Environmental DNA reveals a mismatch between diversity facets of Amazonian fishes in response to contrasting geographical, environmental and anthropogenic effects

Abstract

Freshwater ecosystems are among the most endangered ecosystem in the world. Understanding how human activities affect these ecosystems requires disentangling and quantifying the contribution of the factors driving community assembly. While it has been largely studied in temperate freshwaters, tropical ecosystems remain challenging to study due to the high species richness and the lack of knowledge on species distribution. Here, the use of eDNA‐based fish inventories combined to a community‐level modelling approach allowed depicting of assembly rules and quantifying the relative contribution of geographic, environmental and anthropic factors to fish assembly. We then used the model predictions to map spatial biodiversity and assess the representativity of sites surveyed in French Guiana within the EU Water Framework Directive (WFD) and highlighted areas that should host unique freshwater fish assemblages. We demonstrated a mismatch between the taxonomic and functional diversity. Taxonomic assemblages between but also within basins were mainly the results of dispersal limitation resulting from basin isolation and natural river barriers. Contrastingly, functional assemblages were ruled by environmental and anthropic factors. The regional mapping of fish diversity indicated that the sites surveyed within the EU WFD had a better representativity of the regional functional diversity than taxonomic diversity. Importantly, we also showed that the assemblages expected to be the most altered by anthropic factors were the most poorly represented in terms of functional diversity in the surveyed sites. The predictions of unique functional and taxonomic assemblages could, therefore, guide the establishment of new survey sites to increase fish diversity representativity and improve this monitoring program.

Steps forward in biomonitoring 2.0: eDNA Metabarcoding and community‐level modelling allow the assessment of complex drivers of Neotropical fish diversity

“…However, distinct bioinformatic treatments and filtering thresholds may affect conclusions resulting in large differences in diversity estimates. Moreover, the use of taxonomy-free approaches instead of species-level identification of the eDNA output would hamper the use of Coutant et al's (2022) eDNA framework to estimate and predict taxonomic and functional biodiversity distribution in species-rich environments and unexplored areas. Coutant et al's (2022) approach highlights the importance of the species-level resolution in eDNA studies and a proper local curated database.…”

“…It is unlikely that eDNA will replace traditional biodiversity assessments that provide unique and valuable ecological information, especially in biodiverse-rich ecosystems. However, Coutant et al (2022) shed light on the great potential of combining knowledge from traditional and state-of-the-art methods in assessing biodiversity. In addition to being a valuable tool for unravelling distribution patterns of diversity in the Amazon, eDNA also has great potential for scaling up the monitoring of freshwater biodiversity throughout the Amazon biome.…”

“…In addition to being a valuable tool for unravelling distribution patterns of diversity in the Amazon, eDNA also has great potential for scaling up the monitoring of freshwater biodiversity throughout the Amazon biome. The framework proposed by Coutant et al (2022) will inspire future studies that will improve our understanding of complex ecological systems, as well as assist in conservation planning of freshwater ecosystems. This is urgently needed in Tropical regions, particularly the Amazon, which host most of the global freshwater biodiversity and are undergoing rapid change due to human activities.…”

“…Nonetheless, the Neotropical realm still represents a great challenge to our understanding of species distribution patterns and the role played by different drivers of biodiversity. The paper by Coutant et al (2022) is a great advance towards a holistic approach to quantifying the contribution of environmental and anthropogenic factors that drive community assembly in the Amazon, and how we can apply such knowledge to guide future monitoring programmes. Disentangling the relative roles played by multiple drivers of biodiversity allowed them to also highlight hotspot areas hosting unique freshwater fish diversity and to pinpoint conservation priorities.…”

“…Moreover, the use of a short eDNA fragment to identify specimens to the species level is challenging, since a curated reference library is needed while the selected molecular marker should also have enough variation to discriminate the entire ichthyofauna. Nonetheless, in some regions such as the river basins studied by Coutant et al (2022), knowledge from previous studies, including a reference database, traditional fish inventories and ecological studies (Cilleros et al, 2019) together with testing for eDNA protocol robustness (Coutant et al, 2021), helped overcome such challenges. For instance, 92% of the 400 freshwater fish species described in French Guiana are represented in their local and curated database of the 12S mtDNA fragment, and only 9 species could not be differentiated to the species level (Coutant et al, 2022).…”