A Prickly Problem: Genome Skimming Reveals Varying Levels of Phylogenetic Diversity in the Freshwater Crayfish Euastacus armatus Complex (Parastacidae) With Implications for Taxonomy and Conservation

Abstract

Accurate resolution of species taxonomies and natural distributions is paramount to enable effective conservation and management. But this can be a challenge in systems that lack sufficient genomic resources and systematic research, and when species ranges are dynamic due to population decline, human‐mediated introduction, or responses to climate change. This is particularly true for many of the world's 690 species of freshwater crayfish, including Australia's endemic spiny crayfish from the Euastacus genus. In this study, we use genome skimming to successfully recover whole mitogenomes and nuclear markers to examine the molecular taxonomy, phylogeography and range uncertainty in a wide‐ranging complex, which includes the nationally Vulnerable Murray crayfish Euastacus armatus , the nationally Endangered Glenelg spiny crayfish E. bispinosus and the Southern Victorian spiny crayfish E. yarraensis . The analyses revealed high levels of genetic structure in both E. armatus and E. yarraensis , including sufficiently divergent lineages within E. yarraensis that potentially warrants independent taxonomic recognition. Furthermore, analyses resolved the status of E. armatus populations persisting outside known contemporary ranges as being relictual and of high conservation importance. Whilst one outlying population of E. bispinosus was confirmed as relictual, another was revealed as being translocated. This study demonstrates genome skimming as a powerful technique for generating molecular data to support key elements of conservation for freshwater crayfish and other species.