35SNP_global_dataset

This dataset consists of 295 individuals, which have been typed at 35 SNP loci drawn from Nussberger et al. (2013) that have been identified as discriminatory between the following two groups; [ (Scottish+ mainland European wildcats) versus (UK+ mainland European domestic cats)]. Justification for the 35 SNP panel used is laid out in detail in Senn and Ogden (2015). Wet-lab methods consist of PCR amplification of the samples with 35 Taqman SNP Probes on a StepOne platform (Senn and Ogden 2015). This dataset was divided into a variety of sub-datasets based on the different methodologies used to collect the samples. Since the focus of collection of wild-living cats has shifted over time, this has been done to assist with understanding how collection bias might influence conclusions drawn from the results (more later). The datasets (summarised in Table 1) are: 35SNP_historical_cats: A dataset of 60 cats collected between 1895 and 1985 by National Museums Scotland, Natural History Museum (London) and the New Walk Museum Leicester. These cats are primarily cats identified as wildcats that were shot by gamekeepers. The samples taken from these animals consisted of fragments of dried or tanned skins taken with sterile scalpels, which were then extracted with Qiagen Investigators kits (Qiagen) according to manufacturer’s instructions. Of these cats, 51 were scored for pelage characters, from the preserved skins by ACK. 35SNP_wildliving_dead_cats: A dataset of 125 cats collected from ~1990-2015 by National Museums Scotland with the assistance of a wide variety of partners. The cats are primarily victims of road-traffic accidents, although in some cases they were shot, or the fate of specimen is unclear. Note that it was not possible to include the samples from theBeaumont et al. (2001) study. Sample type consists of skeletal muscle tissue, which was extracted with Fuji film or Qiagen blood and tissue kits according to manufacturers’ instructions. Of these samples 33 have pelage scores taken from photographs of dead cats or their tanned skins by ACK. 35SNP_wildliving_survey_cats: This dataset contains 19 cats trapped as part of the Survey of the Priority Areas conducted prior to the initiation of the current action plan (SNH 2014, Commissioned Report No. 768.). Sample type of these cats consists of EDTA blood extracted with Fuji film or Qiagen blood and tissue kits (Qiagen), according to manufacturers’ instructions. Of these, 18 samples have pelage scores (following Kitchener et al. 2005), scored from photographs taken when the cat was under anaesthesia in the field under Scottish Natural Heritage Animal Licence number 21463 and Animals Scientific Procedures Act personal licence number 70/25690. 35SNP_captive_cats: A dataset of 72 wildcats, which represented 100% of the potential breeding population within the UK captive breeding programme as of May 2017. Sample type for these cats consists of EDTA blood taken during routine health screening, extracted with Fuji film or Qiagen blood and tissue kits (Qiagen), according to manufacturers’ instructions. Of these samples 28 have pelage scores, taken from photographs taken when the cats were under anaesthesia for routine health screening (http://www.scottishwildcataction.org/media/42346/protocol-for-photographing-dead-or-anaesthetised-wildliving-cat-dr-andrew-kitchener.pdf). 35SNP_domestic_cat: A dataset of 19 domestic cat samples collected from across the City of Edinburgh region. Pelage data are not available for this dataset.