Science Advances

Supplementary Materials

The PDF file includes:

  • Section S1. Rationale for baboon taxonomy and nomenclature
  • Section S2. Rationale for mutation rate used in PSMC analyses
  • Section S3. Sequencing and assembly of olive baboon genome
  • Section S4. Annotation and gene content of the baboon genome
  • Section S5. Identification of SNVs and small indels within baboon species
  • Section S6. Validation of species identity within the diversity panel
  • Section S7. Lineage-specific Alu insertion in OWMs and hominoids
  • Section S8. Alternative methods for constructing phylogenetic trees
  • Section S9. Identification of admixture through asymmetric allele sharing
  • Section S10. Polymorphic AluY insertions across Papio species
  • Section S11. Bayesian concordance analyses of gene trees devoid of coding sequences
  • Section S12. CoalHMMs of admixture trees and events
  • Section S13. Locus-specific phylogenetic trees for chromosomal segments containing annotated genes
  • Fig. S1. Panu3.0 genome assembly process.
  • Fig. S2. Workflow used in variant calling pipeline.
  • Fig. S3. Details regarding SNV calls.
  • Fig. S4. Maximum likelihood and Bayesian phylogenetic trees based on SNV data.
  • Fig. S5. Test of phylogeny reconstruction using PoMo.
  • Fig. S6. Identification of admixture using f-statistics.
  • Fig. S7. Evidence for admixture from haplotyping sharing.
  • Fig. S8. A cladogram of Papio individuals from the diversity panel.
  • Fig. S9. Bayesian concordance analysis.
  • Fig. S10. Bootstrap analysis of timing of divergence events.
  • Fig. S11. Confidence intervals for baboon admixture proportions.
  • Fig. S12. Results for simulated admixture analysis.
  • Fig. S13. Results for correction factor adjustment of admixture history.
  • Fig. S14. Model used to estimate specific divergence and admixture history.
  • Fig. S15. Unbiased estimates dating divergences and admixture events.
  • Fig. S16. Phylogeny representing cluster 1 genic regions.
  • Fig. S17. Phylogeny representing cluster 2 genic regions.
  • Fig. S18. Phylogeny representing cluster 3 genic regions.
  • Table S1. Assembly statistics.
  • Table S2. Annotation of baboon genome assemblies.
  • Table S3. DNA samples used for diversity analysis.
  • Table S4. SNV variation among 15 Papio baboons and a gelada.
  • Table S5. Full-length AluY insertions and lineage-specific insertions in primate genomes.
  • Table S6. Effect of admixture on branch lengths measured in substitutions per site.
  • Table S7. Bayes factors comparing alternate phylogenies.
  • Table S8. Divergence time estimates across triplets.
  • Table S9. Admixture proportion estimates across triplets.
  • Legend for table S10
  • References (6178)

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Other Supplementary Material for this manuscript includes the following:

  • Table S10 (Microsoft Excel format). GO terms associated with genes falling in clusters 1 to 3 of genic regions.

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