Biology subjects

Schuster, A.

Publications and source records attributed to Schuster, A..

11 recordsLinked to original sources

bioRxiv2026

Morphogenomic description of Cranifera cranifera (Chitwood, 1932) Kloss, 1960 from captive Blaptica dubia Serville, 1838 cockroach

Nematodes of the superfamily Thelastomatoidea are found in the digestive system of various arthropods, feeding on their host microbiome. They are sometimes considered to be ecologically intermediate forms between free-living rhabditids and parasitic Spirurina, while phylogenetically they are nested within the latter. In addition to new morphological data on the male morphology, this manuscript presents the first nuclear genome assembly of a thelastomatid species, Cranifera cranifera, using long-read sequencing approach, making a total of three nuclear genomes available for superfamilyThelastomatoidea. The C. cranifera nuclear genome assembly presented here is 246 Mb long, consists of 7563 contigs, has an N50 of 43 kb and includes 94% of the BUSCO nematoda_odb12 genes. The mitochondrial genome is 24646 bases long, includes a complete set of protein coding, rRNA and tRNA genes, and a repetitive region 9731 bases long, which includes multiple copies of tRNA-Asn(gtt) and tRNA-Lys(ttt). The nuclear assembly also contained two sequence variants of the 28S rRNA gene, highlighting the presence of intragenomic variation within rRNA operon. The newly generated assemblies (nuclear and organelle) will add to a growing body of genomic resources for underrepresented and understudied animal parasitic nematodes from the Clade 3, enabling comprehensive studies in their phylogeny and trait evolution in the future.

zoology↗

bioRxiv2026

Chromosome-level genome assembly and annotation of the parthenogenetic nematode Acrobeloides nanus

Acrobeloides nanus is a species of widely distributed bacteria-feeding nematodes belonging to the family Cephalobidae. It reproduces parthenogenetically, making it a valuable system for studying the consequences of obligate asexuality, and exhibits early developmental processes that differ significantly from the model organism Caenorhabditis elegans. Additionally, the species has demonstrated remarkable resistance in extreme conditions, surviving near-complete desiccation through anhydrobiosis. This new chromosome-level genome assembly provides a high-quality reference to study these traits. Combining Nanopore, amplified PacBio HiFi, and Hi-C sequencing, we generated a chromosome-level assembly spanning 188.9 Mb over six chromosomes. The genome features a 48.1% repeat content, dominated by Mutator-like elements, and contains 24,912 predicted genes. Structural analysis reveals the conservation of ancestral nematode linkage groups. This resource significantly improves upon previous fragmented assemblies, offering a new framework for identifying genomic adaptations in the family Cephalobidae.

genomics↗

bioRxiv2025

Genomes of ancient asexual mites appear streamlined in their architecture

The long-term persistence of obligate asexual lineages represents one of the most enduring and critical paradoxes in evolutionary biology. Sexual reproduction, through meiotic recombination and segregation, enables the efficient removal of deleterious mutations and facilitates rapid adaptation to shifting environmental pressures. Lineages that lose sex are therefore classically predicted to experience genomic decay and face rapid extinction. Oribatid mites (Acari, Sarcoptiformes) represent a unique system for testing these predictions, as they feature multiple, ancient, and independent transitions to asexuality, providing a natural experiment on the evolutionary fate of asexual genomes. We compared four sets of sister sexual and asexual species using high-quality nuclear genome assemblies to investigate the genomic consequences of long-term asexuality. Our study revealed a profound, reproductive-mode-dependent dichotomy in the evolution of genome architecture. Contrary to their expected genomic decay, asexual species have mostly streamlined genomes with less novel genes than their sexual sister species. In contrast, sexual species have acquired genetic innovations, encompassing both gene and transposable element content. These results challenge classical expectations of genomic deterioration in asexual species and might explain the long-term evolutionary persistence of oribatid mites.

genomics↗

bioRxiv2025

Decoding Demosponge Diversity: Bayesian Analysis of Biodiversity, Extinction Events and Environmental Influences throughout the Phanerozoic

