Use of environmental DNA in assessment of fish functional and phylogenetic diversity

• Published in: Conservation biology 2021-12, Vol.35 (6), p.1944-1956
• Main Authors: Marques, Virginie, Castagné, Paul, Polanco, Andréa, Borrero‐Pérez, Giomar Helena, Hocdé, Régis, Guérin, Pierre‐Édouard, Juhel, Jean‐Baptiste, Velez, Laure, Loiseau, Nicolas, Letessier, Tom Bech, Bessudo, Sandra, Valentini, Alice, Dejean, Tony, Mouillot, David, Pellissier, Loïc, Villéger, Sébastien
• Format: Article
• Language: English
• Subjects: accumulation curves; Animals; arrecifes tropicales; biodiversidad; Biodiversity; Biodiversity and Ecology; caracterización genética con ADNa; características funcionales; Census; Censuses; Conservation of Natural Resources; curvas de acumulación; Deoxyribonucleic acid; DNA; DNA Barcoding, Taxonomic; DNA, Environmental; eDNA metabarcoding; Environmental DNA; Environmental Monitoring; Environmental Sciences; Fish; Fishes - genetics; Fishing; functional traits; Global Changes; Hunting; Malpelo; Marine fish; Marine parks; marine protected area; Marine protected areas; Marine systems; Phylogenetics; Phylogeny; Protected areas; Species; Species diversity; Taxonomy; tropical reefs; Underwater; Video; área marina protegida; 功能性状; 海洋保护区; 热带珊瑚礁; 环境DNA宏条形码; 生物多样性; 累积曲线; 视频; 马尔佩洛岛
• ISSN: 0888-8892; 1523-1739
• DOI: 10.1111/cobi.13802

Assessing the impact of global changes and protection effectiveness is a key step in monitoring marine fishes. Most traditional census methods are demanding or destructive. Nondisturbing and nonlethal approaches based on video and environmental DNA are alternatives to underwater visual census or fishing. However, their ability to detect multiple biodiversity factors beyond traditional taxonomic diversity is still unknown. For bony fishes and elasmobranchs, we compared the performance of eDNA metabarcoding and long‐term remote video to assess species’ phylogenetic and functional diversity. We used 10 eDNA samples from 30 L of water each and 25 hr of underwater videos over 4 days on Malpelo Island (pacific coast of Colombia), a remote marine protected area. Metabarcoding of eDNA detected 66% more molecular operational taxonomic units (MOTUs) than species on video. We found 66 and 43 functional entities with a single eDNA marker and videos, respectively, and higher functional richness for eDNA than videos. Despite gaps in genetic reference databases, eDNA also detected a higher fish phylogenetic diversity than videos; accumulation curves showed how 1 eDNA transect detected as much phylogenetic diversity as 25 hr of video. Environmental DNA metabarcoding can be used to affordably, efficiently, and accurately census biodiversity factors in marine systems. Although taxonomic assignments are still limited by species coverage in genetic reference databases, use of MOTUs highlights the potential of eDNA metabarcoding once reference databases have expanded. Uso de ADN Ambiental en la Evaluación de la Diversidad Funcional y Filogenética de los Peces Resumen La evaluación del impacto de los cambios globales y la efectividad de la protección es un paso fundamental para el monitoreo de peces marinos. La mayoría de los métodos tradicionales de censos son demandantes o destructivos, por lo que las estrategias no letales y no intrusivas basadas en videograbaciones y en el ADN ambiental (ADNa) son alternativas a los censos visuales submarinos y a la pesca. Sin embargo, todavía no se conoce la habilidad que tienen estos métodos para detectar diferentes factores de la biodiversidad más allá de la diversidad taxonómica. Para los peces óseos y los elasmobranquios, comparamos el desempeño de la caracterización genética con ADNa y del video remoto de larga duración para evaluar la diversidad funcional y filogenética de las especies. Usamos diez muestras de ADNa tomadas de 30 litr