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Microarrays can be a cost-effective alternative to high-throughput sequencing for discovering novel single-nucleotide polymorphisms (SNPs). Illumina’s iScan platform dominates the market, but their commercial microarray products are designed for model organisms. Further, the platform outputs data in a proprietary format. This cannot be easily converted to human-readable genotypes or be merged with pre-existing data. To address this, we present and validate a novel pipeline to facilitate data analysis from cross-species application of Illumina microarrays. This facilitates the generation of a compatible VCF from iScan data and the merging of this with a second VCF comprising genotypes derived from other samples and sources. Our pipeline includes a custom script, iScanVCFMerge (presented as a Python package), which we validate using iScan data from three great ape genera. We conclude that cross-species application of microarrays can be a rapid, cost-effective approach for SNP discovery in non-model organisms. Our pipeline surmounts the common challenges of integrating iScan genotypes with pre-existing data.

Based on “Presence data”, we assessed the habitat quality according to the physical factor utilized by Tibetan fox in Gouli Township, Dulan County, Qinghai Province, China. The spatial carrying capacity of Tibetan fox was also estimated according to their minimum space requirements. A total of 4 topographical factors, elevation, slope, terrain ruggedness and slope position, were used to conduct habitat assessment for Tibetan fox. The suitability of habitat factors were determined by comparing the utilization by Tibetan fox and its availability based on 95% Bonferroni confidence interval. A comprehensive assessment criterion was set up for all topographic factors. For Tibetan fox, the elevations of 4 050 - 4 300 m, the slopes of 5 − 20°, the upper and lower slope positions were suitable habitat. Tibetan fox use terrain ruggedness non-selectively. According to the utilization of Tibetan fox on different topographic factors and the consistence of habitat utilization by different fox individuals, we set the comprehensive criterion as: Xi = (X2elevation x X2slope positionx Xslope x Xterrainrug gadness)1/6. The area of suitable habitat is about 17.4 km2, which take a percentage of 38.8% of research area. The area of most suitable habitat is only 0.4 km2. The home range of Tibetan fox ranges from 2.53 km2 to 4.99 km2, and the overlap index (OI) of different individuals were 0.16 − 0.66. The minimum space requirements of Tibetan fox are 2.09 − 3.55 km2, and the spatial carrying capacity of Tibetan fox in suitable habitat is 7−12. According to the habitat resource and monitoring results, we infer that the Tibetan fox population is keeping steady.