the need that we have to keep material documents, the specimens, in still-increasing numbers.
Another future issue concerning collections is related to the development of metagenomics. Developed by microbiologists, this technique makes it possible to obtain global DNA samples from an environmental sample (soil, water, etc.) (Tringe and Rubin 2005). It does not distinguish between the individual organisms analyzed, but rather extracts the overall DNA of a given sample. It therefore does not allow us to return to individual specimens and to the material origin of the data obtained. When the sequenced taxa are unknown at the molecular level, they cannot be identified in a taxonomic sense and thus linked to the existing body of knowledge (Pellens et al. 2016, pp. 375–383). A huge study of plankton in the world’s oceans, for example, reports over 100,000 operational taxonomic units (OTUs) detected by metagenomics, of which only a little over 11,000, at best, are described with a name in the scientific literature (Vargas et al. 2015). Initiatives with similar implications are developing with respect to fungi, for which molecular identification is preferred to the uneasy linkage to traditional taxonomy that is difficult to conduct on microscopic organisms with limited access to direct sampling (Nilsson et al. 2019).
Initially, all these developments occur without too many problems because they are based directly on existing knowledge and the taxon naming system. Nevertheless, it seems quite obvious that a second cycle of knowledge acquisition, on the occasion of future studies, with mixed reference to traditional taxa and molecular entities defined in the meantime, may lead to a great confusion, a lack of global coherence and a lack of capitalization in knowledge.
Unfortunately, there is no miracle solution to this duality between collections or traditional taxonomy and metagenomics, except by organizing crossover studies between these different fields of activity and thus reinforcing the links between species, taxa and molecular OTUs. Collections remain as indispensable as ever in this context and it is simply necessary to ensure that the links with molecular data, which are already very lax, are, at last, adequately rewoven.
2.7. Conclusion
Natural history collections are alive and well and guarantee us a rich future of diachronic or large-scale scientific studies. The usual criticisms of their deficiencies or biases (Beck et al. 2012) do not hold if we rightly consider that we need to resample collections for every new study we conduct instead of considering that they should be improved according to an ideal universal protocol.
Their future study can be very fruitful but their future enrichment can very quickly become a problem and slow down significantly if we do not modify our behavior by making our data properly available and if we do not create the necessary bridges between collections, taxonomy and new forms of sampling. These are open science objectives which must be rigorously implemented in relation to the FAIR data concept.
The permanence and coherence of knowledge on biodiversity come at this price. All the knowledge we have on biodiversity is scattered in a huge and diverse literature and only the taxonomic names and the specimens that are potentially associated with them allow for this knowledge to be united.
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