Human Populations: Origins and Evolution


The origins of modern human diversity have long been debated within a framework set by two hypotheses: ‘Out‐of‐Africa’ versus multiregional evolution. Humans are genetically closer to each other than members of all other primate species, most of our genetic diversity is accounted for by individual differences within populations, and only a small fraction of the species' genetic variance represents differences among populations or geographic groups. All these findings are hard to reconcile with the notion of parallel evolution in different continents, implicit in the multiregional model; the alternative hypotheses are now better described as either complete replacement of archaic human populations, or as partial assimilation into anatomically modern populations. Critical information about human demographic history has emerged from analyses of genomic diversity, clearly supporting an African origin of our species, followed by dispersal of rather small groups of people in the other continents. However, ancient deoxyribonucleic acid from fossil specimens seems to suggest low, but significant, levels of hybridisation between anatomically archaic and modern humans in the course of the latter's expansion from Africa, although alternative explanations of the data cannot be ruled out.

Key Concepts:

  • Genetic differences between humans are smaller than in any other primate species.

  • Genetic differences between human populations account for a minor fraction of the species' diversity.

  • Most human polymorphic alleles are present in all continents.

  • Each population contains an ample subset of human allelic variants.

  • African populations show the highest genome diversity worldwide, and alleles in other continents can largely be regarded as subsets of African diversity.

  • Differences between populations are structured in the geographical space, showing evidence of repeated founder effects as humans expanded to colonise the whole planet.

  • Models of genetic replacement, partial or total, of archaic human forms by anatomically modern humans account for current diversity better than any alternative models.

  • Non‐African people consistently show an excess of DNA similarity with the Neandertal genome, which is often (but not necessarily) interpreted as a consequence of archaic hybridisation between Neandertals and anatomically modern people dispersing from Africa.

Keywords: genomic diversity; DNA diversity; out‐of‐Africa; multiregional evolution; coalescence; neandertal; admixture

Figure 1.

Four main models of human evolution (top) and the relative contribution of African genes to the gene pool of non‐African populations implied by each of them (bottom). In each of the four panels corresponding to the different models, the past is at the root and the present is at the tips of the tree. The assimilation and replacement models do not rule out the possibility of genetic exchanges between different continental populations (represented by the thin horizontal arrows for the model of multiregional evolution). Reproduced with permission from Stoneking . © Nature Publishing Group.

Figure 2.

A comparison of the model assuming hybridisation between modern humans dispersing from Africa and Neandertals (top) and of the model of ancient population structure in Africa (bottom). The colours of the dots suggest levels of genotype similarity. In both (a) and (d) (corresponding to perhaps 800 000 years ago) the Neandertals' ancestors move from Northern Africa into Europe, but in (d) African populations are genetically structured, with a North–South difference. In (b) and (e) (corresponding to perhaps 60 000 years ago) anatomically modern people move from Africa into the Near East; however, in (b) they admix with Neandertals (as indicated by the red arrow) whereas in (e) they do not (as indicated by the diagonal red line). In (c) and (f) (corresponding to any time between 29 000 years ago and the present) Neandertals have gone extinct, but in both cases Europeans are genetically closer to them than Africans, either because they have incorporated some Neandertal genes (darker edge of the dots in (c)), or because they share a set of recent ancestors (similar colours of the dots in (e)).

Figure 3.

A highly schematic view of the origins of current genome diversity, under a replacement model of human evolution. This scheme is also valid, with modest modifications, under a model of limited assimilation of anatomically archaic populations. Dates along the black lines are years before present, dots of different colours represent different genotypes, the distribution of which roughly corresponds to archaeological evidence on human occupation of different regions. Dots of new colours appear in the maps in the course of time (e.g., red and violet in Africa at 70 000 BP, burgundy in India at 10 000 BP), representing the effect of mutation. As only part of the African alleles (yellow, orange and light green dots) are carried into Eurasia by dispersing Africans from 60 000 years bp, diversity in modern Eurasian populations is largely a subset of African diversity. Moreover note how the expansion in Eurasia generates broad gradients of genotype frequencies. Reproduced with permission from Barbujani et al..




