Abstract
Tropical rainforests harbor extraordinary biodiversity. The Amazon basin is thought to hold 30% of all river fish species in the world. Information about the ecology, reproduction, and recruitment of most species is still lacking, thus hampering fisheries management and successful conservation strategies. One of the key understudied issues in the study of population dynamics is recruitment. Fish larval ecology in tropical biomes is still in its infancy owing to identification difficulties. Molecular techniques are very promising tools for the identification of larvae at the species level. However, one of their limits is obtaining individual sequences with large samples of larvae. To facilitate this task, we developed a new method based on the massive parallel sequencing capability of next generation sequencing (NGS) coupled with hybridization capture. We focused on the mitochondrial marker cytochrome oxidase I (COI). The results obtained using the new method were compared with individual larval sequencing. We validated the ability of the method to identify Amazonian catfish larvae at the species level and to estimate the relative abundance of species in batches of larvae. Finally, we applied the method and provided evidence for strong temporal variation in reproductive activity of catfish species in the Ucayalí River in the Peruvian Amazon. This new time and cost effective method enables the acquisition of large datasets, paving the way for a finer understanding of reproductive dynamics and recruitment patterns of tropical fish species, with major implications for fisheries management and conservation.
Highlights
The Amazon basin is thought to hold 30% of all river fish species described to date [1]
We developed a new method based on the massive parallel sequencing capability of generation sequencing (NGS) coupled with hybridization capture
The study of their recruitment is difficult. These migratory fish species represent over 80% of fishery catches in the Amazonian basin, and most of them belong to the orders Characiformes and Siluriformes [8,9,10]
Summary
The Amazon basin is thought to hold 30% of all river fish species described to date [1]. The study of their recruitment is difficult These migratory fish species represent over 80% of fishery catches in the Amazonian basin, and most of them belong to the orders Characiformes and Siluriformes (catfish) [8,9,10]. The larvae drift downstream to their nursery area in the Amazon estuary where they grow before migrating upriver to join the breeding adults in the headwaters [14,15,16,17,18] This long-distance migratory life cycle is threatened by human activities, overfishing and the construction of hydroelectric dams, which could drastically limit larval recruitment, the renewal of fisheries resources. The technique has already been successfully used to identify adult siluriform species [21,22,23] More recently this approach was extended to the identification of larvae [24,25] using individual Sanger sequencing. It is very easy to extrapolate from a proof-of-concept on a single marker to several markers, whole mitochondria, or even several thousand nuclear genes [33]
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