Science Advances

Supplementary Materials

The PDF file includes:

  • Fig. S1. PCA plot of red panda whole-genome SNPs data, with PC1, PC2, and PC3 explaining 28.5, 4.1, and 3.6% of the observed variations, respectively.
  • Fig. S2. Phylogenetic tree based on 41 mitochondrial genome haplotypes, showing two significant species lineages (A. fulgens and A. styani).
  • Fig. S3. Phylogenetic tree based on eight Y chromosome SNPs haplotypes, showing two significant species lineages (A. fulgens and A. styani).
  • Fig. S4. Bayesian skyline plot (BSP) analysis results based on mitochondrial genomes.
  • Fig. S5. Four alternative population divergence models for Fastsimcoal2 simulations, with the maximum estimated likelihood values shown.
  • Fig. S6. Residual fit from the maximum likelihood tree estimated by TreeMix.
  • Table S1. Summary of the morphological differences between the Himalayan and Chinese red pandas.
  • Table S2. Sample information for whole-genome resequencing, Y chromosome SNP genotyping, mitochondrial genome assembly, and Fastsimcoal2 analysis.
  • Table S3. Summary of whole-genome resequencing data for 65 red panda individuals that include the individuals for PSMC analysis.
  • Table S4. Summary of SNP calling based on 65 red panda individuals.
  • Table S5. Cross-validation error result for varying values of K in the ADMIXTURE analysis.
  • Table S6. PCR primer information for validating the six male-specific Y-scaffolds of red pandas.
  • Table S7. PCR primer information for amplifying the SNPs on the male-specific Y-scaffolds.
  • Table S8. Eight Y-SNP haplotypes identified from 27 Y-SNPs of 49 male red panda individuals.
  • Table S9. Confidence intervals of key parameters for the best population divergence and demographic model estimated by Fastsimcoal2.
  • Table S10. Genetic diversity of whole genome, Y chromosome, and mitochondrial genome for different species and populations of red pandas.
  • Legends for tables S11 to S16

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Other Supplementary Material for this manuscript includes the following:

  • Table S11 (Microsoft Excel format). The 146 genes under selection with top 5% maximum FST values and top 5% minimum θπ1π2 values in the Himalayan red panda (MH).
  • Table S12 (Microsoft Excel format). Significantly enriched KEGG pathways for the 146 genes under selection in the Himalayan red panda (MH).
  • Table S13 (Microsoft Excel format). Significantly enriched GO terms of biological processes for the 146 genes under selection in the Himalayan red panda (MH).
  • Table S14 (Microsoft Excel format). The 178 genes under selection with top 5% maximum FST values and top 5% minimum θπ1π2 values in the Chinese red panda (EH-GLG, XXL-LS, and QL).
  • Table S15 (Microsoft Excel format). Significantly enriched KEGG pathways for the 178 genes under selection in the Chinese red panda (EH-GLG, XXL-LS, and QL).
  • Table S16 (Microsoft Excel format). Significantly enriched GO terms of biological processes for the 178 genes under selection in the Chinese red panda (EH-GLG, XXL-LS, and QL).

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