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

Zheng HX, Yan S, Qin ZD, Jin L - Sci Rep (2012)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: MOE Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.

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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Related in: MedlinePlus

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.
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f1: 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.

Mentions: In the 1000 Genome Project, 313 African samples from 4 populations were collected, most of which (97.9%) were from Macrohaplogroup L excluding M and N under L3 (Table S1), and were also confirmed as autochthonous in African. Detailed information for the populations was annotated in Methods. Besides Macrohaplogroup L, we could find some Native American components which belong to A2, C1 and D1 (3 individuals in ASW), while there were also low frequent M32 which was common in Southeast of Africa (1 individual in ASW) and U6 which had the North African origin (1 individual in ASW and 1 in YRI). From the median-joining network constructed by 313 African samples, 16 expansion lineages were identified, not including the very old expansion L3 lineage (see Figure 1). Nearly all the lineages with star-like structure were shared by at least 2 populations except for L3b1a1 that is LWK-specific, indicating that most of these expansions might have occurred in the African ancestral populations before the divergence of these populations and these star lineages were a representative of the African maternal evolution. Among the 16 expansion haplogroups, 5 lineages (L0a1a2, L2a1f, L3b1a1, L3e2a1b, and L3e3b) showed coalescence time less than 10 kya at least by three of five estimates mentioned in Methods, while the remaining 11 lineages (L0a1a, L1b1a3, L1b1a, L2a1a, L2a1c, L2a1, L3b1a, L3e1, L3e2a, L3e2b and L3d1–5) expanded before 10 kya (see Table S2). Specially, the expansion of lineage L3d1–5 took place before the LGM. From the ages estimated above, we found that most lineages shared among populations (11/15) expanded before 10 kya, i.e. the first occurrence of farming in the land of Africa. Thus, the result of lineage expansions showed that maternal African growth could be mainly attributed to pre-Neolithic expansion.


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

Zheng HX, Yan S, Qin ZD, Jin L - Sci Rep (2012)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3475341&req=5

f1: 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.
Mentions: In the 1000 Genome Project, 313 African samples from 4 populations were collected, most of which (97.9%) were from Macrohaplogroup L excluding M and N under L3 (Table S1), and were also confirmed as autochthonous in African. Detailed information for the populations was annotated in Methods. Besides Macrohaplogroup L, we could find some Native American components which belong to A2, C1 and D1 (3 individuals in ASW), while there were also low frequent M32 which was common in Southeast of Africa (1 individual in ASW) and U6 which had the North African origin (1 individual in ASW and 1 in YRI). From the median-joining network constructed by 313 African samples, 16 expansion lineages were identified, not including the very old expansion L3 lineage (see Figure 1). Nearly all the lineages with star-like structure were shared by at least 2 populations except for L3b1a1 that is LWK-specific, indicating that most of these expansions might have occurred in the African ancestral populations before the divergence of these populations and these star lineages were a representative of the African maternal evolution. Among the 16 expansion haplogroups, 5 lineages (L0a1a2, L2a1f, L3b1a1, L3e2a1b, and L3e3b) showed coalescence time less than 10 kya at least by three of five estimates mentioned in Methods, while the remaining 11 lineages (L0a1a, L1b1a3, L1b1a, L2a1a, L2a1c, L2a1, L3b1a, L3e1, L3e2a, L3e2b and L3d1–5) expanded before 10 kya (see Table S2). Specially, the expansion of lineage L3d1–5 took place before the LGM. From the ages estimated above, we found that most lineages shared among populations (11/15) expanded before 10 kya, i.e. the first occurrence of farming in the land of Africa. Thus, the result of lineage expansions showed that maternal African growth could be mainly attributed to pre-Neolithic expansion.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: MOE Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.

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.

Show MeSH
Related in: MedlinePlus