DOI: 10.5061/dryad.79cnp5j27
title: Single Nucleotide Polymorph and location metadata for Turbo militaris from Eastern Australia

description: 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.
description: Eight rocky shore locations (0 to 5m depth) were selected for
 sampling spanning the<br>known range of T. militaris from Hastings
 Point (northern NSW) to Jervis Bay (southern NSW)<br> representing a
 seven-degree latitudinal and a 3.9°C annual mean sea surface
 temperature<br>gradient. Between 25 and 30 T. militaris individuals
 were collected from<br>each location. <br><br>For single
 nucleotide polymorphism (SNP) genotyping, extracted DNA was sent
 to<br>Diversity Arrays Technology Pty Ltd (Canberra, Australia)
 (DArT). The DArT organisation<br>provides a process pipeline of
 whole-genome profiling, without the need for a reference genome.
 High-throughput DArTseq technology was used to genotype
 Turbo<br>militaris DNA. Here, the PstI-based complexity reduction
 method (Wenzl et al. 2004) was<br>applied for the enrichment of
 genomic representation with single copy sequences. This
 method<br>involved the digestion of DNA samples with a cutting
 enzyme PstI, paired with a set of<br>secondary frequently cutting
 restriction endonucleases, ligation with site-specific adapters,
 and<br>amplification of adapter-ligated fragments. Post digestion
 with a restriction enzyme pair, a PstI-<br>overhang-compatible
 oligonucleotide adapter was ligated, and the adapter-ligated
 fragments<br>were amplified in adherence to standard protocol (Wenzl
 et al, 2004). To develop SNPs, the<br>DArTseq technology was
 optimized using two PstI-compatible adapters corresponding to
 two<br>different restriction enzyme overhangs. The genomic
 representations were generated following<br>the procedures described
 by Kilian et al. (2012 ). Next-generation sequencing technology
 was<br>implemented using HiSeq2000 (Illumina, USA) to detect SNP
 markers. Sequence data was<br>analysed using DarTsoft14 and
 DArTdb.
description: # Australian Turbo militaris SNP data and metadata
 [https://doi.org/10.5061/dryad.79cnp5j27](https://doi.org/10.5061/dryad.79cnp5j27) This dataset contains single nucleotide polymorph SNP 2 data generated by Divertisty Arrays Technologies DArT sequencing process - see https://www.diversityarrays.com/ for the marine turbinid gastropod Turbo militaris from across its entire range in NSW, Australia. Analysis using standard SNP population genetics scripts in R revealed panmixia across its range. ## Description of the data and file structure There are two data files - both. csv files. The first is a SNP data set generated by DArT next generation sequencing technologies. The second is the site metadata for each of the individuals in the SNP dataset. File structure in the SNP dataset is as per the proprietary outputs from DaRT technologies. Data in this file can be analysed using the standardised DArT workflow analysis. ## Sharing/Access information Data are stored in the Dryad Repository. ## Code/Software