Science Advances

Supplementary Materials

The PDF file includes:

  • Legends for tables S1 to S3
  • Table S4. D statistics results with spotted hyena as H1 and H2 and cave hyena as H3.
  • Table S5. D statistics results with cave hyena as H1 and H2 and spotted hyena as H3.
  • Table S6. Parameter estimates from fastsimcoal.
  • Table S7. List of orthologous domestic cat genes found in windows showing signs of admixture from cave hyena into spotted hyena.
  • Table S8. List of protein classes of the orthologous domestic cat genes found in windows showing signs of admixture from cave hyena into spotted hyena.
  • Table S9. List of biological processes of the orthologous domestic cat genes found in windows showing signs of admixture from cave hyena into spotted hyena.
  • Table S10. List of orthologous domestic cat genes found in windows showing signs of admixture from spotted hyena into cave hyena.
  • Table S11. List of protein classes of the orthologous domestic cat genes found in windows showing signs of admixture from spotted hyena into cave hyena.
  • Table S12. List of biological processes of the orthologous domestic cat genes found in windows showing signs of admixture from spotted hyena into cave hyena.
  • Table S13. Modern spotted hyena sample information.
  • Table S14. Pleistocene cave hyena sample information.
  • Table S15. Spotted hyena mapping values.
  • Table S16. Cave hyena mapping values.
  • Table S17. Genomic features and substitution model within each partition determined using Partionfinder2 on the Hyaenidae mitochondrial genomes.
  • Table S18. Distance matrix used to calculate divergence time between spotted and cave hyena.
  • Fig. S1. Bayesian dated phylogenetic tree of the Hyaenidae family constructed using complete mitochondrial genomes.
  • Fig. S2. Spotted and cave hyena cladogram consensus tree constructed using 467 maximum likelihood phylogenetic trees from 2 Mbp nonoverlapping windows along the nuclear genome.
  • Fig. S3. PCA constructed using only Pleistocene cave hyena individuals.
  • Fig. S4. PCA constructed using only modern spotted hyena individuals.
  • Fig. S5. Cumulative size distributions of regions returning putative admixture topologies, determined by counting the number of consecutive 100-kb blocks showing a putative admixture topology.
  • Fig. S6. MapDamage results for cave hyena genome data.

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Other Supplementary Material for this manuscript includes the following:

  • Table S1 (Microsoft Excel format). Results from the five-taxon topology test for admixture when considering only Ccsp040 and Ccsp041 as C1 and C2 and all combinations of spotted hyena.
  • Table S2 (Microsoft Excel format). Results from the five-taxon topology test for admixture when considering only Ccsp040 and Ccsp042 as C1 and C2 and all combinations of spotted hyena.
  • Table S3 (Microsoft Excel format). Results from the five-taxon topology test for admixture when considering only Ccsp041 and Ccsp042 as C1 and C2 and all combinations of spotted hyena.

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