Minimalist barcodes for sponges: a case study classifying African freshwater Spongillida

Abstract

African sponges, particularly freshwater sponges, are understudied relative to demosponges in most other geographical regions. Freshwater sponges (Spongillida) likely share a common ancestor; however, their evolutionary history, particularly during their radiation into endemic and allegedly cosmopolitan groups, is unclear. Freshwater sponges of at least 58 species of 17 genera and four families are described from Central and Eastern Africa, but the diversity is underestimated due to limited distinguishable morphological features. The discovery of additional cryptic species is very likely with the use of molecular techniques such as DNA barcoding. The Royal Museum of Central Africa (MRAC, Tervuren, Belgium) hosts one of the largest collections of (Central) African freshwater sponge type material. Type specimens in theory constitute ideal targets for molecular taxonomy; however, the success is frequently hampered by DNA degradation and deamination, which are a consequence of suboptimal preservation techniques. Therefore, we genotyped African demosponge holotype material of the MRAC with specific short primers suitable for degenerated tissue and compare the results with the current, morphology-based classification. Our results demonstrate the utility of minimalistic barcodes for identification of sponges, potentially enabling efficient identification of individuals in taxonomic or metabarcoding studies, and highlight inconsistencies in the current freshwater sponge classification.

Genetic analysis confirms the freshwater origin of the endemic Caspian sponges (Demospongiae, Spongillida, Metschnikowiidae)

“…Our results support the monophyly of Lubomirskiidae, the sponges of Lake Baikal. They form a strongly supported monophyletic clade with Ephydatia muelleri as a sister species, which is consistent with preceding analyses (Itskovich et al 2008(Itskovich et al , 2015Erpenbeck et al 2019). However, Radiospongilla turns out to be paraphyletic.…”

“…This clade also supports the hypothesis of the formation of endemic species from cosmopolitan founders (Meixner et al 2007;Erpenbeck et al 2011). The high variability of the ITS spacers makes it difficult to align them unambiguously, which leads to low support for deeper nodes (Erpenbeck et al 2019). Therefore, more markers are required for improving resolution of the trees.…”

“…Except for this, the obtained results are in accordance with the previous data. They demonstrate the unresolved phylogeny of Spongillida at the family level (Erpenbeck et al 2011(Erpenbeck et al , 2019Carballo et al 2018). We believe the revision of the taxonomy of Spongillida at the family level requires the addition of other molecular markers and genomic data.…”

Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage

“…An important application is, for example, to search for the position of a previously unknown species in an existing phylogenetic tree, the so-called phylogenetic placement [31]. In this situation, low-pass sequencing can be an attractive alternative to phylogenetic barcoding based on selected marker genes [30,13] to identify the phylogenetic position of an unknown species. As read-to-read comparison with Read-Spam still produces reliable results for sequencing coverage down to 2 −3 X, it is possible to estimate phylogenetic distances between strains or species for which assembled genomes are not available.…”

Study of variability of ITS1 and ITS2 spacers of rDNA of freshwater sponges (Porifera, Spongillida)

“…Molecular analyses based mostly on the internal transcribed spacer (ITS) region and COXI sequences have provided us with a better understanding of freshwater sponge phylogeny (Itskovich et al, 2017;Schuster et al, 2018;Erpenbeck et al, 2019). This finding also indicates that the taxonomy of freshwater sponges needs urgent revision.…”