Sponges (phylum Porifera) have been essential to marine ecosystems for over 600 million years, contributing to nutrient cycling, reef building, and ecological stability. Despite their evolutionary importance, the drivers of their diversity dynamics remain poorly understood. This study investigates the diversification patterns of Demospongiae, the largest class of sponges with a well-documented fossil record throughout the Phanerozoic Eon (541-0 Ma). Using fossil occurrence data and a Bayesian framework, we modeled origination and extinction rates to understand their evolutionary history. Our findings reveal key extinction events, including three previously unrecognized events in the Cambrian, Late Silurian, and Late Jurassic, alongside known events such as the Permian-Triassic and Triassic-Jurassic extinctions. Notably, there was no statistical evidence for mass extinction during the Late Ordovician or Late Devonian. Additionally, Demosponges underwent a significant decline prior to the Cretaceous-Paleogene extinction. To explore abiotic influences, we applied the Multivariate Birth-Death (MBD) model across all extinction events. This analysis identified correlations between major speciation and extinction events and key variables, including temperature, continental fragmentation, oxygen levels, and sea level, as well as geochemical proxies such as sulfur and strontium, which may reflect underlying drivers like anoxia, weathering, or tectonic activity. Temperature and oxygen levels, in particular, correlated with speciation and extinction during the Permian-Triassic extinction. These findings underscore the role of environmental fluctuations in shaping demosponge diversity and highlight the complex interplay between changes in abiotic factors and sponge evolution. Our work provides critical insights into the factors driving sponge biodiversity and offers perspectives on how modern sponges might respond to ongoing climate change. Significance StatementSponges are ancient and ecologically pivotal marine organisms that have persisted through Earths major environmental upheavals. Despite their resilience, the mechanisms driving their evolutionary responses to past climate shifts remain unclear. By leveraging the fossil record of Demospongiae, this study identifies previously unrecognized extinction events and elucidates how abiotic factors, including temperature and oxygen levels, shaped their diversity during these crises. These findings enhance our understanding of sponge evolutionary dynamics and resilience, offering critical insights into the vulnerability of marine ecosystems under current and future climate change scenarios.

paleontology↗

bioRxiv2024

Independent origins of spicules reconcile the evolutionary history of sponges

Sponges (Porifera) play a critical role in global biogeochemical processes. However, their evolutionary timeline remains unclear hampering our understanding of Neoproterozoic paleoecology. Molecular data suggest a Tonian or Cryogenian origin, while the oldest confirmed sponge fossils, represented by siliceous spicules, date to the Ediacaran. To understand this 150-million-year discrepancy, we compiled a new phylogenomic dataset, revised fossil evidence, derived a new dated sponge phylogeny, and tested whether ancestral sponges were aspiculated or not. We infer the last common sponge ancestor to have been early Ediacaran in age and aspiculated. Siliceous spicules evolved independently at least four times, and calcareous spicules at least two times in crown sponges. We performed a diversification rate analysis showing that siliceous spicules did not drive species radiations. Our study reconciles molecular and fossil evidence, indicating that while sponges emerged in the early Ediacaran, they are largely absent from the Neoproterozoic fossil record because they had not yet evolved spicules. TeaserSponges emerged in the Precambrian, were soft-bodied and did not produce mineralized spicules, which emerged multiple times independently.

evolutionary biology↗

bioRxiv2023

Transcriptomic responses of sponge holobionts to in situ, seasonal anoxia and hypoxia

Deoxygenation can be fatal for many marine animals; however, some sponge species are tolerant of hypoxia and anoxia. Indeed, two sponge species, Eurypon sp. 2 and Hymeraphia stellifera, survive seasonal anoxia for months at a time. To understand their tolerance mechanisms, we performed differential gene expression analyses on the sponges, their mitochondria and their microbial symbionts under in situ conditions of normoxia, hypoxia and anoxia. Each species possessed a unique microbiome, but the microbiomes of each species were dominated by a species-specific Thaumarchaeon and a Gammaproteobacterium. Holobiont gene expression was species-and oxygen-level dependent, though there were some shared interspecific responses to deoxygenation. In general, few changes occurred in the expression of sponge metabolic genes as a function of oxygenation level, indicating that they may remain metabolically active under anoxia. However, ATP synthesis genes were significantly upregulated under hypoxia when compared to normoxia, and genes for DNA replication were downregulated. Mitochondrial gene expression was effectively unchanged under both hypoxia and anoxia. Nevertheless, both anoxia and hypoxia caused upregulation of heat shock proteins (HSPs), indicating cellular level adaptations to deoxygenation stress. A meta-analysis demonstrated that sponge transcriptional responses to anoxia were distinct from those displayed by other invertebrates while dormant, and the hypothesis of sponge dormancy under anoxia was not supported. Thaumarchaeota symbionts also upregulated stress response genes in hypoxia, while maintaining expression of oxygen-dependent metabolic pathways under hypoxia and anoxia. Gammaproteobacteria symbionts showed relatively few noteworthy changes in gene expression in response to anoxia but decreased metabolic gene expression in hypoxia. There was no clear evidence of upregulated anaerobic respiration in the transcriptomes of the sponge holobionts under anoxia or hypoxia. The tolerance of some sponges to prolonged anoxia warrants further investigation and could give them an advantage in future oceans following climate change as well as in ancient oceans when oxygen concentrations were lower than at present.

