Genotype-by-sequencing of Arctocephalus pusillus pusillus: flipper or ear tissue from pup
Flipper and ear tissue samples were collected from 95 Cape fur seal (CFS Arctocephalus pusillus pusillus) pups between 2019 and 2024 at colonies in Southern Africa (see Spanjaard et al., 2026). Only pups younger than eight months of age were sampled, using non-destructive methods. DNA was extracted using a NucleoSpin Tissue Kit (Macherey-Nagel). Genotype-by-sequencing (GBS) libraries were prepared using the PstI and MspI enzymes, followed by sequencing on an Illumina NovaSeq X PE150 lane. One negative control was included during extraction and sequencing and is included in the submission.  FASTQ files were demultiplexed, filtering reads with Phred scores < 20 and cleaning barcodes and restriction sites using the PROCESS_RADTAGS program in Stacks v2.59. Samples were provided by the Sea Search Research and Conservation (SSRC) and the Department of Forestry, Fisheries and the Environment (DFFE). Samples were frozen at  -1820 and/or stored in 70% ethanol until DNA extraction. Namibian specimens were collected by Sea Search Research and Conservation under permits granted by the National Commission on Research, Science and Technology (NCRST) and the Namibian Chamber of Environment (NCE; permits AN20200702, RCIV00042018) and/or in collaboration with the Ministry of Fisheries and Marine Resources. These samples were transported to South Africa in compliance with CITES (Permits 0064261, 257533). Permission to collect South African specimens was granted by the DFFE (Permits RES2023-38, RES2024-46) and Cape Nature (CN44-87-31079). Ethical approval for the collection and use of specimens was obtained from the Stellenbosch University Institutional Research Ethics Committee for Animal Care and Use, South Africa (Reference No. ACU-2021-15015, ACU-2021-21659, ACU-2024-30229).