The global genetic diversity of planktonic foraminifera reveals the structure of cryptic speciation in plankton

• Published in: Biological Reviews
• Main Authors: Morard, Raphaël, Darling, Kate, Weiner, Agnes K. M., Hassenrueck, Christiane, Vanni, Chiara, Cordier, Tristan, Henry, Nicolas, Greco, Mattia, Vollmar, Nele M., Milivojevic, Tamara, Rahman, Shirin Nurshan, Siccha, Michael, Meilland, Julie, Jonkers, Lukas, Quillévéré, Frédéric, Escarguel, Gilles, Douady, Christophe J., de Garidel-Thoron, Thibault, Vargas, Colomban de, Kucera, Michal
• Other Authors: Ministerio de Ciencia e Innovación (España), European Commission, Centre National de la Recherche Scientifique (France), Natural Environment Research Council (UK), German Research Foundation, Agencia Estatal de Investigación (España)
• Format: Article in Journal/Newspaper
• Language: English
• Published: John Wiley & Sons 2024
• Subjects: Protists; Planktonic foraminifera; Cryptic diversity; Molecular taxonomy; Automated delimitation; Barcoding; Metabarcoding; Ecology; Biogeography; Biodiversity; Conserve and sustainably use the oceans; seas and marine resources for sustainable development
• Online Access: http://hdl.handle.net/10261/365784; https://doi.org/10.1111/brv.13065

24 pages, 12 figures, 1 table, supporting information https://doi.org/10.1111/brv.13065.-- Data Availability: The data that support the findings of this study are provided as supporting information and are openly available at Zenodo (10.5281/zenodo.10454474); the R script is provided on GitHub (https://github.com/Raph-forams/Forams_Cryptic_Diversity) The nature and extent of diversity in the plankton has fascinated scientists for over a century. Initially, the discovery of many new species in the remarkably uniform and unstructured pelagic environment appeared to challenge the concept of ecological niches. Later, it became obvious that only a fraction of plankton diversity had been formally described, because plankton assemblages are dominated by understudied eukaryotic lineages with small size that lack clearly distinguishable morphological features. The high diversity of the plankton has been confirmed by comprehensive metabarcoding surveys, but interpretation of the underlying molecular taxonomies is hindered by insufficient integration of genetic diversity with morphological taxonomy and ecological observations. Here we use planktonic foraminifera as a study model and reveal the full extent of their genetic diversity and investigate geographical and ecological patterns in their distribution. To this end, we assembled a global data set of ~7600 ribosomal DNA sequences obtained from morphologically characterised individual foraminifera, established a robust molecular taxonomic framework for the observed diversity, and used it to query a global metabarcoding data set covering ~1700 samples with ~2.48 billion reads. This allowed us to extract and assign 1 million reads, enabling characterisation of the structure of the genetic diversity of the group across ~1100 oceanic stations worldwide. Our sampling revealed the existence of, at most, 94 distinct molecular operational taxonomic units (MOTUs) at a level of divergence indicative of biological species. The genetic diversity only doubles the number of formally ...