Pleistocene Legacies in the Contemporary Population Genetic Structure of an Acid-Specialised Crayfish, the Threatened Sand Yabby Cherax robustus.

Following decades of clearing, fragmentation and degradation of coastal heathlands in southeast Queensland, many endemic species are now threatened with extinction, including the vulnerable sand yabby Cherax robustus (Parastacidae), a freshwater crayfish restricted to 200km2 of acidic wetlands. Dramatic fluctuations in the distribution and extent of these wetlands, particularly during the glacial cycles of the Pleistocene, likely shaped the distribution and genetic structure of acid-specialist species, yet their historic and contemporary connectivity remains poorly understood, despite these species being particularly sensitive to habitat fragmentation and environmental change. Here, we investigate the genetic structure of two island and two mainland C. robustus populations within peatlands using DArTseq next-generation DNA sequencing. Analysis of over 7000 SNP markers indicates population divergence occurred during the mid-to-late Pleistocene, with no detectable gene flow between most sites for between 50,000 and 120,000 years. Consistent with long-term isolation, we found slight heterozygote deficiency in all populations, and evidence of genetic erosion in only one population, which should continue to be monitored, though the effect appears to predate European arrival in Australia. Evidently, sand yabbies are not naturally rare within stable environments but have become vulnerable through anthropogenic pressures of habitat loss and degradation. The strong population structuring observed means that each population represents a unique genetic lineage and should be managed as an independent unit. Protecting all remaining habitat and preventing any further degradation is therefore critical to the conservation of this species as well as the wider ecosystem.