ecology↗

bioRxiv2023

Formate Promotes Invasion and Metastasis by Activating Fatty Acid Synthesis and Matrix Metalloproteinases

Metabolic rewiring is essential to enable cancer onset and progression. One important metabolic pathway that is often hijacked by cancer cells is the one-carbon cycle, in which the third carbon of serine is oxidized to formate. We have previously shown that formate production in cancer cells often exceeds the anabolic demand, resulting in formate overflow. Furthermore, we observed that high extracellular formate promotes the in vitro invasiveness of glioblastoma (GBM) cells. However, additional data supporting this in vitro observation and mechanistic details remained elusive so far. In the present study, we now demonstrate that inhibition of formate overflow results in a decreased invasiveness of GBM cells ex vivo and in vivo. Additionally, we observed that exposure to exogeneous formate can induce a transiently stable pro-invasive phenotype that results in increased metastasis formation in vivo. All in all, these results suggest that a local formate increase within the tumor microenvironment may be one factor that can promote cancer cell motility and dissemination. Mechanistically, we uncover a previously undescribed interplay where formate acts as a trigger to alter fatty acid metabolism and matrix metalloproteinase (MMP) activity which in turn impacts cancer cell invasiveness. We thus highlight the role of formate as a pro-invasive metabolite. Gaining a deeper understanding of formate overflow and how it promotes invasion in cancer, may open new therapeutic opportunities to prevent cancer cell dissmination.

cancer biology↗

bioRxiv2021

Metagenomic data for Halichondria panicea from Illumina and Nanopore sequencing and preliminary genome assemblies for the sponge and two microbial symbionts.

ObjectivesThese data were collected to generate a novel reference metagenome for the sponge Halichondria panicea and its microbiome for subsequent differential expression analyses. Data descriptionThese data include raw sequences from four separate sequencing runs of the metagenome of a single individual of Halichondria panicea - one Illumina MiSeq (2x300 bp, paired-end) run and three Oxford Nanopore Technologies (ONT) long-read sequencing runs, generating 53.8 and 7.42 Gbp respectively. Comparing assemblies of Illumina, ONT and an Illumina-ONT hybrid revealed the hybrid to be the best assembly, comprising 163 Mbp in 63,555 scaffolds (N50: 3,084). This assembly, however, was still highly fragmented and only contained 52% of core metazoan genes (with 77.9% partial genes), so it was also not complete. However, this sponge is an emerging model species for field and laboratory work, and there is considerable interest in genomic sequencing of this species. Although the resultant assemblies from the data presented here are suboptimal, this data note can inform future studies by providing an estimated genome size and coverage requirements for future sequencing, sharing additional data to potentially improve other suboptimal assemblies of this species, and outlining potential limitations and pitfalls of the combined Illumina and ONT approach to novel genome sequencing.

genomics↗

bioRxiv2020

The effects of seasonal anoxia on the microbial community structure in demosponges in a marine lake (Lough Hyne, Ireland)

Climate change is expanding marine oxygen minimum zones (OMZs), while anthropogenic nutrient input depletes oxygen concentrations locally. The effects of deoxygenation on animals are generally detrimental; however, some sponges (Porifera) exhibit hypoxic and anoxic tolerance through currently unknown mechanisms. Sponges harbor highly specific microbiomes, which can include microbes with anaerobic capabilities. Sponge-microbe symbioses must also have persisted through multiple anoxic/hypoxic periods throughout Earth history. Since sponges lack key components of the hypoxia-inducible factor (HIF) pathway responsible for hypoxic responses in other animals, it was hypothesized that sponge tolerance to deoxygenation may be facilitated by its microbiome. To test this hypothesis, we determined the microbial composition of sponge species tolerating seasonal anoxia and hypoxia in situ in a semi-enclosed marine lake, using 16S rRNA amplicon sequencing. We discovered a high degree of cryptic diversity among sponge species tolerating seasonal deoxygenation, including at least nine encrusting species of the orders Axinellida and Poecilosclerida. Despite significant changes in microbial community structure in the water, sponge microbiomes were species specific and remarkably stable under varied oxygen conditions, though some symbiont sharing occurred under anoxia. At least three symbiont combinations, all including large populations of Thaumarchaeota, corresponded with deoxygenation tolerance, and some combinations were shared between distantly related hosts. We propose hypothetical host-symbiont interactions following deoxygenation that could confer deoxygenation tolerance. ImportanceThe oceans have an uncertain future due to anthropogenic stressors and an uncertain past that is becoming clearer with advances in biogeochemistry. Both past and future oceans were, or will be, deoxygenated compared to present conditions. Studying how sponges and their associated microbes tolerate deoxygenation provides insights into future marine ecosystems. Moreover, sponges form the earliest branch of the animal evolutionary tree and they likely resemble some of the first animals. We determined the effects of variable environmental oxygen concentrations on the microbial communities of several demosponge species during seasonal anoxia in the field. Our results indicate that anoxic tolerance in some sponges may depend on their symbionts, but anoxic tolerance was not universal in sponges. Therefore, some sponge species could likely outcompete benthic organisms like corals in future, reduced-oxygen ecosystems. Our results support the molecular evidence that sponges and other animals have a Neoproterozoic origin, and that animal evolution was not limited by low-oxygen conditions.

