Science Advances

Supplementary Materials

This PDF file includes:

  • fig. S1. Assessment of the effect of genealogical discordance on branch-site tests of positive selection.
  • fig. S2. Assessment of divergence between domestic cat and Panthera species in windows containing genes with signatures of interspecies introgression and positive selection.
  • fig. S3. Maximum-likelihood phylogeny constructed with a supermatrix consisting of 2151 concatenated single-copy orthologs for 11 mammals, derived from our phylome analysis.
  • fig. S4. Enrichment analysis for the site model test.
  • table S1. DNA sequencing information for the reference jaguar individual.
  • table S2. Jaguar genome assembly quality metrics.
  • table S3. Annotated protein-coding genes.
  • table S4. Summary of the jaguar transcriptome sequencing results.
  • table S5. DNA sequencing information for the leopard genome.
  • table S6. Tree topology frequencies in window- and gene-based analyses.
  • table S7. Tree topology frequencies for 3732 genes and their introns.
  • table S8. Detailed results of the ABBA/BABA tests.
  • table S9. Branch-site results for the jaguar.
  • table S10. Branch-site results for the lion.
  • table S11. Branch-site results for the snow leopard.
  • table S14. Results of coalescent simulations based on jaguar exome data.
  • table S15. Summary of repeat annotation for the jaguar genome.
  • table S16. Tandem repeat annotation for the jaguar genome.
  • table S17. Forty largest microsatellite families in the jaguar genome.
  • table S18. Statistics on noncoding RNA annotation in the jaguar genome.
  • table S20. Previously reported genomic resources used in our multispecies analyses.
  • table S21. Consensus genome information (using the tiger assembly as a reference).
  • table S27. Detailed information on the samples used in the exome capture experiment.
  • table S28. Enrichment results for the jaguar branch-site test.
  • table S29. Enrichment results for the lion branch-site test.

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Other Supplementary Material for this manuscript includes the following:

  • table S12 (Microsoft Excel format). Branch-site results for the tiger.
  • table S13 (Microsoft Excel format). Site model results.
  • table S19 (Microsoft Excel format). Annotation of nuclear insertions of mitochondrial DNA (NUMTS) in the jaguar genome.
  • table S22 (Microsoft Excel format). Outlier window test results.
  • table S23 (Microsoft Excel format). Outlier Window KEGG enrichment results.
  • table S24 (Microsoft Excel format). Outlier Window Pathway Commons enrichment results.
  • table S25 (Microsoft Excel format). Outlier Window Phenotype enrichment results.
  • table S26 (Microsoft Excel format). Outlier Window Disease enrichment results.
  • table S30 (Microsoft Excel format). Tiger Pathway Commons enrichment results.
  • table S31 (Microsoft Excel format). Tiger KEGG enrichment results.
  • table S32 (Microsoft Excel format). Tiger Disease enrichment results.
  • table S33 (Microsoft Excel format). Site model Pathway Commons enrichment results.
  • table S34 (Microsoft Excel format). Site model KEGG enrichment results.
  • table S35 (Microsoft Excel format). Site model Disease enrichment results.
  • table S36 (Microsoft Excel format). Site model Biological Process enrichment results.
  • table S37 (Microsoft Excel format). Site model Molecular Function enrichment results.

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