The taxonomic quagmire of northern Australian snake-necked turtles (Testudines: Chelidae): Chelodina kuchlingi—Extinct or hiding in plain sight?

Abstract Using mitochondrial genomes and nine nuclear loci, we examined genetic variation in snake-necked turtles (Chelodina sensu lato), with a focus on northern Australian taxa. The mitochondrial phylogeny of the genus is confounded by multiple introgression events, rendering the subgenera Chelodina sensu stricto and Chelydera non-monophyletic. However, in the analyses of our nuclear dataset (6071 bp), the recognition of the subgenera is supported. The morphologically most distinct taxa (Chelodina expansa, C. longicollis, C. oblonga, C. parkeri, C. steindachneri) are well differentiated genetically. However, many other species are not or only weakly distinct, calling their validity into question. Our dataset includes sequences from historical museum material and the holotype of C. kuchlingi, a species currently listed as Critically Endangered by the Biodiversity Conservation Act of Western Australia. Resequencing its mitogenome using protocols optimized for formalin-preserved specimens provides evidence that the formerly reported mitochondrial distinction of C. kuchlingi was based on a sequencing artifact. Two historical specimens of C. kuchlingi are genetically indistinguishable from snake-necked turtles living today on the Ord River floodplain. In addition, C. walloyarrina, a geographically close taxon with introgressed mitochondria from another species, is not differentiated on the nuclear genomic level. We conclude that Chelodina walloyarrina (McCord & Joseph-Ouni, 2007) is a junior synonym of Chelodina kuchlingi Cann, 1997 and that the extant snake-necked turtles from the Ord River floodplain are conspecific. This implies that morphological traits used in the past to diagnose the involved taxa are less important than previously thought. The redefined species C. kuchlingi is distributed on the sandstone plateau and associated escarpments as well as on the lowland coastal plains of the Kimberley region of tropical northern Australia. It no longer qualifies as Critically Endangered and has to be downlisted, pending a new status evaluation. Our results underline the importance of a robust taxonomy for conservation decisions. Further research is warranted to examine the validity of the remaining weakly differentiated Chelodina taxa, which could not be resolved in our analyses.