Fitak, Robert; Naidu, Ashwin; Thompson, Ron; Culver, Melanie (2014): PumaPlex 1.0: Data generated during the development of the SNP markers and SNP genotypes of pumas [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.835154,

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Supplement to: Fitak, R et al. (2016): PumaPlex 1.0: a new panel of SNP markers for the genetic management of North American pumas (Puma concolor). 7(1), 13-27, https://doi.org/10.3996/112014-JFWM-080

Pumas are one of the most studied terrestrial mammals because of their widespread distribution, substantial ecological impacts, and conflicts with humans. Extensive efforts, often employing genetic methods, are undertaken to manage this species. However, the comparison of population genetic data is difficult because few of the microsatellite loci chosen are shared across research programs. Here, we describe the development of PumaPlex, a high-throughput assay to genotype 25 single nucleotide polymorphisms in pumas. We validated PumaPlex in more than 700 North American pumas (Puma concolor couguar), and demonstrated its ability to generate reproducible genotypes and accurately identify individuals. Furthermore, we compared PumaPlex with traditional genotyping of 12 microsatellite loci in fecal DNA samples and found that PumaPlex produced significantly more genotypes with fewer false alleles. PumaPlex promotes the cross-laboratory comparison of genotypes, is easily expandable in the future, and is a valuable tool for the genetic monitoring and management of North American puma populations.

Summary of the files (tab-delimited text format) in this Puma_SNP_Data.zip archive:

1. Puma_cDNA_transcriptome.tab - this file contains the transcriptome assembly which includes all contigs >100 bp in length. The first column is the sequence identifier, the second column is the sequence.

2. Raw_SNPs_identified.vcf.tab - this file contains the initial SNPs identified in this study coded in the in the standard VCF format. VCF format is a tab-delimited format described as part of the 1,000 genomes project (see the attached file VCFv4.1.pdf for a description). All lines beginning with a '#' are comment/header lines.

3. Puma_SNP_genotypes.tab - this file contains SNP genotypes and geographic information for the 727 pumas described in this study. The first column is the puma identifier, the second column is the latitude, the third column is the longitude, fourth column is the group (AZ or CULVER), and the remaining columns are the genotypes for loci PP01-PP25. Missing genotypes are shown as a '0'.

4. Puma_Fecal_SNP_genotypes.tab - this file contains SNP genotype data for the 46 fecal DNA samples used in this study. The first column in the fecal DNA identified, the second column is the replicate number, then the remaining columns are genotypes at the 25 SNP and 12 microsatellite loci. Missing genotypes are shown as a '0'.