Table 1.
Summary statistics for the 20 unlinked, noncoding autosomal regions.
Figure 1.
Minor allele and derived allele frequency spectra.
(A) Minor allele frequency (MAF) and (B) derived allele frequency (DAF) spectra computed by merging the 20 non coding autosomal DNA sequences. The expected MAF and DAF spectra (grey bars) were obtained assuming constant population sizes (Material and Methods). To focus on low frequency bins, the MAF spectrum display values lower than 35 counts in each continental population. To show the derived alleles that are fixed in each continental population, we arbitrarily removed intermediate bins in the DAF spectrum.
Figure 2.
Sequenced-based summary statistics in Africans, Europeans and East-Asians.
Biplots of Tajima's D and Fu and Li's F* computed for each genomic region separately, in Africans (A), Europeans (B) and East-Asians (C). Significant Tajima's D values (P<0.05) are indicated in blue, in green for Fu and Li's F* only, and in red for both. Biplots of the number of haplotypes (K) and polymorphisms (S) computed for each genomic region separately in Africans (D), Europeans (E) and East-Asians (F). Significant K values (P<0.05) are indicated in blue, in green for S, and in red for both. The grey dots indicate the expected values of each genomic region simulated assuming a constant population size model (simulation procedure and significance of each region are described in the Materials and Methods section).
Figure 3.
Model and parameter best-fitted estimations.
(A) Simulations considering different levels of replacement of archaic hominids by modern humans. We performed 8 sets of 105 simulations: one set for a replacement rate δ = 0, one for δ = 1, 3 sets for 0≤δ≤0.01, 0≤δ≤0.1 and 0≤δ≤0.5, and 3 sets for δ≥0.5, δ≥0.9 and δ≥0.99. For each of the 8 sets, we considered three models of ancestral migration (represented by black arrows): a residual ancestral migration rate (m0∼10−10), an ancestral migration rate with the same range (10−6 to 4×10−3) as m the current migration rate (represented by gray arrows), and an ancestral migration twice higher than m. Among the 24 models tested, the model assuming a complete replacement rate of archaic hominids (δ = 1) and a residual ancestral migration (m0∼10−10) exhibited the significantly highest ψ1 except when compared with the model assuming an almost complete replacement rate of archaic hominids (δ≥0.99). This best-fitted range of parameters (δ≥0.99 and m0∼10−10), indicated by the yellow/orange/white area (A), was therefore used to simulate the African expansion (B) and the non African bottleneck (C). We performed three sets of 105 simulations for the onset tA: 0≤tA≤25 Kyears, 25≤tA≤50 Kyears and 50≤tA≤75 Kyears. For each of the three sets, we considered 5 models of growth rate αA parameters; αA = 0, 0≤αA≤0.005, 0.005≤αA≤0.01, 0.01≤αA≤0.015 and 0.015≤αA≤0.02. Among the 15 models tested, the best-fitted ranges of parameters (ψ1 significantly higher than ψ1 of the constant size model αA = 0, P<0.01) are indicated by the yellow/orange/white area (B). Likewise, we performed 5 sets of 105 simulations assuming bottlenecks intensities βOoA, starting at the time of the out-of-Africa exodus (TOoA) and ending at the independent Neolithic expansions in Europe and east-Asia: βOoA = 1, 1≤βOoA≤2, 2≤βOoA≤20, 20≤βOoA≤40 and 40≤βOoA≤60. The best-fitted range of parameter (ψ1 significant higher than ψ1 of the constant size model βOoA = 1, P<0.01), indicated by the yellow/orange/white area (C), was obtained with the set of priors 2≤βOoA≤20. The distributions used are specified in Table S4.
Table 2.
Prior distributions of the parameters for the best-fit (RAOEB) model.
Figure 4.
Models of recent African origin involving different dispersal scenarios.
(A) General RAOEB model best fitting the data, with parameter ranges given in Table 2. This model assumes a single out-of-Africa dispersal followed by the European and East-Asian split. (B) RAOEB model involving two independent, concomitant dispersals out of Africa, each giving rise to Europeans and East-Asians. (C) RAOEB model involving two independent dispersals out of Africa occurring at different times, the earlier giving rise to Europeans. (D) RAOEB model involving two independent dispersals out of Africa occurring at different times, the earlier giving rise to East Asians. For models B–D, the ranges of parameters are the same as those given in Table 2. The alternative dispersal model B (two independent dispersals at the same time) was performed using a split of the two non Africans populations concomitant with the time of out-of-Africa exodus (TOoA) simulated with the same prior reported in Table 2. The two alternative dispersal models C and D (two independent dispersals at different times) were simulated using times for the first out-of-Africa exodus drawn from the first half of the prior distribution of TOoA (Table 2), while times for the second out-of-Africa exodus were drawn from the second half of the prior distribution of TOoA. (E) Posterior probability estimated for the 4 possible dispersal models represented in A, B, C, and D.
Figure 5.
Approximate posterior distributions of historical and demographic parameters.
This figure gives the estimated ABC posterior distributions of the historical and demographic parameters (Table 3) using the RAOEB model (Figure 4A) with best-fitted priors (Table 2). Black lines represent the prior distributions and grey bars the posterior distributions. The times were translated into years using a generation time equal to 25 years. The posterior distributions of the parameters where the estimations were not validated by means of the accuracy evaluation procedure are not presented (i.e. NA and δ).
Table 3.
Historical and demographic parameters estimated under the favored RAOEB model.