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Figure S1 Flow chart illustrating the read-processing pipeline. Settings used for custom scripts and other programs are detailed in the main text.

Figure S2 BLAST + MEGAN taxonomic classifications for the sequenced contaminant libraries.

Figure S3 Mitochondrial 12S ribosomal DNA maximum likelihood phylogeny of the Bovidae.

Figure S4 Frequency histograms showing the proportion of contaminant reads per operational taxonomic unit (OTU) for each library. OTUs are shown on the x-axis.

Figure S5 12S operational taxonomic unit (OTU) classifications summarized to the genus rank.

Figure S6 16S operational taxonomic unit (OTU) classifications summarized to the genus rank.

Figure S7 cox1 operational taxonomic unit (OTU) classifications summarized to the genus rank.

Figure S8 trnL intron operational taxonomic unit (OTU) classifications summarized to the genus rank.

Table S1 Summary of PCR assays modified from D'Costa et al. (2011) to include details for the cox1 assay.

Table S2 Summary of Bear Creek (BC) sample PCR results, modified from D'Costa et al. (2011) to include cox1 results and the complete set of controls for the project.

Table S3 Summary of the BC1 + BC4 quality reads for each marker before removing contaminant sequences.

Table S4 Summary of sequenced contaminants.

Table S5 Summary of mitochondrial 12S rDNA reads classified to the genus rank.

Table S6 Summary of 16S rDNA reads classified to the genus rank.

Table S7 Summary of mitochondrial cox1 reads classified to the genus rank.

Table S8 Summary of chloroplast trnL intron reads classified to the genus rank.

Table S9 Summary of reads, clustered into OTUs, that could not be taxonomically assigned to any rank using BLAST + MEGAN.

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