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Environmental DNA (eDNA) analysis is a revolutionary method to monitor marine biodiversity from animal DNA traces. Examining the capacity of eDNA to provide accurate biodiversity measures in species‐rich ecosystems such as coral reefs is a prerequisite for their application in long‐term monitoring. Here, we surveyed two Colombian tropical marine reefs, the island of Providencia and Gayraca Bay near Santa Marta, using eDNA and underwater visual census (UVC) methods. We collected a large quantity of surface water (30 L per filter) above the reefs and applied a metabarcoding protocol using three different primer sets targeting the 12S mitochondrial DNA, which are specific to the vertebrates Actinopterygii and Elasmobranchii. By assigning eDNA sequences to species using a public reference database, we detected the presence of 107 and 85 fish species, 106 and 92 genera, and 73 and 57 families in Providencia and Gayraca Bay, respectively. Of the species identified using eDNA, 32.7% (Providencia) and 18.8% (Gayraca) were also found in the UVCs. We further found congruence in genus and species richness and abundance between eDNA and UVC approaches in Providencia but not in Gayraca Bay. Mismatches between eDNA and UVC had a phylogenetic and ecological signal, with eDNA detecting a broader phylogenetic diversity and more effectively detecting smaller species, pelagic species and those in deeper habitats. Altogether, eDNA can be used for fast and broad biodiversity surveys and is applicable to species‐rich ecosystems in the tropics, but improved coverage of the reference database is required before this new method could serve as an effective complement to traditional census methods.

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 hours 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 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 hours 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.

Estuaries are characterized by a tidal regime and are strongly influenced by hydrodynamics and host diverse and highly dynamic habitats, from fresh, brackish, or saltwater to terrestrial, whose biodiversity is especially difficult to monitor. Here, we investigated the potential of environmental DNA (eDNA) metabarcoding, with three primer sets targeting different regions of the mitochondrial DNA 12S ribosomal RNA gene, to detect vertebrate diversity in the estuary of the Don Diego River in Colombia. With eDNA, we detected not only aquatic organisms, including fishes, amphibians, and reptiles, but also a large diversity of terrestrial, arboreal, and flying vertebrates, including mammals and birds, living in the estuary surroundings. Further, the eDNA signal remained relatively localized along the watercourse. A transect from the deep outer section of the estuary, across the river mouth toward the inner section of the river, showed marked taxonomic turnover from typical marine to freshwater fishes, while eDNA of terrestrial and arboreal species was mainly found in the inner section of the estuary. Our results indicate that eDNA enables the detection of a large diversity of vertebrates and could become an important tool for biodiversity monitoring in estuaries, where water integrates information across the ecosystem.

Las relaciones simbióticas en comunidades coralinas mesofóticas y de profundidad han sido ampliamente reconocidas en las últimas décadas. Teniendo en cuenta la importancia de los corales como formadores de hábitat en zonas profundas por sus tamaños y formas tridimensionales y la estrecha relación que históricamente han mantenido con diferentes grupos de invertebrados y peces, este estudio se centró en las asociaciones entre ofiuras y octocorales encontradas entre 70 y 270 m de profundidad en La Guajira y en el Parque Nacional Natural Corales de Profundidad - PNNCP (Bolívar). Los ejemplares en asociación se recolectaron durante el Proyecto ICP realizado en el 2013 por el Invemar en convenio con Ecopetrol, mediante arrastres de diez minutos con redes de tipo semi-balón (9,5 m de ancho de la boca). Para dilucidar las relaciones existentes entre octocorales y ofiuros, se realizó la identificación de las diferentes especies involucradas a partir de fotografías y claves taxonómicas. En total fueron revisados 11 ofiuras y 11 colonias/fragmentos de octocoral; los cuales pertenecen a nueve especies, tres ofiuras de los géneros Asteroschema y Hemieuryale , y seis octocorales de los géneros Nicella y Heterogorgia . Las asociaciones aquí encontradas fueron identificadas como Epibiosis/comensalismo y Epibiosis/parasitismo, siendo la primera el tipo de asociación más común entre los especímenes revisados. La mayoría de los especímenes en asociación se encontraron en el PNNCP y solo una de estas en el área de La Guajira. Algunas de las especies de ofiuros y octocorales encontrados constituyen nuevos registros para el Caribe colombiano y el Caribe suroccidental, lo cual permite ampliar su intervalo de distribución geográfica, y en algunos casos su distribución batimétrica. Finalmente, para contribuir a la historia de vida de cada una de las especies identificadas se describen las asociaciones y se presentan descripciones detalladas de la morfología y distribución geográfica y batim

This work investigates the systematics of the genus Holothuria in the Mediterranean Sea and Northeastern Atlantic in the light of a wider molecular phylogenetic hypothesis of Holothuriidae, and it also provides a time-scale for the family diversification using mitochondrial markers and the molecular clock hypothesis. The subgenera Holothuria and Roweothuria are retrieved as paraphyletic. At least four separate lineages, with quite different time frameworks were identified. There are at least three species with an apparent long evolutionary history, H. forskali, H. sanctori and H. impatiens and six species belonging to Holothuria, Roweothuria and Vaneyothuria, which have diverged relatively recently.