Museomics reveals the phylogenetic position of the extinct Moroccan troutSalmo pallaryi

Abstract

The authors used museomics to reconstruct the mitochondrial genome from two individuals of the Moroccan, endemic and extinct trout, Salmo pallaryi. They 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. mtDNA 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. Phylogenetic discordance between mtDNA and nuclear DNA phylogenies is briefly discussed. As several specimens that were extracted failed to produce DNA of sufficient quality, the authors discuss potential reasons for the failure.They 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 20th century.

Phylogenomics of Fresh and Formalin Specimens Resolves the Systematics of Old World Mud Snakes (Serpentes: Homalopsidae) and Expands Biogeographic Inference

“…The inclusion of degraded samples from natural history collections has been useful for determining the phylogenetic placement (Delling et al, 2023) and biogeography (Garg et al, 2022) of poorly known or extinct lineages. In this study, we phylogenetically place five genera and six species for the first time, each of which are known from only a few voucher specimens, and use these results to formulate hypotheses regarding homalopsid evolution.…”

Travelling in the omics time machine: uncovering mysteries of the extinct Moroccan trout (Salmo pallaryi)

“…Sadly, authors highlight that the Moroccan trout is now classified as extinct, largely due to the introduction of invasive species into lake Sidi Ali, such as common carp. Despite this, from the successfully acquired sequence data, Delling et al (2023) were able to uncover some final secrets from the Moroccan trout. S. pallaryi was seen to have a species‐specific mitochondrial haplotype, showing its distinct phylogenetic signal, likely caused by the long‐term isolation in lake Sidi Ali.…”

“…However, ancient DNA is not the only source of DNA that gives us a glimpse into the past. In this issue, Delling et al (2023) look into the more recent past, between 1924‐1936, utilizing preserved museum specimens of the now extinct Moroccan trout ( Salmo pallaryi ). Authors had six museum specimens with the desirable white‐eyed indicator of probable ethanol fixation and storage and thus viable DNA (rather than the alternative DNA busting formalin fixation)(De Bruyn et al, 2011) and so they began sequencing.…”