Fig 1.
Schematic of MSMC2 and MSMC-IM.
(A) MSMC2 analyses patterns of mutations between pairs of haplotypes to estimate local coalescence times along the genome. (B) MSMC-IM fits an isolation-migration model to the pairwise coalescence rate estimates, with time-dependent population sizes and migration rate. (C) As a result, we obtain the migration rate over time, m(t), and the cumulative migration probability, M(t), which denotes the probability for lineages to have merged by the time t and which we use to estimate fractions of ancestry contributed by lineages diverged deeper than time t.
Fig 2.
(A) Clean-split scenario: Two populations with constant size 20,000 each diverged at split time T in the past, varying from 15kya to 150kya. (B) Split-with-migration scenario. Similar to A), with T varying between 15-150kya, and a post-split time period of symmetric migration (amounting to a total migration rate of 0.5 in both directions) between 10 and 15kya. (C) Split-with-archaic-admixture scenario: Similar to A), with T = 75kya, and population 1 receiving an admixture pulse at 30kya from an unsampled population that separates from the ancestral population at 1 million years ago. The admixture rate varies from 0% to 20%. (D) Split-with-archaic-admixture&bottleneck scenario: Similar to C), but with an added population bottleneck with factor 30 in population 1 between 40-60kya. Solid red lines indicate split times in all panels. In all plots, the blue light blue shading indicates the interval between 1–99% of the cumulative migration probability, the dark blue shading from 25–75%, and the black dashed vertical line indicates the median.
Fig 3.
Evaluating admixture proportions through M(t).
(A) The cumulative migration probability M(t) is shown for selected simulation scenarios described in Fig 2B, 2C and 2D. Plateaus of M(t) indicate periods of isolation, with the level of the plateau indicating how much ancestry has merged before. (B) Schematic coalescence in the Split-with-archaic-admixture scenario. In this scenario, a fraction 1-α of lineages sampled from the two extant populations merges at time T, and the rest, of proportion α merges as time Ta. (C) For the split-with-archaic-admixture scenarios (with and without bottleneck), we can use the level of the plateau in M(t) to estimate 1-α, and thus α. The level of the plateau is measured at time t = 300kya.
Fig 4.
Migration rate profiles for selected pairs of African populations.
(A) Migration rates. Dashed lines indicate the time point where 50% of ancestry has merged, and shading indicates the 1%, 25%, 75% and 99% percentiles of the cumulative migration probability (see Fig 2). (B) Cumulative migration probabilities M(t). Dashed lines indicate the relative cross coalescence rate obtained from MSMC2, for comparison. See S4 Fig for the full set of figures.
Fig 5.
Selected migration profiles between Yoruba and 7 non-African populations.
(A) Migration rates. Dashed lines indicate the time point where 50% of ancestry has merged, and shading indicates the 1%, 25%, 75% and 99% percentiles of the cumulative migration probability (see Fig 2). (B) Cumulative migration probabilities M(t). Dashed lines indicate the relative cross coalescence rate obtained from MSMC2. See S4 Fig for the full set of figures.
Fig 6.
Selected migration profiles within non-African populations.
(A) Migration rates. Dashed lines indicate the time point where 50% of ancestry has merged, and shading indicates the 1%, 25%, 75% and 99% percentiles of the cumulative migration probability (see panel B). (B) Cumulative migration probabilities M(t). Dashed lines indicate the relative cross coalescence rate obtained from MSMC2. See S4 Fig for the full set of figures.
Fig 7.
Summary profiles for divergence processes for 81 pairs of populations from 15 populations.
(A) Boxes show the 25% to 75% quantiles of the cumulative migration probability M(t), with bi-directional elongated error bars representing 1% and 99% percentiles. Colorcode: Red for African/African, blue for African/Non-African and orange for Non-African/Non-African pairs. (B) Barchart showing the amount of ancestry due to lineages older than 300, 600, 800kya and 1 million years ago, based on the cumulative migration probability M(t).