Dirk Erpenbeck 1,2§; Fabian Deister 1; Merrick Ekins 3,4,5; Nora Dotzler 1; John N.A. Hooper 3,5; Toufiek Samaai 6,7,8; Simone Schätzle 1; Joëlle van der Sprong 1; Sergio Vargas 1; Gert Wörheide 1,2,9
1 Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
2 GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
3 Biodiversity Program, Queensland Museum, South Brisbane, QLD, Australia
4 School of Biological Sciences, University of Queensland, St Lucia, Queensland, 4072 Australia
5 Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, Australia
6 Department of Forestry, Fisheries and the environment, Oceans and Coasts Research, Cape Town, South Africa
7 University of the Western Cape, Biodiversity Conservation Department, Bellville, Cape Town, South Africa
8 Iziko Museums of South Africa, Marine Biology, Gardens, Cape Town, South Africa
9 Bavarian State Collection of Palaeontology and Geology, Munich, Germany
§ corresponding author: [email protected]
Marine biodiversity collections are critical resources for understanding biodiversity and evolutionary patterns. However, their taxonomic utility is limited due to challenges in morphological identification and cryptic speciation, particularly in sponges (Porifera). This study applied a novel target-enriched multilocus assay to a decades-old unidentified collection of Tethyidae from the Queensland Museum. Target-specific baits were designed based on Tethya genome data, enabling the sequencing of nuclear ultraconserved elements (UCEs) and mitochondrial genomes, even from degraded samples. In the study, 40 specimens were sequenced, and we found up to 4,440 UCEs per sample. The phylogenies were based on up to 2,788 loci and demonstrated overall high bootstrap support. Results include robust support for earlier findings on the non-monophyly of Tethya, with lineages linking to other genera (e.g., Stellitethya, Tethycometes), suggesting that Tethya is a paraphyletic group foundational to Tethyidae. Morphological subgroupings, previously hypothesized, were validated genetically, though several novel relationships emerged. This approach highlights the suitability of target-enriched multilocus assays for archival collections, enabling detailed biodiversity assessments using collection material initially not sampled for molecular work. Our Tethya case study underlines that this methodology provides a framework for broader applications in marine biodiversity conservation, facilitating the understanding and preservation of past and present biodiversity to guide future efforts.
This repository includes the following:
- UCE alignments of 25%, 35%, 45%, 55%, 65%, 75% and 85% coverage sets. ("UCE-alignments.zip")
- full mtDNA protein alignment and tree ("mt_Protein_alignment.nex")
- 28S rRNA alignment and RAxML tree ("28SrRNA_alignment.nex")
- custom Perl-scripts
For the following information we recommend to consult the following github page: https://github.com/PalMuc/HaploTC