Single Nucleotide Polymorph and location metadata for Turbo militaris from Eastern Australia

Studies of population genomics have been increasingly used to identify climate change vulnerability and explore the potential resilience of harvested marine species. The turban snail, Turbo militaris is a commercially and culturally harvested marine gastropod snail from eastern Australia. The species has exhibited a climate-driven poleward range shift over the last two decades and continued climate change presents an ongoing challenge for sustainable fisheries management. This study investigates the likely resilience of Turbo militaris to future climate change effects using genotype-by-sequencing to explore patterns of gene flow and local adaptation across the entire species distribution. We provide evidence of a single admixed, and potentially panmictic, demographic unit with no evidence of genetic subdivision across the species range. Furthermore, significant genotype associations with heterogeneous habitat features were observed, including associations with sea surface temperature, ocean currents, and nutrients, indicating possible adaptive genetic differentiation among sample locations. These findings suggest that standing genetic variation may be available for selection to counter future environmental change, assisted by widespread gene flow, high fecundity and short generation time in this species. We discuss the findings of this study in the content of future fisheries management and conservation.

Methods
Eight rocky shore locations (0 to 5m depth) were selected for sampling spanning the
known range of T. militaris from Hastings Point (northern NSW) to Jervis Bay (southern NSW)
 representing a seven-degree latitudinal and a 3.9°C annual mean sea surface temperature
gradient. Between 25 and 30 T. militaris individuals were collected from
each location. 

For single nucleotide polymorphism (SNP) genotyping, extracted DNA was sent to
Diversity Arrays Technology Pty Ltd (Canberra, Australia) (DArT). The DArT organisation
provides a process pipeline of whole-genome profiling, without the need for a reference genome. High-throughput DArTseq technology was used to genotype Turbo
militaris DNA. Here, the PstI-based complexity reduction method (Wenzl et al. 2004) was
applied for the enrichment of genomic representation with single copy sequences. This method
involved the digestion of DNA samples with a cutting enzyme PstI, paired with a set of
secondary frequently cutting restriction endonucleases, ligation with site-specific adapters, and
amplification of adapter-ligated fragments. Post digestion with a restriction enzyme pair, a PstI-
overhang-compatible oligonucleotide adapter was ligated, and the adapter-ligated fragments
were amplified in adherence to standard protocol (Wenzl et al, 2004). To develop SNPs, the
DArTseq technology was optimized using two PstI-compatible adapters corresponding to two
different restriction enzyme overhangs. The genomic representations were generated following
the procedures described by Kilian et al. (2012 ). Next-generation sequencing technology was
implemented using HiSeq2000 (Illumina, USA) to detect SNP markers. Sequence data was
analysed using DarTsoft14 and DArTdb.