Unique Population or Unique Species? Genetic Insights Into the Pygmy Freshwater Crocodiles of Northern Australia

Isolated populations of Australian freshwater crocodiles (Crocodylus johnstoni) in few elevated, rocky escarpment areas of the Northern Territory of Australia reach sexual maturity earlier and generally have an adult size half that of their downstream counterparts. There is debate over whether these "pygmy" or "dwarf" crocodile populations are the result of extreme phenotypic plasticity or the origins of a unique species through peripatric speciation. This debate is of conservation concern as these populations face immediate threats from invasive species and climate change, and species classification can affect conservation management strategies. We used mitochondrial DNA control region and cytochrome b sequences to investigate whether mtDNA haplotype variation supports any evidence of speciation between the pygmy and standard-size freshwater crocodiles. Additionally, we used genotyping by sequencing (dd-RADseq) to examine genetic clustering. Separated and concatenated control region and cytochrome b haplotypes were shared between pygmy and standard-size crocodile populations. Principle Component Analysis and STRUCTURE analyses on dd-RADseq data showed pygmy and standard-size crocodiles cluster by geographic location as much as by phenotype. We found no clear and objective genetic evidence to suggest that the pygmy freshwater crocodiles should be considered a separate species from any other population of the standard-size crocodiles. However, the isolation and environmental adaptability of these unique pygmy freshwater crocodile populations make them ecologically unique and valuable for conservation, and worth safeguarding against potential threats.