Biology subjects

van der Sprong, J.

Publications and source records attributed to van der Sprong, J..

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↗

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

Barcoding-inferred biodiversity of shallow-water Indo-Pacific demosponges

AimThe Indo-Pacific is the worlds largest marine biogeographic region. It is characterised by different degrees of connectivity among its subregions, and harbours the majority of demosponge species currently known to science. Comparisons between several regional sponge faunas have been undertaken in the past, mostly based on identifying the sponge species morphologically. The Sponge Barcoding Project, in tandem with other regional DNA taxonomy campaigns, provides one of the largest DNA-based taxonomic data collections from sponges of the Indo-Pacific. Here, we utilise the sponge barcoding data in the largest molecular biodiversity study of sponges to date, which reveals patterns of shallow-water demosponge faunal connectivity, endemism, and distribution in the Indo-Pacific with a level of resolution unavailable in prior morphology-based studies. LocationDemosponge specimens in this study cover 13 marine provinces of the Indo-Pacific, from the Red Sea to South East Polynesia. MethodsWe classified demosponge barcodes using the ribosomal subunit (28S rDNA) of 1,910 sponge samples into molecular operational taxonomic units (MOTUs). MOTU composition of the 13 marine provinces was compared based on Jaccard and Sorenson dissimilarities, and other biodiversity indices. ResultsOur data corroborated high levels of endemism among demosponges. Faunal overlaps were revealed between the Red Sea and the Gulf, which displayed relatively small connectivity with other marine provinces of the Western Indian Ocean. In the Western Indian Ocean, we observed a strong faunistic boundary to the Central Indo-Pacific. The Polynesian sponge faunas were comparatively isolated marine provinces of the Central Indo-Pacific. Main conclusionsOur data corroborate case studies on sponges that generally reject the presence of cosmopolitan or otherwise widespread sponge species, instead revealing high levels of regional endemism. This is consistent with similar observations and hypotheses in other marine invertebrates. Connectivity among Indo-Pacific marine provinces differs for demosponges in many aspects from that of other marine taxa, such as corals and fishes, probably due to their shorter pelagic larval phase.

zoology↗