Data associated with "Implications of past and present genetic connectivity for management of the saltwater crocodile (Crocodylus porosus)"

\nThis collection contains genetic data and associated meta data information generated\nfrom 1,176 saltwater crocodiles sampled from across the coastal habitat of \nQueensland, Australia. These data were generated in a collaborative analysis \nbetween the Queensland Department of Environment and Science (DES) and the\nCommonwealth Scientific and Industrial Research Organisation (CSIRO). The \nmethods and results are discussed in a scientific manuscript titled "Implications \nof past and present genetic connectivity for the management of the saltwater \ncrocodile (Crocodylus porosus)". \n\nThe README details the genetic data is its original formats, which was generated\nby DArT Pty Ltd, and a 'processed' format. The details of quality control used\nto generate the processed formats are provided in the manuscript. \nLineage: Saltwater crocodile samples (n = 1,176) were collected between August 1997 and September 2021 across ten of twelve crocodile bioregions in the Queensland, Australia study area. Samples collected between August 1997 and October 2005 were sourced from the Queensland Museum (n = 482) and the remainder collected by Queensland Department of Science and Environment staff between May 2018 and July 2021 (n = 694). The number of samples taken from each bioregion comprises Fitzroy (n = 23), Coastal Plains: Ayr - Proserpine - Rockhampton (APrR) (n = 105), Coastal Plains: Cooktown - Ayr (CA) (n = 255), Coastal Plains: Cape Melville - Cooktown (CMC) (n = 2), Princess Charlotte Bay (n = 239), North East Cape York (n = 12), North West Cape York (n = 406), Gulf Plains: Mitchell-Gilbert drainage (MGD) (n = 13), Gulf Plains: Norman-Flinders drainage (NFD) (n = 111), and Gulf Plains: Albert-Leichardt drainage (ALD) (n = 8). \n\nTissue was sampled from free-swimming crocodiles > 600 mm TL using a non-lethal biopsy punch method (Barrow and Halford, 2019). This involved a needle head (3 mm x 25 mm) modified to fit the end of a 3 m long Rangoon cane pole that was plunged into the base of the crocodile’s tail from a moving boat at night. For smaller crocodiles (< 600 mm TL) a single piece of tail scute was removed. Genetic material (using both methods) was also collected from problem crocodiles by the Department of Environment and Science (DES) during routine management activities required by departmental guidelines (Queensland Department of Environment and Science, 2008) under the Nature Conservation Act 1992. All genetic material was stored in 70% ethanol. Sampling was conducted under the Department of Agriculture and Fisheries Animal Ethics Committee Reference numbers SA 2018-07-644, and SA 2021-07-793. All activities were undertaken in accordance with the Code of Practice on the Humane Treatment of Wild and Farmed Australian Crocodiles (Natural Resource Management Ministerial Council, 2009).\n\nPilot Genetic Data - To minimise ascertainment bias, 188 crocodiles from within five of the most sample abundant bioregions were included in the SNP discovery phase. Specifically, 41, 39, 38, 31 and 39 samples were taken from Cairns, Lakefield, Norman River, Proserpine and Wenlock regions respectively (Supplementary Table 1). DNA extraction and quality control was performed by Diversity Arrays Technology (DArT Pty Ltd, Canberra) and samples were genotyped using DArTseqTM as described by (Grewe et al., 2015). A set of 4,799 short-listed DArTSeq markers was deemed adequate and taken forward for DArTcap analysis.\n\n\tDArTcap genotyping involves adding a hybridisation-based enrichment step before the DArTseq libraries are sequenced, which dramatically lowers the cost per sample when sample sizes are large. The hybridisation step uses custom synthesised biotinylated RNA MYbaits (Arbor Bioscience) designed based on the chosen DArTseq markers. The 4,799 DArTSeq markers short-listed for the DArTcap panel were put through a selection process using a DArT P/L proprietary algorithm that assesses sequence length and complexity in order to limit nonspecific capture. \n\nThese DArTcap enriched libraries, one per sample, were sequenced on an Illumina HiSeq. SNP calling for DArT reporting was again performed using DArT P/L’s proprietary SNP-calling algorithms. DArT P/L reported 6,754 variants from 1,176 individuals (of an original set of 1,204 samples, 28 failed the internal quality control protocols at DArT).\n