Lowland central Amazonia is characterized by heterogeneous riverscapes dominated by two chemically divergent water types: black (ion-poor, rich in dissolved organic carbonate and acidic) and white (rich in nutrient and turbid) waters. Recent phylogeographic and genomic studies have associated the ecotone formed by these environments to an ecologically driven genetic divergence between fish present in both water types. With the objective of better understanding the evolutionary forces behind the central 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 divergence at the junction of these ecotones. Results obtained through our genetic assessment based on 41,268 SNPs contrast with previous findings and support a low influence of diverging water physicochemical characteristics on the genetic structuration of M. festivus populations. Conversely, we detected patterns of isolation by downstream water current and evidence of past events of vicariance potentially linked to the Amazon River formation. Using a combination of population genetics, phylogeographic analysis and environmental association models, we decomposed the spatial and environmental genetic variances to assess which evolutionary forces shaped inter-population differences in M. festivus’ genome. Our sampling design, comprising three confluences of black and white water rivers, supports the main role of evolution by allopatry. While an ecologically driven evolution admittedly played a role in Amazonian fish 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.

Here we present an annotated, chromosome-anchored, genome assembly for Lake Trout (Salvelinus namaycush) – a highly diverse salmonid species of notable conservation concern and an excellent model for research on adaptation and speciation. We leveraged Pacific Biosciences long-read sequencing, paired-end Illumina sequencing, proximity ligation (Hi-C), and a previously published linkage map to produce a highly contiguous assembly composed of 7,378 contigs (contig N50 = 1.8 mb) assigned to 4,120 scaffolds (scaffold N50 = 44.975 mb). 84.7% of the genome was assigned to 42 chromosome-sized scaffolds and 93.2% of Benchmarking Universal Single Copy Orthologs were recovered, putting this assembly on par with the best currently available salmonid genomes. Estimates of genome size based on k-mer frequency analysis were highly similar to the total size of the finished genome, suggesting that the entirety of the genome was recovered. A mitome assembly was also produced. Self-vs-self synteny analysis allowed us to identify homeologs resulting from the Salmonid specific autotetraploid event (Ss4R) and alignment with three other salmonid species allowed us to identify homologous chromosomes in other species. We also generated multiple resources useful for future genomic research on Lake Trout including a repeat library and a sex averaged recombination map. A novel RNA sequencing dataset was also used to produce a publicly available set of gene annotations using the National Center for Biotechnology Information Eukaryotic Genome Annotation Pipeline. Potential applications of these resources to population genetics and the conservation of native populations are discussed.