Nuclear DNA reveals multiple waves of colonisation, reticulate evolution and a large impact of stocking on trout in north-west Africa

Using nuclear DNA sequences we studied the phylogeny and genetic structure of trout in Morocco, and estimated the impact of stocking upon natural populations. We supplemented the sample set from a previous study with new sample localities and with specimens from the main hatchery in Morocco. Phylogeny was performed using Bayesian inference, identification of genetic clusters and the genetic structure of populations were assessed from microsatellite polymorphism using discriminant analysis of principal components, and genealogical relationships among mitochondrial haplotypes were re-estimated with an unrooted phylogenetic network using statistical parsimony. Nuclear DNA sequences demonstrated the existence of three major clades in north-west Africa: (1) an Afro-Atlantic clade in Moroccan Mediterranean coastal rivers and the Sous drainage, stemming from a colonisation wave of the Atlantic lineage from Iberia, (2) a relict and native Draa clade (Dades trout), which has maintained an incipient nuclear DNA and mitochondrial DNA signature, and (3) a native Atlas clade, sister to Draa, in which only Atlantic mitochondrial DNA was found, suggesting invasion by Atlantic trout that introgressed into local populations and resulted in a reticulate evolutionary event. Microsatellite analysis and the distribution of the haplotypes revealed a large impact of hatchery trout stocking on wild populations.