DOI: 10.5061/dryad.0k6djhb96
title: Data from: Recommendations for population and individual diagnostic SNP selection in non-model species

description: Despite substantial reductions in the cost of sequencing over the last
 decade, genetic panels remain relevant due to their cost-effectiveness and
 flexibility across a variety of sample types. In particular, single
 nucleotide polymorphism (SNP) panels are increasingly favored for
 conservation applications. SNP panels are often used because of their
 adaptability, effectiveness with low-quality samples, and cost-efficiency
 for use in population monitoring and forensics. However, the selection of
 diagnostic SNPs for population assignment and individual identification
 can be challenging. The consequences of poor SNP selection are
 under-powered panels, inaccurate results, and monetary loss. Here, we
 develop a novel user-friendly SNP selection pipeline for population
 assignment and individual identification, mPCRselect. mPCRselect allows
 any researcher, who has sufficient SNP-level data, to design a successful
 and cost-effective SNP panel for species of conservation concern.
description: 13 tigers from each of the Amur and Bengal subspecies, and 13
 Generic (N = 39 individuals total from Armstrong et al., 2024) were
 selected for this dataset. Unrelated individuals were previously
 identified in Armstrong et al., 2024. Then, we created a subset of 10,000
 markers randomly sampled from across the genome using the remaining
 markers in linkage equilibrium. This dataset is provided as the test data
 for the mPCRselect pipeline (https://github.com/ellieearmstrong/mPCRselect). References: Armstrong et al. 2024, DOI: 10.1073/pnas.2402924121
description: # Data from: Recommendations for Population and Individual Diagnostic SNP
 Selection in Non-Model Species
 [https://doi.org/10.5061/dryad.0k6djhb96](https://doi.org/10.5061/dryad.0k6djhb96) ## Description of the data and file structure Tiger data from Armstrong et al. 2024 and Armstrong et al. 2021. File contains tigers from five tiger subspecies and generic (admixed) tigers which are unrelated. Data has been filtered down to two chromosomes (B1 and F2) and is filtered as described in manuscript. Test dataset for mPCRselect pipeline. ### Files and variables #### File: tiger\_pop.csv **Description:** Information corresponding to individuals contained in the VCF and their population assignment. ##### Variables * Sample: Tiger samples correspond to individuals from Armstrong et al. 2024 (see Supplementary Table 1) * Population: One of five tiger subspecies (Amur, Bengal, Indochinese, Malayan, Sumatran) or admixed population (Generic) #### File: tiger\_chromosomes.txt **Description:** Names of chromosomes contained in VCF file. #### File: PanTig-genmap1.0.chromrename.bed **Description:** File containing sites to be filtered from VCF which contain low mappability scores/repetitive regions. #### File: tiger.vcf.gz **Description:** VCF containing single nucleotide polymorphisms from tiger individuals. #### File: PanTig1.0-chrrename.fa **Description:** Reference genome file containing two chromosomes. ## Access information Data was derived from the following sources: * Armstrong, E. E., Khan, A., Taylor, R. W., Gouy, A., Greenbaum, G., Thiéry, A., ... & Ramakrishnan, U. (2021). Recent evolutionary history of tigers highlights contrasting roles of genetic drift and selection. *Molecular Biology and Evolution*, *38*(6), 2366-2379. * Armstrong, E. E., Mooney, J. A., Solari, K. A., Kim, B. Y., Barsh, G. S., Grant, V. B., ... & Hadly, E. A. (2024). Unraveling the genomic diversity and admixture history of captive tigers in the United States. *Proceedings of the National Academy of Sciences*, *121*(39), e2402924121.