The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans  Sriram Sankararaman, Swapan Mallick, Nick Patterson, David Reich  Current Biology  Volume 26, Issue 9, Pages 1241-1247 (May 2016) DOI: 10.1016/j.cub.2016.03.037 Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 1 More Recent Date of Denisovan than Neanderthal Admixture Average linkage disequilibrium (Lewontin’s D) as a function of distance in Oceanians for SNPs informative of Neanderthal (red) and Denisovan (blue) ancestry. The Denisova decay is slower, implying a more recent date. See also Table S1. Current Biology 2016 26, 1241-1247DOI: (10.1016/j.cub.2016.03.037) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 2 Variation in Denisovan Ancestry Proportion (A) Proportion of the genome inferred to be Denisovan in ancestry in diverse non-Africans. The color scale is not linear to allow saturation of the high Denisova proportions in Oceania (bright red) and better visualization of the peak of Denisova proportion in South Asia. (B) Proportion of the genome confidently inferred to be Denisovan in ancestry in mainland Eurasians plotted against the rate of allele sharing of each sample with non-West Eurasians as measured by an f4 statistic. Error bars (1 SE) were obtained from a block jackknife. The Denisovan ancestry estimates in South Asians are systematically above expectation (fitted trend line) (p = 0.0013). See also Table S3. Current Biology 2016 26, 1241-1247DOI: (10.1016/j.cub.2016.03.037) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 3 Fine-Scale Maps of Denisovan and Neanderthal Introgression (A) Non-overlapping 100 kb windows that have non-zero inferred archaic ancestry in each of six populations (blue, Denisova; red, Neanderthal). In the innermost rings, we plot deserts (windows >10 Mb). See also Tables S4 and S5. (B) Correlation of confidently inferred archaic ancestry (Neanderthal ancestry in six non-African populations and Denisovan ancestry in Oceanians) across populations in non-overlapping windows of size 100 kb, 1 Mb, and 10 Mb. (C) We plot the median of the proportion of Denisovan and Neanderthal ancestry within quintiles of a B statistic measuring intensity of linked selection (low B indicates the regions most affected by linked selection). See also Tables S6 and S7. Current Biology 2016 26, 1241-1247DOI: (10.1016/j.cub.2016.03.037) Copyright © 2016 Elsevier Ltd Terms and Conditions