro methods to complex metazoans. Main find of the workCd chronic exposure under environmental realistic concentrations did not exert mutagenicity; It is questionable to transfer in vitro mutagenicity assessments to complex metazoans.

pharmacology and toxicology↗

bioRxiv2019

A high-quality genome assembly from short and long reads for the non-biting midge Chironomus riparius (Diptera)

BackgroundChironomus riparius is of great importance as a study species in various fields like ecotoxicology, molecular genetics, developmental biology and ecology. However, only a fragmented draft genome exists to date, hindering the recent rush of population genomic studies in this species.\n\nFindingsMaking use of 50 NGS datasets, we present a hybrid genome assembly from short and long sequence reads that make C. riparius genome one of the most contiguous Dipteran genomes published, the first complete mitochondrial genome of the species and the respective recombination rate as one of the first insect recombination rates at all.\n\nConclusionsThe genome and associated resources will be highly valuable to the broad community working with dipterans in general and chironomids in detail. The estimated recombination rate will help evolutionary biologist gain a better understanding of commonalities and differences of genomic patterns in insects.

genomics↗