How Robust are Multispecies Coalescent Species Delimitations in Taxonomically Complex Systems? A Genomic Assessment using Mediterranean Tethya Sponges
Joëlle van der Sprong 1,§; Frine Cardone 2,3; Sebastian Höhna 1,4; Simone Schätzle 1; Fabian Deister 1; Dirk Erpenbeck 1,4; Gert Wörheide 1,4; Sergio Vargas 1,§
1 Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
2 Stazione Zoologica Anton Dohrn Napoli, Naples, Italy
3 National Centre for Future Biodiversity, Palermo, Italy
4 GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
§ corresponding authors: j.vandersprong@uni-goettingen.de & s.vargas@lmu.de
This repository accompanies the manuscript above and contains the data and code needed to reproduce the analyses presented in the paper. It includes all scripts for data processing and the multispecies-coalescent species-delimitation analyses (in BEAST2 and BPP), example input datasets, the associated configuration files and model outputs. See the sections/folders for a description of each component and instructions for re-running the workflow.
An archived, release of this repository is also available on Zenodo: https://doi.org/10.5281/zenodo.15519666.
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.
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