Museomics reveals the phylogenetic position of the extinct Moroccan trout Salmo pallaryi.

We used museomics to reconstruct the mitochondrial genome from two individuals of the Moroccan, endemic and extinct trout, Salmo pallaryi. We further obtained partial data from 21 nuclear genes previously used for trout phylogenetic analyses. Phylogenetic analyses including publicly available data from the mitochondrial control region and the cytochrome b gene, and the 21 nuclear genes place S. pallaryi among other North African trouts. Mitochondrial DNA places S. pallaryi close to Salmo macrostigma within a single North African clade. Although the nuclear coverage of the genome was low, both specimens were independently positioned as sisters to one of two distantly related North African clades, viz. the Atlas clade with the Dades trout, Salmo multipunctatus as sister. Phylogenetic discordance between mitochondrial DNA and nuclear DNA phylogenies is briefly discussed. As several specimens that were extracted failed to produce DNA of sufficient quality, we discuss potential reasons for that. We suggest that museum specimens in poor physical condition may be better for DNA extraction compared to better-preserved ones, possibly related to the innovation of formalin as a fixative before ethanol storage in the early 20 th century. This article is protected by copyright. All rights reserved.