Unveiling biogeographical patterns of the ichthyofauna in the Tuichi basin, a biodiversity hotspot in the Bolivian Amazon, using environmental DNA

detected at the site sampled immediately downstream. Of the species identified at the Arana river site (point c on Fig 1B), 23 species are not identified at the Tuichi8 site (point 9 on Fig 1B) located only 3.7 km downstream. These 23 species have an average detection rate at the Arana site of 71% and for 9 of these species it is 100% (i.e. identified in all Arana libraries). Given that sampling in lakes was carried out in the dry season without water entering from the main river, DNA detected was emitted only by species present in the lake and in its tributaries. Therefore, in lakes, as well as in rivers, the eDNA approach provides a localized view of species distribution by site which is estimated at a few km in our case study, as evidenced by the strong structure of the species distribution observed among 4 clusters totally independent of the geo- graphical distance, hence of the stream flow (Fig 3B). Environmental factors correlated to the biogeographic structure. The NMDS based on Jac- card distances between sites in fish composition had a stress value of 0.09 showing that the representation was highly reliable. Fish populations are differentiated between ecotypes, rivers and lakes (r2 = 0.52, p-value < 0.0001) (Fig 6A and S4 and S5 Figs for details) and the analysis of variance using distance matrix confirmed a significant separation between the four biogeo- graphic entities defined by the hierarchical clustering (p-value = 0.0009). Fig 4. Occurrence map representing the presence (blue) or absence (white) of taxa (rows) for each site (columns).

Sites and species dendrograms are constructed using Jaccard’s binary distance and a Ward clustering method. The colours associated with the site dendrogram correspond to the biogeographic entities defined by the hierarchical analysis. The colour associated with each leaf in the species dendrogram corresponds to its taxonomic Order. A detailed dendrogram of the taxa with their names is available in S6 Fig. The names of the sites are those shown in Fig 1 (details in S3 Table). https://doi.org/10.1371/journal.pone.0262357.g004 PLOS ONE Fish diversity and distribution in the Tuichi basin PLOS ONE | https://doi.org/10.1371/journal.pone.0262357 January 4, 2022 12 / 25