Solving classification questions in sponge biology
In this blog Dr Dirk Erpenbeck talks about his co-authored paper Nothing in (sponge) biology makes sense – except when based on holotypes which featured in the New Frontiers in Sponge Science special issue from Journal of the Marine Biological Association.
Organismal taxonomy is nowadays a rather neglected discipline despite the fact that it provides all fundamental groundwork to understand evolution, assess biota, monitor and predict biodiversity changes, and much more. Even in the current Genomic Era we need to identify organisms and require unambiguous ways for their distinction.
Especially classical taxonomy (i.e., morphology-based) resulted in the descriptions of currently about 1.2 million eukaryotic species. These descriptions are based on type material, which was examined for this purpose and is now deposited (and ideally meticulously curated) in natural history collections as reference for this species. Morphological taxonomy, however, clearly faces its limitations for most organisms when diagnostic characters are few (e.g., due to a simple bauplan) or plastic (e.g., due to environmental factors).
Sponges (Porifera) constitute an ecologically and biotechnologically important group of marine organisms, in which both a simple bauplan and environmental plasticity hamper unambiguous identification, even for experts. Molecular taxonomic tools, however, have the potential to surmount the shortcomings of morphological taxonomy – if used adequately.
Comparing sponge DNA sequences against public databases will likely return a “matching” sponge sequence once submitted under a given species name – but is the identification of this reference match reliable? Specialized curated taxonomic databases such as the Sponge Barcoding Project identified this problem and aim to provide the most reliable reference sequences in return. However, the best reference for a species is by definition the (holo)type material. Unfortunately, holotypes are older than their species descriptions and may already have passed the hands of Carl v. Linné in the 1750s. Therefore, scientists frequently hesitate using holotype material for molecular systematic approaches because under non-optimal tissue preservation DNA experiences rapid degradation (preventing PCR) and depurination (causing base changes during PCR).
We show in a few case studies the feasibility and potential of molecular work with holotype material. Samples used in this study go back to the late 19th century and produce sequences solving questions in classification, phylogeny and biochemistry with taxonomic certainty. Although not always successful, the reliability of the reference sequence clearly outweighs any hassle of holotype material acquisition and sequencing. Nevertheless, the most important factor for successful holotype sequencing is simple – it must be attempted.