Shedding the mitochondrial blinkers: A long-overdue challenge for species delimitation in herpetology

The advent of molecular methods has revolutionised the field of species delimitation and description, one of the key tasks of systematic biology. In animal taxonomy, one marker, the mitochondrial DNA (mtDNA) molecule, has acquired and retained disproportionate influence. This is despite its uniparental, clonal mode of inheritance, as a result of which the entire molecule acts as a single locus, and that precludes its use as a test for admixture between putative lineages, a key consideration in species delimitation. To establish the extent to which the limitations of mtDNA affect present-day taxonomy in non-avian reptiles, I surveyed species descriptions and delimitations published during the years 2023–2024, determined the markers used, and whether analyses of different markers were set up to critically test or just to confirm mtDNA-inspired candidate species. Mitochondrial DNA remains the dominant molecular marker in reptile taxonomy, being used in 84% of species descriptions and delimitations, and as the sole molecular marker in 44%. Despite the immense progress in next generation sequencing (NGS) technologies and their increasing affordability, only 3.4% of descriptions used NGS approaches. In 61% of descriptions, taxa were identified primarily through mtDNA divergence, and additional data (morphology, single-copy nuclear gene sequences) were used as confirmatory evidence rather than as rigorous tests of mitochondrially inferred species limits. I reiterate the importance of truly integrative species delimitation that critically tests species limits first hypothesised from mtDNA, and suggest ways of improving the robustness of species delimitations by optimising the allocation of resources to more appropriate markers and through analytical approaches that critically test the evolutionary independence of putative species.