Reassessing leatherback turtle lineages and unveiling the first evidence of nuclear mitochondrial DNA in sea turtles

A recent study proposed a new genetic lineage of leatherback turtles (Dermochelys coriacea) based on genetic analysis, environmental history, and local ecological knowledge (LEK), suggesting the existence of two possible species or subspecies on the beaches of Oaxaca, diverging similar to 13.5 Mya. However, this hypothesis may be influenced by nuclear mitochondrial DNA segments (NUMTs), which could have been misamplified as true mtDNA. NUMTs are sequences that have migrated from the mitochondrial genome to the nuclear genome and can co-amplify with mtDNA, potentially leading to erroneous phylogenetic interpretations. We re-examined the evidence for this proposed lineage by reviewing taxonomic literature and additional genetic data. Our analysis indicates that the divergent sequences, previously associated with a new lineage of D. coriacea, are NUMTs rather than true mitochondrial sequences. This is the first evidence of NUMTs in sea turtles. We also proposed a more specific primer for the mitochondrial control region (D-loop) for leatherback turtles to avoid amplifying nuclear copies. Our findings highlight the importance of rigorous genetic validation in conservation genetics, where misinterpretations can significantly impact species management. Finally, we developed a general protocol for detecting NUMTs applicable to any species.