1000 Genomes Project Consortium (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56–65.

Ahn SM, Kim TH, Lee S et al. (2009) The first Korean genome sequence and analysis: full genome sequencing for a socio‐ethnic group. Genome Research 19: 1622–1629.

Barbujani G and Belle EMS (2006) Genomic boundaries between human populations. Human Heredity 61: 15–21.

Barbujani G and Colonna V (2010) Human genome diversity: frequently asked questions. Trends in Genetics 26: 285–295.

Barbujani G, Ghirotto S and Tassi F (2013) Nine things to remember about human genome diversity. Tissue Antigens 82: 155–164.

Behar DM, Villems R, Soodyall H et al. (2008) The dawn of human matrilineal diversity. American Journal of Human Genetics 82: 1130–1140.

Blum MGB and Jakobsson M (2011) Deep divergences of human gene trees and models of human origins. Molecular Biology and Evolution 28: 889–898.

Briggs AW, Good JM, Green RE et al. (2009) Targeted retrieval and analysis of five neandertal mtDNA genomes. Science 325: 318–321.

Campbell MC and Tishkoff SA (2008) African genetic diversity: implications for human demographic history, modern human origins, and complex disease mapping. Annual Review of Genomics and Human Genetics 9: 403–433.



Currat M and Excoffier L (2004) Modern humans did not admix with Neanderthals during their range expansion into Europe. PLoS Biology 2: e421.

DeGiorgio M, Jakobsson M and Rosenberg NA (2009) Out of Africa: Modern human origins special feature: explaining worldwide patterns of human genetic variation using a coalescent‐based serial founder model of migration outward from Africa. Proceedings of the National Academy of Sciences of the USA 106: 16057–16062.

Eriksson A and Manica A (2012) Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. Proceedings of the National Academy of Sciences of the USA 109: 13956–13960.

Fagundes NJ, Ray N, Beaumont M et al. (2007) Statistical evaluation of alternative models of human evolution. Proceedings of the National Academy of Sciences of the USA 104: 17614–17619.

Foley R and Lewin R (2004) Principles of Human Evolution. Oxford: Blackwell.

Garrigan D, Kingan SB, Pilkington MM et al. (2007) Inferring human population sizes, divergence times and rates of gene flow from mitochondrial, X and Y chromosome resequencing data. Genetics 177: 2195–2207.

Ghirotto S, Tassi F, Benazzo A and Barbujani G (2011) No evidence of neandertal admixture in the mitochondrial genomes of early European modern humans and contemporary Europeans. American Journal of Physical Anthropology 146: 242–252.

Green RE, Krause J, Briggs AW et al. (2010) A draft sequence of the neandertal genome. Science 328: 710–722.

Grossman SR, Andersen KG, Shlyakhter I et al. (2013) Identifying recent adaptations in large‐scale genomic data. Cell 152: 703–713.

Henn BM, Botigué LR, Gravel S et al. (2012) Hunter–gatherer genomic diversity suggests a southern African origin for modern humans. Proceedings of the National Academy of Sciences of the USA 108: 5154–5162.

Hunley KL, Healy ME and Long JC (2009) The global pattern of gene identity variation reveals a history of long‐range migrations, bottlenecks, and local mate exchange: implications for biological race. American Journal of Physical Anthropology 139: 35–46.

Jakobsson M, Scholz SW, Scheet P et al. (2008) Genotype, haplotype and copy‐number variation in worldwide human populations. Nature 451: 998–1003.

Jorde LB and Wooding SP (2004) Genetic variation, classification and race. Nature Genetics 36(suppl): S28–S33.

Kaessmann H, Wiebe V, Weiss G and Pääbo S (2001) Great ape DNA sequences reveal a reduced diversity and an expansion in humans. Nature Genetics 27: 155–156.

