Biology subjects

Schaetzle, S.

Publications and source records attributed to Schaetzle, S..

4 recordsLinked to original sources

bioRxiv2026

How Robust are Multispecies Coalescent Species Delimitations in Taxonomically Complex Systems? A Genomic Assessment Using Mediterranean Tethya Sponges

Reliable species delimitation underpins biodiversity assessment but remains difficult for organisms with plastic morphology and few diagnostic characters. Multispecies coalescent (MSC) methods can delimit species from genomic data, yet they are rarely tested in taxonomically complex, marine invertebrate groups where they are arguably most needed. We used the three Mediterranean species of the genus Tethya, a rare, well-characterised system within the otherwise taxonomically difficult phylum Porifera--distinguished by multiple independent morphological and ecological characters--to evaluate how robust MSC-based delimitation is in such groups. Analysing 64 single-copy nuclear loci in BEAST2 and BPP, we compared constrained, hypothesis-testing approaches (BFD*, BFdriver, A10) with freer, heuristic ones (SPEEDEMON, A11), and examined their sensitivity to data type, clock model, priors, and the species-collapse threshold. All methods recovered the three recognised Mediterranean species, but the resolution of within-lineage structure was method-dependent. The hypothesis-testing approaches consistently supported six lineages, robustly across data types and model assumptions, whereas the heuristic approaches proved less stable. Configurations without a priori species hypotheses often failed to converge or were computationally intractable, a problem compounded by the relaxed clock. In SPEEDEMON the outcome changed with the collapse threshold. Because our system lacks an independent reference point to calibrate this threshold, any delimitation based on it is poorly constrained. We conclude that constrained, hypothesis-testing delimitation is the most robust and reproducible MSC approach, yielding a quantitative, model-based hypothesis that can be weighed against other lines of evidence to inform taxonomic decisions. By clarifying how these methods behave and how their outcomes should be interpreted, our study offers a practical guide for researchers working on comparably complex systems.

evolutionary biology↗

bioRxiv2026

Ecological Filtering is a Better Predictor of Microbiome Assembly than Coevolution in Marine Sponges

Understanding how microbiomes evolve in concert with their hosts is crucial for understanding the evolutionary dynamics of complex holobionts. Phylosymbiosis describes a pattern in which microbial community relationships parallel host phylogeny. Although often interpreted as evidence for host-microbiome co-diversification, phylosymbiosis can also arise from ecological filtering, a process in which hosts with similar physiology or morphological characteristics select for similar microbial communities independent of host relatedness. Here, we test co-diversification and ecological filtering as alternative explanations for phylosymbiosis in marine sponges (Order Haplosclerida) from the Red Sea. We inferred a robust host phylogeny using 1,153 target-captured genome-wide loci from 144 specimens and characterised their prokaryotic microbiomes via V4 16S rRNA gene amplicon sequencing. Host clade identity explained [~]50% of the microbiome. However, topological analyses revealed high incongruence between host phylogeny and microbial community composition, and phylogenetic distance was only weakly correlated with microbiome dissimilarity. Partial Mantel tests confirmed that geography did not affect this signal. Trait-based analyses comparing high versus low microbial abundance (HMA-LMA) phenotypes, that are linked to sponge filtration physiology, revealed that this classification was a better predictor of microbiome composition than phylogenetic distance. Furthermore, phylogenetically distant clades with convergent HMA characteristics harboured similar microbiome profiles but had unique amplicon sequence variant (ASV) compositions, with between-trait dissimilarity exceeding within-trait dissimilarity. This demonstrates that sponge-microbiome associations are more influenced by ecological filtering than by host-microbe co-diversification, and suggests that sponge holobionts may be better understood as ecological consortia than as coevolved units.

microbiology↗

bioRxiv2020

Deep sequencing of B cell receptor repertoires from COVID-19 patients reveals strong convergent immune signatures

Deep sequencing of B cell receptor (BCR) heavy chains from a cohort of 19 COVID-19 patients from the UK reveals a stereotypical naive immune response to SARS-CoV-2 which is consistent across patients and may be a positive indicator of disease outcome. Clonal expansion of the B cell memory response is also observed and may be the result of memory bystander effects. There was a strong convergent sequence signature across patients, and we identified 777 clonotypes convergent between at least four of the COVID-19 patients, but not present in healthy controls. A subset of the convergent clonotypes were homologous to known SARS and SARS-CoV-2 spike protein neutralising antibodies. Convergence was also demonstrated across wide geographies by comparison of data sets between patients from UK, USA and China, further validating the disease association and consistency of the stereotypical immune response even at the sequence level. These convergent clonotypes provide a resource to identify potential therapeutic and prophylactic antibodies and demonstrate the potential of BCR profiling as a tool to help understand and predict positive patient responses.

immunology↗

bioRxiv2017

Identification of Tumor-Reactive B Cells and Systemic IgG in Breast Cancer Based on Clonal Frequency in the Sentinel Lymph Node

A better understanding of antitumor immune responses is key to advancing the field of cancer immunotherapy. Endogenous immunity in cancer patients, such as circulating anticancer antibodies or tumor-reactive B cells, has been historically yet incompletely described. Here, we demonstrate that tumor-draining (sentinel) lymph node (SN) is a rich source for tumor-reactive B cells that give rise to systemic IgG anticancer antibodies circulating in the bloodstream of breast cancer patients. Using a synergistic combination of high-throughput B-cell sequencing and quantitative immunoproteomics, we describe the prospective identification of tumor-reactive SN B cells (based on clonal frequency) and also demonstrate an unequivocal link between affinity-matured expanded B-cell clones in the SN and antitumor IgG in the blood. This technology could facilitate the discovery of antitumor antibody therapeutics and conceivably identify novel tumor antigens. Lastly, these findings highlight the unique and specialized niche the SN can fill in the advancement of cancer immunotherapy.\n\nSIGNIFICANCEUsing high-throughput molecular cloning and antibody proteomics to study coordinated antitumor immunity in breast cancer patients, we simultaneously demonstrate that the sentinel lymph node is a localized source of expanded antitumor B cells undergoing affinity maturation and that their secreted antibodies are abundant as systemic IgG circulating in blood.

immunology↗