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. 2012:2:745.
doi: 10.1038/srep00745. Epub 2012 Oct 18.

MtDNA analysis of global populations support that major population expansions began before Neolithic Time

Hong-Xiang Zheng  1 , Shi Yan, Zhen-Dong Qin, Li Jin
Affiliations

MtDNA analysis of global populations support that major population expansions began before Neolithic Time

Hong-Xiang Zheng et al. Sci Rep. 2012.

Abstract

Agriculture resulted in extensive population growths and human activities. However, whether major human expansions started after Neolithic Time still remained controversial. With the benefit of 1000 Genome Project, we were able to analyze a total of 910 samples from 11 populations in Africa, Europe and Americas. From these random samples, we identified the expansion lineages and reconstructed the historical demographic variations. In all the three continents, we found that most major lineage expansions (11 out of 15 star lineages in Africa, all autochthonous lineages in Europe and America) coalesced before the first appearance of agriculture. Furthermore, major population expansions were estimated after Last Glacial Maximum but before Neolithic Time, also corresponding to the result of major lineage expansions. Considering results in current and previous study, global mtDNA evidence showed that rising temperature after Last Glacial Maximum offered amiable environments and might be the most important factor for prehistorical human expansions.

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Figures

Figure 1
Figure 1. African expansion lineages from median-joining network.
Star expansions were selected from median-joining network of 313 African mtDNA coding region sequences corresponding to rCRS positions 577–16023.Blue, LWK; purple, ASW; yellow, YRI. Red squares and numbers indicate clusters with distinct expansions. 1, L3e2a; 2, L3e2a1b; 3, L3e2b; 4, L1b1a; 5, L1b1a3; 6, L3d1–5; 7, L3e3b; 8, L0a1a; 9, L0a1a2; 10, L3b1a; 11, L3b1a1; 12, L3e1; 13, L2a1; 14, L2a1a; 15, L2a1c; 16, L2a1f. Branch length is proportional to steps of mutations and red arrows indicate the root.
Figure 2
Figure 2. mtDNA Bayesian skyline plot showing the size trend of 10 global populations.
The y-axis is the product of maternal effective size and generation time.The x-axis is the time from present in units of years. The thick solid line is the median estimate and the thin lines (blue) show the 95% highest posterior density limits. Detailed settings refer to Methods.
Figure 3
Figure 3. Time estimation of each observed expansion in 3 African populations and Bayesian skyline plot for 3 African populations together.
(A)Time estimation of each observed expansion in 3 African populations: ρ statistic-based method with Soares complete genome rate, Soares synonymous rate and modified Mishmar coding region rate, Bayesian MCMC method by BEAST using Ho and Endicott rate, and Atkinson rate respectively.(B) mtDNA Bayesian skyline plot showing size trend of the 3 African populations together, detailed settings refer to Methods. The grey area shows the time after LGM and before Neolithic Time.
Figure 4
Figure 4. European expansion lineages from median-joining network.
Star expansions were selected from median-joining network of 413 European mtDNA coding region sequences corresponding to rCRS positions 577–16023.Blue, GBR; purple, FIN; yellow, CEU; Cyan, TSI; Green, IBS. Red squares and numbers indicate clusters with distinct expansions. 1, HV; 2, H; 3, H1; 4, H3; 5, V; 6, T2; 7, T2b; 8, T1; 9, U5a; 10, U5a1; 11, J1c; 12, J1c3; 13, W; 14, U2'3'4'7'8'9; 15, K1. Branch length is proportional to steps of mutations and red arrows indicate the root.
Figure 5
Figure 5. Time estimation of each observed expansion in 5 European populations and Bayesian skyline plot for 5 European populations together.
(A)Time estimation of each observed expansion in 5 European populations.(B) mtDNA Bayesian skyline plot showing size trend of the 5 European populations together, detailed setting refers to Methods. The grey area shows the time after LGM and before Neolithic Time.
Figure 6
Figure 6. American expansion lineages from median-joining network.
Star expansions were selected from median-joining network of 184 Ameican mtDNA coding region sequences corresponding to rCRS positions 577–16023.Blue, CLM; yellow, MXL; Green, PUR. Red squares and numbers indicate clusters with distinct expansions. 1, A2; 2, A2w; 3, B2; 4, B2d; 5, C1; 6, D1. Branch length is proportional to steps of mutations and red arrows indicate the root.
Figure 7
Figure 7. Time estimation of each observed expansion in 3 American populations and Bayesian skyline plot for 3 American populations together.
(A)Time estimation of each observed expansion in 3 American populations.(B) mtDNA Bayesian skyline plot showing size trend of the 3 American populations together, detailed settings refer to Methods. The grey area shows the time after LGM and before Neolithic Time.
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