The black piranha (Serrasalmus rhombeus), a widely spread species in the rivers of the Amazon basin, plays a vital role as both key predator and important prey. Despite its essential contribution to ecosystem stability, there is a lack of information regarding its genetic diversity and population dynamics in the central Amazon region. As the Amazon continues to undergo environmental changes in the context of growing anthropogenic threats, such knowledge is fundamental for assist in the conservation of this species. This study is the first to analyze the genetic diversity and population structure of S. rhombeus in the central Amazon region using high-resolution genomic data. We employed a Genotyping-by-Sequencing approach with 248 samples across 14 study sites from various tributaries, encompassing diverse water types (black, white and clear water) and characterized by 34 physiochemical parameters. The data reveals low diversity accompanied by pronounced signs of inbreeding in half of the sites and robust genetic differentiation and variation among sites and within-sites. Surprisingly, we also found evidence of higher dispersal capacity than previously recognized. Our analysis exposed a complex and high population structure with genetic groups exclusive to some sites. Gene flow was low and some groups presented ambiguous genealogical divergence index (gdi) signals, suggesting the occurrence of potential cryptic species. Moreover, our results suggest that the the population structure of black piranha appears more influenced by historical events than contemporary factors. These results underscore the need to give greater attention to this keystone species, for which no regulatory framework or conservation strategies is presently in effect.

Amazonia is characterized by very heterogeneous riverscapes dominated by two drastically divergent water types: black (ion-poor, dissolved organic carbonate rich and acidic) and white (nutrient rich and turbid) waters. Recent phylogeographic and genomic studies have associated the ecotone formed by these environments to ecologically driven speciation in fishes. With the objective of better understanding the evolutionary forces behind the Amazonian Teleostean diversification, we sampled 240 Mesonauta festivus from 12 sites on a wide area of the Amazonian basin. These sites included three confluences of black and white water environments to seek for repeated evidences of ecological speciation at these ecotones. Results obtained through our genetic assessment based on 41,268 SNPs contrast with previous findings and supports a low structuring power of water types. Conversely, we detected a strong pattern of isolation by unidirectional downstream water current and evidence of past events of vicariance potentially linked to the Amazon River formation. Using a combination of population genetic, phylogeographic analysis and environmental association models, we decomposed the spatial variance from the environmental genetic variance specifically to assess which evolutive forces have shaped inter-population differences in M. festivus’ genome. Our sampling design comprising four major Amazonian rivers and three confluences of black and white water rivers supports the possibility that past studies potentially confounded ecological speciation with a site effect unrepresentative of the full Amazonian watershed. While ecological speciation admittedly played a role in Amazonian fish species diversification, we argue that neutral evolutionary processes explain most of the divergence between M. festivus populations.

Associations between host genotype and the microbiome of holobionts have been shown in a variety of animal clades, but studies on teleosts mostly show weak associations. Our study aimed to explore these relationships in four sympatric Serrasalmidae (i.e. piranha) teleosts from an Amazonian lake, using datasets from the hosts genomes (SNPs from GBS), skin and gut microbiomes (16S rRNA metataxonomics), and diets (COI metabarcoding) from the same fish individuals. Firstly, we investigated whether there were significant covariations of microbiome and fish genotypes at the inter and intraspecific scales. We also assessed the extent of co-variation between Serrasalmidae diet and microbiome, to isolate genotypic differences from dietary effects on community structure. We observed a significant covariation of skin microbiomes and host genotypes at interspecific (R2=24.4%) and intraspecific (R2=6.2%) scales, whereas gut microbiomes correlated poorly with host genotypes. Serrasalmidae diet composition was significantly correlated to fish genotype only at the interspecific scale (R2=5.4%), but did not covary with gut microbiome composition (Mantel R=-0.04; only 6 microbiome taxa involved). Secondly, we tested whether microbial taxa represent reliable host traits to complement host genotypic variations in these species. By using an NMDS ordination-based approach, we observed that subsets of the skin and gut microbiomes selected by a machine-learning Random Forest algorithm can complement host genotypic variations by increasing significantly the average interspecific differentiation. The complementarity of genome and microbiome variations suggests that combining both markers could potentially benefit our understanding of the evolution of Serrasalmidae in future studies.