Science Advances

Supplementary Materials

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  • Section S1. Current demographic models cannot explain the CSFS
  • Section S2. The CSFS cannot be explained by departures from panmixia in the ancestor of archaics and modern humans
  • Section S3. Exploration of models of introgression into the ancestors of present-day Africans
  • Section S4. Parameter exploration of model A
  • Section S5. Estimating parameters for the best-fit model of archaic introgression
  • Section S6. Continuous migration versus a single pulse
  • Section S7. Local ancestry inference
  • Section S8. Extended discussion
  • Section S9. ms command lines
  • Fig. S1. Demographic model from Prüfer et al. ( 15) (see section S1 for details).
  • Fig. S2. Demographic model topologies for introgression into the ancestors of present-day Africans simulations in figs. S20, S22, S24, S26, S28, and S30.
  • Fig. S3. Demographic model topologies for mathematical results.
  • Fig. S4. CSFS from 1000 Genomes Phase 3 data across all African populations included in the dataset.
  • Fig. S5. CSFS from 1000 Genomes Phase 3 data in the Luhya population.
  • Fig. S6. CSFS from 1000 Genomes Phase 3 data in the CEU and CHB.
  • Fig. S7. Robustness of CSFS in YRI across mutation types and the Phase 1 1000 Genomes dataset.
  • Fig. S8. Robustness of CSFS in YRI to genotype quality thresholds in archaic genomes.
  • Fig. S9. CSFS in YRI when using alternate sources for the ancestral allele.
  • Fig. S10. CSFS in YRI when controlling for biased gene conversion and background selection.
  • Fig. S11. Simulations of the baseline model (section S1) with both ancestral misidentification (e1) and genotyping error in the archaic (e2).
  • Fig. S12. Mutation rate and recombination rate variation.
  • Fig. S13. Simulations of the demographic model inferred from Hsieh et al. (19) relating the Yoruba, Baka, and Biaka populations.
  • Fig. S14. Simulations of a demographic model with structure and gene flow in Africa.
  • Fig. S15. Models with continuous migration (m in units of migrants per generation) since the introgressing lineages lineage splits.
  • Fig. S16. Current demographic models from the literature cannot explain the shape of the CSFS observed in fig. S4.
  • Fig. S17. Models involving structure in the ancestor of modern humans and archaics cannot explain the observed CSFS.
  • Fig. S18. Models involving ancestral structure from the literature cannot explain the observed CSFS.
  • Fig. S19. Model A.1: Gene flow from the modern human ancestor branch back into the modern human ancestor before the out-of-Africa event.
  • Fig. S20. Model sA.1: Simplified model of gene flow from the modern human ancestor branch back into the modern human ancestor before the out-of-Africa event.
  • Fig. S21. Model A.2: Gene flow from the modern human ancestor branch into the African branch after the out of Africa event.
  • Fig. S22. Model sA.2: Simplified model of gene flow from the modern human ancestor branch into the African branch after the out of Africa event.
  • Fig. S23. Model B.1: Gene flow from the archaic branch into the modern human ancestor before the out-of-Africa event.
  • Fig. S24. Model sB.1: Simplified model of gene flow from the archaic branch into the modern human ancestor before the out-of-Africa event.
  • Fig. S25. Model B.2: Gene flow from the archaic branch into the African branch after the out-of-Africa event.
  • Fig. S26. Model sB.2: Simplified model of gene flow from the archaic branch into the African branch after the out-of-Africa event.
  • Fig. S27. Model C.1: Gene flow from an unknown archaic branch into the modern human ancestor before the out-of-Africa event.
  • Fig. S28. Model sC.1: Simplified model of gene flow from an unknown archaic branch into the modern human ancestor before the out-of-Africa event.
  • Fig. S29. Model C.2: Gene flow from an unknown archaic branch into the African branch after the out-of-Africa event.
  • Fig. S30. Model sC.2: Simplified model of gene flow from an unknown archaic branch into the African branch after the out-of-Africa event.
  • Fig. S31. Simulations of the best-fitting parameters for models A, B, C (section S3).
  • Fig. S32. Model A.2 with a population size of 0:01 Na in the introgressing population.
  • Fig. S33. Model A.2 with a population size of 1 × 10−4 Na in the introgressing population.
  • Fig. S34. Model A.2 with a population size of 1 × 10−4 Na in the introgressing population and migration between CEU and YRI over the last 20 ka B.P.
  • Fig. S35. Model A.2 with a population size of 1 × 10−5 Na in the introgressing population, which branches off 200 ka B.P.
  • Fig. S36. Model A.2 where the introgressing population splits at the same time as the archaic population (550 ka B.P.) with a population size of 0.01 Na.
  • Fig. S37. Model A.2 where the introgressing population splits at the same time as the archaic population, 765 ka B.P.
  • Fig. S38. Parameter estimates using ABC for model A.1 including ancestral misidentification (e1) and genotyping error in the archaic (e2).
  • Fig. S39. Parameter estimates using ABC for model A.2 including ancestral misidentification (e1) and genotyping error in the archaic (e2).
  • Fig. S40. Marginalized joint CSFS of YRI and CEU from simulations.
  • Fig. S41. Distribution of allele frequencies for neutral archaic SNPs from model C with 13% introgression and an introgression time of 42 ka B.P.
  • Fig. S42. Archaic segment frequency map for MSL and YRI.
  • Fig. S43. CSFS from the baseline model allowing for recurrent mutations.
  • Table S1. Description of the models examined in this work.
  • Table S2. We simulated data from the Prüfer et al. (15) model and added in ancestral misidentification error and genotyping error in the archaic.
  • Table S3. Model fits for null models including structure and departures from panmixia in the Modern Human (MH) ancestor.
  • Table S4. Model fits for alternate models including admixture from other lineages.
  • Table S5. Model fits for alternate models using a simplified demography.
  • Table S6. Model fits for variations of model A.
  • Table S7. Best-fitting parameter values for all populations using ABC.
  • Table S8. P values of a test of goodness of fit for the best-fitting parameters for each class of demographic models.
  • Appendix A. The CSFS is uniform under structure in the archaic population.
  • Appendix B. The CSFS is symmetric under model A.
  • References (4355)

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