Andrea Polanco Fernandez

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Polanco Fernandez

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Andrea

ORCID

0000-0001-6121-5214

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Publications 1 - 10 of 14

Detecting aquatic and terrestrial biodiversity in a tropical estuary using environmental DNA
Polanco Fernandez, Andrea; Mutis Martinezguerra, Maria; Marques, Virginie; et al. (2021)
Biotropica
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. Abstract in Spanish is available with online material.
Similar trait structure and vulnerability in pelagic fish faunas on two remote island systems
Steinberg, Madeline; Juhel, Jean-Baptiste; Marques, Virginie; et al. (2022)
Marine Biology
The link between biodiversity and ecosystem functioning has been the topic of considerable research, but it remains unclear how biodiversity decline is compromising ecosystem functionality, particularly in the pelagic realm. Here, we explore how pelagic fish species diversity relates to functional diversity by sampling two locations, which, on the basis of biogeography, environmental conditions and human pressures, were expected to host pronounced differences in species composition and abundances and therefore functionality. Strings of five drifting mid-water Baited Remote Underwater Video Systems were used to survey pelagic vertebrate diversity and abundance in two isolated oceanic island systems, the Malpelo Fauna and Flora Sanctuary – a large, 25-year-old marine protected area – and an unprotected area in Cape Verde. Functional diversity, which offers insight into a community’s resilience against disturbance, was analysed using six key functional traits of marine fishes. Abundance was recorded as MaxN, the maximum number of individuals of a given species in a single frame during the 2-h deployment time. Cape Verde showed high overall abundance (Total MaxN 873) and low biomass (3559 kg), with a predominance of smaller fishes. Malpelo showed high biomass (7839 kg) but lower abundance (Total MaxN 465), with a predominance of large species. Species and functional diversity were marginally different between locations. Multivariate analysis of species relative abundances showed significant divergence between locations, although community functional traits overlapped strongly, suggesting that both communities share a similar structure and vulnerability. The existence of a common functional ‘backbone’ in diverging species communities across the oceans, under different productivity regimes, and under different protection levels, suggests that although pelagic communities may differ considerably in terms of species composition, this does not translate into a differing functional structure and resilience potential. Whether this vulnerability is a common feature of pelagic communities and how this contrasts with benthic systems warrants further research.
Use of environmental DNA in assessment of fish functional and phylogenetic diversity
Marques, Virginie; Castagné, Paul; Polanco Fernandez, Andrea; et al. (2021)
Conservation Biology
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.
Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes
Polanco Fernandez, Andrea; Marques, Virginie; Fopp, Fabian; et al. (2021)
Environmental DNA
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.
Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding
Mathon, Laetitia; Marques, Virginie; Mouillot, David; et al. (2022)
Proceedings of the Royal Society B: Biological Sciences
Increasing speed and magnitude of global change threaten the world's biodiversity and particularly coral reef fishes. A better understanding of large-scale patterns and processes on coral reefs is essential to prevent fish biodiversity decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns on these highly diverse and threatened ecosystems. We analysed 226 environmental DNA (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central and Southwest Pacific, Coral Triangle and Western Indian Ocean) and compared those to 2047 underwater visual censuses from the Reef Life Survey in 1224 stations. Environmental DNA reveals a higher (16%) fish biodiversity, with 2650 taxa, and 25% more families than underwater visual surveys. By identifying more pelagic, reef-associated and crypto-benthic species, eDNA offers a fresh view on assembly rules across spatial scales. Nevertheless, the reef life survey identified more species than eDNA in 47 shared families, which can be due to incomplete sequence assignment, possibly combined with incomplete detection in the environment, for some species. Combining eDNA metabarcoding and extensive visual census offers novel insights on the spatial organization of the richest marine ecosystems.
Ecological indices from environmental DNA to contrast coastal reefs under different anthropogenic pressures
Polanco Fernandez, Andrea; Waldock, Conor; Keggin, Thomas; et al. (2022)
Ecology and Evolution
Human activities can degrade the quality of coral reefs and cause a decline in fish species richness and functional diversity and an erosion of the ecosystem services provided. Environmental DNA metabarcoding (eDNA) has been proposed as an alternative to Underwater Visual Census (UVC) to offer more rapid assessment of marine biodiversity to meet management demands for ecosystem health indices. Taxonomic information derived from sequenced eDNA can be combined with functional traits and phylogenetic positions to generate a variety of ecological indices describing ecosystem functioning. Here, we inventoried reef fish assemblages of two contrasting coastal areas of Curacao, (i) near the island's capital city and (ii) in a remote area under more limited anthropogenic pressure. We sampled eDNA by filtering large volumes of seawater (2 x 30 L) along 2 km boat transects, which we coupled with species ecological properties related to habitat use, trophic level, and body size to investigate the difference in fish taxonomic composition, functional and phylogenetic indices recovered from eDNA metabarcoding between these two distinct coastal areas. Despite no marked difference in species richness, we found a higher phylogenetic diversity in proximity to the city, but a higher functional diversity on the more isolated reef. Composition differences between coastal areas were associated with different frequencies of reef fish families. Because of a partial reference database, eDNA only partly matched those detected with UVC, but eDNA surveys nevertheless provided rapid and robust species occurrence responses to contrasting environments. eDNA metabarcoding coupled with functional and phylogenetic diversity assessment can serve the management of coastal habitats under increasing threat from global changes.