Labuda D, Zietkiewicz E and Yotova V (2000) Archaic lineages in the history of modern humans. Genetics 156: 799–808.

Lachance J, Vernot B, Elbers CC et al. (2012) Evolutionary history and adaptation from high‐coverage whole‐genome sequences of diverse African hunter–gatherers. Cell 150: 457–469.

Lahr MM and Foley RA (1994) Multiple dispersals and modern human origins. Evolutionary Anthropology 3: 48–60.

Li JZ, Absher DM, Tang H et al. (2008) Worldwide human relationships inferred from genome‐wide patterns of variation. Science 319: 1100–1104.

Liu H, Prugnolle F, Manica A and Balloux F (2006) A geographically explicit genetic model of worldwide human‐settlement history. American Journal of Human Genetics 79: 230–237.


Marques‐Bonet T, Kidd JM, Ventura M et al. (2009) A burst of segmental duplications in the genome of the African great ape ancestor. Nature 457: 877–881.

McEvoy BP, Powell JE, Goddard ME and Visscher PM (2011) Human population dispersal “Out of Africa” estimated from linkage disequilibrium and allele frequencies of SNPs. Genome Research 21: 821–829.

Ramachandran S, Deshpande O, Roseman CC et al. (2005) Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proceedings of the National Academy of Sciences of the USA 102: 15942–15947.

Reich D, Patterson N, Kircher M et al. (2011) Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. American Journal of Human Genetics 89: 516–528.

Rosenberg N (2011) A population‐genetic perspective on the similarities and differences among worldwide human populations. Human Biology 83: 659–684.

Rosenberg N, Pritchard JK, Weber JL et al. (2002) Genetic structure of human populations. Science 298: 2381–2385.

Rosenberg NA, Mahajan S, Ramachandran S et al. (2005) Clines, clusters, and the effect of study design on the inference of human population structure. PLoS Genetics 1: e70.

Schuster SC, Miller W, Ratan A et al. (2010) Complete Khoisan and Bantu genomes from southern Africa. Nature 463: 943–947.

Stoneking M (2008) Human origins. The evolutionary perspective. EMBO Reports 9: S46–S50.

Thalmann O, Fischer A, Lankester F, Pääbo S and Vigilant L (2007) The complex evolutionary history of gorillas: insights from genomic data. Molecular Biology and Evolution 24: 146–158.

Tishkoff SA, Dietzsch E, Speed W et al. (1996) Global patterns of linkage disequilibrium at the CD4 locus and modern human origins. Science 271: 1380–1387.

Veeramah KR, Wegmann D, Woerner A et al. (2012) An early divergence of KhoeSan ancestors from those of other modern humans is supported by an ABC‐based analysis of autosomal resequencing data. Molecular Biology and Evolution 29: 617–630.

Wall JD, Yang MA, Jay F et al. (2013) Higher levels of neanderthal ancestry in East Asians than in Europeans. Genetics 194: 199–209.

Wu DD, Irwin DM and Zhang YP (2011) De novo origin of human protein‐coding genes. PLoS Genetics 7: e1002379.

Zhao Z, Yu N, Fu YX and Li WH (2006) Nucleotide variation and haplotype diversity in a 10‐kb noncoding region in three continental human populations. Genetics 174: 399–409.

Further Reading

Balding D, Bishop M and Cannings C (2007) Handbook of Statistical Genetics, 3rd edn. New York: Wiley.

Jobling M, Hollox E, Hurles M and Kivisild T (2013) Human Evolutionary Genetics. New York: Garland Science.

Relethford JH (2001) Genetics and the Search for Modern Human Origins. New York: Wiley.

Stringer C (2012) Lone Survivors: How We Came to Be the Only Humans on Earth. New York: Henry Holt.

Tattersall I (2012) Masters of the Planet: The Search for Our Human Origins. New York: Palgrave MacMillan.

Contact Editor close

* Required Field

How to Cite close
Barbujani, Guido, and Colonna, Vincenza(Oct 2013) Human Populations: Origins and Evolution. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0001794.pub3]