A Continuum of Biodiversity: Revealing Marine Tropical Fish Diversity From Intra‐ to Interspecific Variation Through Environmental DNA

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Abstract
Describing and understanding diversity patterns from populations to communities remains a fundamental challenge in ecology and evolutionary biology. The main barriers to address this challenge are linked to the difficulty of concurrently assessing diversity from intra‐ to interspecific level and of obtaining genetic data for multiple species, particularly for hyperdiverse taxa like tropical reef fishes. Here, we propose environmental DNA (eDNA) metabarcoding with level‐specific primers (the conserved 12S and the hypervariable D‐loop) as a standardized approach to bridge this gap. Using 21 eDNA samples from the Caribbean Sea, we estimated species diversity across all teleosts (378 Molecular Operational Taxonomic Units, MOTUs) and intraspecific haplotype diversity for several grunt species ( Haemulon 1149 Amplicon Sequence Variants, ASVs). Our results revealed no covariation between the haplotype diversity of Haemulon and the overall species richness detected. However, we detected isolation‐by‐distance patterns at the interspecific level and species‐dependent isolation‐by‐distance at the intraspecific level. Notably, the effect of distance led to a positive covariation between fish species dissimilarity and Haemulon plumierii haplotype dissimilarity across samples. By enabling simultaneous, standardized monitoring of biodiversity across scales, eDNA opens new perspectives on unifying biodiversity assessments and understanding the eco‐evolutionary processes that shape diversity patterns from genes to communities.
Funding Information
  • Agence Nationale de la Recherche (ANR‐18‐CE02‐0016)
  • Agence Nationale de la Recherche (ANR‐21‐CE02‐0032)
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF‐205556)

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