Abstract
To date, more than 2400 valid fish species have been recorded in the Amazon basin. However, some regions remain poorly documented. This is the case in the Beni basin and in particular in one of its main sub-basins, the Tuichi, an Andean foothills rivers flowing through the Madidi National Park in the Bolivian Amazonia. The knowledge of its ichthyological diversity is, however, essential for the management and protection of aquatic ecosystems, which are threatened by the development of infrastructures (dams, factories and cities), mining and deforestation. Environmental DNA (eDNA) has been relatively little used so far in the Amazon basin. We sampled eDNA from water in 34 sites in lakes and rivers in the Beni basin including 22 sites in the Tuichi sub-basin, during the dry season. To assess the biogeographical patterns of the amazonian ichthyofauna, we implemented a metabarcoding approach using two pairs of specific primers designed and developed in our laboratory to amplify two partially overlapping CO1 fragments, one of 185bp and another of 285bp. We detected 252 fish taxa (207 at species level) among which 57 are newly identified for the Beni watershed. Species compositions are significantly different between lakes and rivers but also between rivers according to their hydrographic rank and altitude. Furthermore, the diversity patterns are related to the different hydro-ecoregions through which the Tuichi flows. The eDNA approach makes it possible to identify and complete the inventory of the ichthyofauna in this still poorly documented Amazon basin. However, taxonomic identification remains constrained by the lack of reference barcodes in public databases and does not allow the assignment of all OTUs. Our results can be taken into account in conservation and management strategies and could serve as a baseline for future studies, including on other Andean tributaries.
Highlights
The Amazon basin hosts the largest freshwater fish diversity on earth with 2,406 native species [1, 2] as well as a high genetic diversity [3], but is facing increasing threats from anthropogenic activities such as deforestation, habitat degradation, overexploitation, hydropower dam building, invasive species and pollution, and from climate change [4,5,6]
5,246 operational taxonomic units (OTUs) made up from 12.59 million sequences were assigned to a fish COI reference, 93.6% at the species level
Since the beginning of the 19th century until recently, 444 species of fish have been identified in the Beni basin [1]
Summary
The Amazon basin hosts the largest freshwater fish diversity on earth with 2,406 native species [1, 2] as well as a high genetic diversity [3], but is facing increasing threats from anthropogenic activities such as deforestation, habitat degradation, overexploitation, hydropower dam building, invasive species and pollution, and from climate change [4,5,6]. The Madeira is one of the most species-rich basins of the Amazon [2]. It includes the Beni watershed, already considered vulnerable to anthropic pressure and where knowledge gaps remain, such as in the Tuichi River [1]. The Tuichi basin is part of the Madidi National Park and Natural Area of Integrated Management (hereafter abbreviated Madidi NP), which is included in the Tropical Andes hotspot of biodiversity [8,9,10] and hosts one of the few identified spawning area for many fish species [11]. It appears urgent to implement conservation and management measures to protect this biodiversity and to fill known gaps in terms of collection and knowledge of fish species [1]
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