Speciation process of iconic Arapaima along the Guayana Shield

The future of the largest freshwater fish species, the Arapaima, requires an improved knowledge onthe population status and structure. We conducted a whole genome study to identify populationspecific adaptations of a clearwater population in the Pirara and a whitewater and a blackwaterpopulation in the Essequibo River, widely isolated from the Amazon Basin by the Guayana Shield.Whole genome shotgun data of six museum specimen of the three populations and publicly availabledata of six fishes from Peru and Brazil was used to assemble mitochondrial genomes and analysevariants in the whole genomes. Despite relatively low overall variability, a whole genome phylogeneticapproach resolved the population structure down to the whitewater and blackwater populations.Analysis of branch specific variants with impact on the coding sequence of genes revealed adaptationto the different Guayana habitats which was further related to observed phenotypical differences. Thedata enable the future development of mitochondrial and nuclear markers to distinguish Arapaimasubspecies in South America and thus to identify scientifically sound conservation management units.