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Determining the dietary niche is an essential part of any conservation strategy, and for modeling the community responses to climate change. DNA metabarcoding methods are revolutionizing such approaches, allowing higher taxonomic resolution than typically possible using microscopy. However, few studies have compared directly the approaches to evaluate the differences in methodology. Here we assess the dietary niches of two genetically diverse populations of Atlantolacerta andreanskyi, a lizard endemic to the Atlas Mountains, Morocco, using DNA metabarcoding of faecal samples, and for one of these we compared the results to two previously published assessments of diets obtained using microscopy of pellets and stomach contents respectively. While results at the Order level were similar, the higher taxonomic resolution obtained in this study provided new insights into the dietary niche of this species. Comparisons between the two populations further highlighted how ecologically distinct these are.

Atlantolacerta andreanskyi (Werner, 1929) is an endemic lizard from the High Atlas Mountains region of Morocco. A previous molecular assessment of this species using mitochondrial and nuclear DNA markers uncovered extensive genetic diversity with seven lineages indicative of a species complex. A morphological assessment of six of these lineages did not establish simple diagnostic features, and proposed these should be considered as a cryptic species, while highlighting the need for greater sampling across the range. In this study, we sampled 8 individuals from 5 previously unsampled localities and carried out genetic analyses to compare these populations to the known variation. Phylogenetic reconstruction based on mitochondrial DNA markers (12S rRNA and ND4) corroborates the previously described lineages and identified a new one. Interestingly, the two samples that account for this newly identified lineage have been collected from distinct localities – M’goun and Toumliline – that form a sister taxon to the population of Jbel Azourki.