microbiology↗

bioRxiv2019

Genome-wide association meta-analysis for early age-related macular degeneration highlights novel loci and insights for advanced disease

BackgroundAdvanced age-related macular degeneration (AMD) is a leading cause of blindness. While around half of the genetic contribution to advanced AMD has been uncovered, little is known about the genetic architecture of the preceding early stages of the diseases. MethodsTo identify genetic factors for early AMD, we conducted a genome-wide association meta-analysis with 14,034 early AMD cases and 91,214 controls from 11 sources of data including data from the International AMD Genomics Consortium (IAMDGC) and the UK Biobank (UKBB). We ascertained early AMD via color fundus photographs by manual grading for 10 sources and by using an automated machine learning approach for >170,000 images from UKBB. We searched for significant genetic loci in a genome-wide association screen (P<5x10-8) based on the meta-analysis of the 11 sources and via a candidate approach based on 13 suggestive early AMD variants from Holliday et al 2013 (P<0.05/13, additional 3,432 early AMD cases and 11,235 controls). For the novel AMD regions, we conducted in-silico follow-up analysis to prioritize causal genes and pathway analyses. ResultsWe identified 11 loci for early AMD, 9 novel and 2 known for early AMD. Most of these 11 loci overlapped with known advanced AMD loci (near ARMS2/HTRA1, CFH, APOE, C2, C3, CETP, PVRL2, TNFRSF10A, VEGFA), except two that were completely novel to any AMD. Among the 17 genes within the two novel loci, in-silico functional annotation suggested CD46 and TYR as the most likely responsible genes. We found the presence or absence of an early AMD effect to distinguish known pathways of advanced AMD genetics (complement/lipid pathways or extracellular matrix metabolism, respectively). ConclusionsOur data on early AMD genetics provides a resource comparable to the existing data on advanced AMD genetics, which enables a joint view. Our large GWAS on early AMD identified novel loci, highlighted shared and distinct genetics between early and advanced AMD and provides insights into AMD etiology. The ability of early AMD effects to differentiate the major pathways for advanced AMD underscores the biological relevance of a joint view on early and advanced AMD genetics.

genetics↗

bioRxiv2017

Divergence times in demosponges (Porifera): firstinsights from new mitogenomes and the inclusion offossils in a birth-death clock model

Approximately 80% of all recent sponge species belong to the class Demospongiae. Yet, despite their diversity and importance, accurate divergence times are still unknown for most demosponge clades. The estimation of demosponge divergence time is key to answering fundamental questions like e.g. the origin of Demospongiae, their diversification and historical biogeography. Molecular sequence data alone is not informative on an absolute time scale, and therefore needs to be \"calibrated\" with additional data such as fossils. Here, we apply the fossilized birth-death model (FBD), which has the advantage, compared to strict node dating with the oldest fossil occurrences, that it allows for the inclusion of young and old fossils in the analysis of divergence time. We use desma-bearing sponges, a diverse group of demosponges that form rigid skeletons and have a rich and continuous fossil record dating back to the Cambrian ([~]500 Ma), aiming to date the demosponge radiation and constrain the timing of key evolutionary events, like the transition from marine to freshwater habitats. To do so, we assembled mitochondrial genomes of six desma-bearing demosponges from size-selected reduced-representation genomic libraries and apply a fossilized birth-death model including 30 fossils and 33 complete demosponge mitochondrial genomes to infer a dated phylogeny of Demospongiae. Our study supports a Neoproterozoic origin of Demospongiae. Novel age estimates for the split of freshwater and marine sponges dating back to the Carboniferous and the previously assumed Recent ([~]18 Ma) diversification of freshwater sponges is supported. Moreover, we provide detailed age estimates for a possible diversification of Tetractinellidae ([~]315 Ma), the Astrophorina ([~]240 Ma), the Spirophorina ([~]120 Ma) and the family Corallistidae ([~]188 Ma) all of which are considered as key groups for dating the Demospongiae, due to their extraordinary rich and continuous fossil history.

evolutionary biology↗