Marine fish diversity in Tropical America associated with both past and present environmental conditions
Polanco Fernandez, Andrea; Fopp, Fabian; Albouy, Camille; et al. (2020)
Journal of Biogeography
Aim Tropical America, including the Tropical Eastern Pacific and the Caribbean Sea, presents a high level of marine biodiversity, but its fish fauna has been poorly documented. In early studies marine species distributions were interpreted based on tectonic activity during the late Cenozoic, while more recent studies have highlighted a link with the present-day environment. Here, we described the assemblage richness and composition of fishes in Tropical America and related these properties to both the past evolution of marine environmental conditions and current environmental gradients. Location Tropical America. Taxon Demersal and benthic fishes. Methods We mapped the distribution of 2,216 demersal and benthic fish species of Tropical America using existing occurrence data. We computed three assemblage indicators: species richness, composition and nestedness, which we explained by environmental gradients. We linked compositional distance to environmental differences using distance-based redundancy analysis, species richness and nestedness using a generalized linear model. We ran simulations of a mechanistic model in which three processes determine the spatial dynamics of biodiversity: speciation, dispersal and extinction. This model yielded estimates for species assemblage properties following palaeogeographic changes in the region that shaped the current coastal habitat configuration. Results Fish species richness in Tropical America peaks around the Florida Peninsula, Bahamas and Greater Antilles. Fish composition varies along a depth gradient, between the Tropical Eastern Pacific and the Caribbean Sea, and forms distinct domains within the Caribbean region. The nestedness component of beta-diversity is lower in shallower assemblages, especially those along the outer section of the Greater Caribbean. Species richness and nestedness are partly explained by current environmental conditions, but model simulations illustrate how this may be further explained by the tectonic history of the region. Main conclusions Species richness peaks in the Greater Caribbean, coinciding with generally favourable current environmental conditions for demersal and benthic fishes. The high species richness and the low nestedness of fish assemblages in the Cuba region are compatible with the results of palaeo-environmental changes that have occurred in that area. Effects of the plate tectonic history might still be present in the organization of fish fauna in this region.
Checklist and new records of coastal-marine fishes of the Department of Atlántico (Colombian Caribbean)
Moreno-Tilano, Jorge Alberto; Gracia Clavijo, María Adriana; Polanco Fernandez, Andrea (2023)
Caldasia
This first checklist of coastal marine fish inhabiting the Department of Atlántico (Colombian Caribbean) was compiled through an exhaustive review of published information, databases, other unpublished sources, and primary data. We recorded 272 fish species, of which twenty were first reported for this re-gion. Carangidae, Lutjanidae, and Scombridae were the richest families, which together represent 14 % of the total number of species. According to the Red List of Marine Fishes of Colombia, 37 species show some degree of threat. Most species are demersal, associated with soft bottoms. However, a significant number of species were also found associated with hard substrates, suggesting that fish congregate around these less abundant substrates, as the coastline is mainly dominated by fine sediments. This study reveals that this region has higher fish richness than previously thought and highlights the need to carry out further studies to increase the knowledge of the ichthyofauna, framed in the environmental setting of the Department’s coastal zone and the anthropogenic influence on the group in question. Bet-ter knowledge of the richness of ichthyic species contributes indirectly to the improvement of current management plans for marine biodiversity conservation.
Environmental DNA highlights fish biodiversity in mesophotic ecosystems
Muff, Marion; Jaquier, Mélissa; Marques, Virginie; et al. (2023)
Environmental DNA
Mesophotic marine ecosystems are characterized by lower light penetration supporting specialized fish fauna. Due to their depths (−30–−150 m), accessibility is challenging, and the structure of mesophotic fish assemblages is generally less known than either shallow reefs or deep zones with soft bottoms which are generally trawled. Environmental DNA metabarcoding from seawater filtered in situ could improve our ability to monitor the diversity of mesophotic ecosystems. Here, we developed and tested a submersible standalone pumping device allowing targeted marine water filtering to explore the biodiversity of two mesophotic ecosystems, one temperate along the Provence coast in the North-Western Mediterranean Sea and one tropical at the seamount La Pérouse in the Western Indian Ocean. We filtered water samples from depths ranging between 0 and 200 m in the Mediterranean Sea and between 60 and 140 m in the Indian Ocean and applied a metabarcoding protocol using the teleo primer pair targeting the 12S mitochondrial rDNA (Actinopterygii and Chondrichthyes). For both study regions, our eDNA surveys were able to recover highly diverse fish assemblages, and the compositional analysis of eDNA samples showed both a marked signal of fish compositional turnover and overlapping taxa between depth zones. Further, we observed that a substantial number of species were found in samples collected in depths beyond their reported depth range suggesting an underestimation of species' depth tolerances. eDNA metabarcoding should thus complement existing knowledge of species' geographic distributions across space and depth. Overall, our results demonstrate the potential of eDNA metabarcoding for future mesophotic surveys as it allows fast and broad biodiversity assessment.
Confirmación de la presencia del pez globo Chilomycterus spinosus (Diodontidae) en el Caribe colombiano
Acosta‐Chaparro, Andrés; Polanco Fernandez, Andrea; Navas-Camacho, Raúl (2023)
Boletin de Investigaciones Marinas y Costeras
Se registra por primera vez en el Caribe colombiano el pez globo Chilomycterus spinosus correspondiente a la familia Diodontidae. Un individuo de esta especie fue avistado en agosto de 2022 en la zona de Bahía Portete a una profundidad de 1.5 m. Se reporta una variación en el rango de profundidad de esta especie, a zonas más someras.

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