Genomic analysis reveals strong population structure in the Giant Sydney Crayfish (Euastacus spinifer (Heller, 1865))

Australia is home to over 140 species of freshwater crayfish (Decapoda: Parastacidae), representing a centre of diversity for this group in the Southern Hemisphere. Species delimitation in freshwater crayfish is difficult because many species show significant variation in colouration and morphology. This is particularly evident in the genus Euastacus, which exhibits large variations in colour and spination throughout its putative range. To understand this variation, we investigated the genetic diversity, population structure, phylogeny, and evolutionary timescale of the Giant Sydney Crayfish (Euastacus spinifer (Heller, 1865)). Our data set is sampled from over 70 individuals from across the ∼600 km range of the species, and includes a combination of two mitochondrial markers and more than 7000 single-nucleotide polymorphisms (SNPs) from the nuclear genome. Data were also obtained for representatives of the close relative, Euastacus vesper McCormack and Ahyong, 2017. Genomic SNP analyses revealed strong population structure, with multiple distinct populations showing little evidence of gene flow or migration. Phylogenetic analyses of mitochondrial data revealed similar structure between populations. Taken together, our analyses suggest that E. spinifer, as currently understood, represents a species complex, of which E. vesper is a member. Molecular clock estimates place the divergences within this group during the Pleistocene. The isolated and highly fragmented populations identified in our analyses probably represent relict populations of a previously widespread ancestral species. Periodic flooding events during the Pleistocene are likely to have facilitated the movement of these otherwise restricted freshwater crayfish within and between drainage basins, including the Murray-Darling and South East Coast Drainages. We present evidence supporting the recognition of populations in the southern parts of the range of E. spinifer as one or two separate species, which would raise the number of species within the E. spinifer complex to at least three. Our results add to the growing body of evidence that many freshwater crayfish exhibit highly fragmented, range-restricted distributions. In combination with the life-history traits of these species, the restricted distributions exacerbate the threats already placed on freshwater crayfish, which are among the five most endangered animal groups globally.

Phylogeography and limited distribution of the endangered freshwater crayfish, Euastacus urospinosus

Conservation plans can benefit from understanding patterns of genetic structure because many endangered species are spatially fragmented. In particular, headwater species in high elevations are expected to exhibit a high level of population structure, as dispersal through lowland streams may be limited. Euastacus urospinosus is an endangered freshwater crayfish that, until recently, was thought to have a distribution of just 200 km2. In the current study, we identified a total of 26 locations for this species across a 1225 km2 region spanning the Brisbane and Mary River catchments of south-east Queensland, Australia. We then used mitochondrial DNA sequence data to investigate the population structure and the phylogeographic divergence between four uplands. We found significant population differentiation for this species, which conforms to the headwater model of genetic structure. Further, we found that fragmentation between these uplands is most likely historical, as the first divergence between lineages dated back 2.1 million years. Overall, we found no reason to remove the conservation rating of ‘endangered’ for this species. Conservation plans should seek to preserve the genetic integrity of these uplands by considering them to be genetically distinct and isolated populations.