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  • Review Article
  • Published:

Learning about human population history from ancient and modern genomes

Nature Reviews Genetics volume 12, pages 603–614 (2011)Cite this article

Subjects

Key Points

  • Studies of human population history have the goal of finding out what happened in our past, in terms of population origins, migrations, relationships, admixture and changes in population size — that is, the demographic history of populations. Genome-wide data sets are now transforming this field.

  • The study of fossil DNA, or ancient DNA, has been revolutionized by technological developments in high-throughput sequencing. Three ancient hominin nuclear genome sequences have now been published: from a Neanderthal; from a recently discovered extinct hominin group from Siberia, Denisovans; and from a native Greenlander (Saqqaq).

  • Many new genome sequences from modern humans have been obtained by the 1000 Genomes Project, as well as by several other human genome and exome sequencing efforts.

  • Genome-wide SNP data are becoming increasingly available from many populations of anthropological interest.

  • Increases in computational power have enabled more sophisticated use of genome-scale data. There have been two important advances for human population studies: unsupervised analyses and model-based analyses.

  • Issues that can be addressed using genome-wide data include the African origin of modern humans and the number of dispersals.

Abstract

Genome-wide data, both from SNP arrays and from complete genome sequencing, are becoming increasingly abundant and are now even available from extinct hominins. These data are providing new insights into population history; in particular, when combined with model-based analytical approaches, genome-wide data allow direct testing of hypotheses about population history. For example, genome-wide data from both contemporary populations and extinct hominins strongly support a single dispersal of modern humans from Africa, followed by two archaic admixture events: one with Neanderthals somewhere outside Africa and a second with Denisovans that (so far) has only been detected in New Guinea. These new developments promise to reveal new stories about human population history, without having to resort to storytelling.

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Figure 1: Model-based analyses of demographic history.
Figure 2: High-throughput sequencing of ancient DNA.
Figure 3: Distinguishing ancient from modern DNA.
Figure 4: Dispersal of modern humans from Africa.

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Acknowledgements

We thank A. Briggs, B. Pakendorf and S. Pääbo for helpful comments. The work of the authors is supported by the Max Planck Society (M.S.) and the University of Tübingen, Germany (J.K.).

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Authors and Affiliations

  1. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, D04103, Germany

    Mark Stoneking

  2. Institute for Archaeological Sciences, University of Tübingen, Germany

    Johannes Krause

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Correspondence to Mark Stoneking.

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1000 Genomes Project

CEPH Human Genetic Diversity Panel

Nature Reviews Genetics series on Applications of next-generation sequencing

Glossary

HapMap

An international project with the goal of identifying genetic similarities and differences among human populations. The project has made large amounts of data publicly available.

Admixture

Gene flow between two (or more) groups that have been separated for a long enough period of time to be genetically distinct.

Demographic history

The history of events that influence the genetic structure of a population, including population size changes, divergence from other populations and migration (gene flow).

SNP arrays

Microarrays that are used to simultaneously genotype several thousand to several hundred thousand SNPs for a single sample.

Hominin

Modern humans, their fossil ancestors, and extinct relatives thereof, up to (but not including) chimpanzees.

Denisovans

Archaic hominins represented by fossil remains from Denisova Cave in southern Siberia; genome sequence data indicate that Denisovans are a sister group to Neanderthals.

Saqqaq

The Saqqaq culture is the archaeological designation of the earliest culture of West and South East Greenland. A 4,000-year-old native Greenlander from the Saqqaq culture, whose hair sample was preserved in permafrost, was used to obtain the first genome sequence from an ancient modern human.

Endogenous DNA

In the ancient DNA field, endogenous DNA usually refers to the original DNA from the actual organism that was sampled. In some publications, endogenous DNA includes the microbial DNA that is common to most ancient samples versus exogenous DNA that is brought onto or into the sample after excavation.

Nucleotide misincorporations

Erroneous incorporations of nucleotides during the synthesis of the complementary DNA strand by a polymerase (for example, during PCR) that are caused by chemical modifications of the template nucleotides. For example, deamination of cytosine leads to uracil, which is read by the DNA polymerase as thymine and as a consequence instead of a guanine an adenine is incorporated into the complementary strand.

Sequencing library

This consists of DNA samples that have been prepared for high-throughput DNA sequencing by adding artificial oligonucleotides to both ends of the template molecules. The adaptors can be used to bind the DNA to a surface and clonally amplify each molecule before or during high-throughput DNA sequencing.

Post-mortem chemical damage

Chemical modifications to DNA that happen after the death of the organism: for example, hydrolytic deamination of cytosine.

Cytosine deamination

In the context of ancient DNA, a post-mortem hydrolytic chemical reaction that changes cytosine to uracil, releasing ammonia in the process.

Ascertainment bias

Sampling bias that arises from how SNPs are chosen for inclusion on SNP arrays; SNPs that are known to be polymorphic in a particular population will overestimate genetic variation in that population relative to other populations.

Hybridization capture

A method that allows selective capture of genomic regions of interest from a complex DNA sample before DNA sequencing. It is based on hybridization between DNA fragments in the sample and chosen 'bait' sequences.

Pleistocene

Geological epoch that spans the time period from about 2.5 million years ago to 12,000 years ago.

Unsupervised analyses

Analyses that are done at the individual instead of the population level and do not require that population labels are applied to individuals.

Ancestry components

A pre-defined number of subgroups with distinctive allele frequencies, inferred from genome-wide data, which are then used to assign the ancestry of each individual without specifying the population to which the individual belongs.

Model-based analyses

Analyses that specify demographic models, investigate which demographic model best fits the genetic data and infer parameters of interest (such as population size changes, divergence times and migration events) for the best-fitting model.

Summary statistics

Statistics that summarize various aspects of genetic data, such as heterozygosity (for within population variation) or FST values (for between population variation). Summary statistics are conventionally used to investigate the fit of demographic models to the actual genetic data.

Sahul

The combined Australia–New Guinea landmass that existed periodically during cold periods in the Pleistocene, including during the initial colonization of Australia and New Guinea about 50,000 years ago, up until rising sea levels separated Australia from New Guinea about 8,000 years ago.

Bougainville

A large island in the Pacific that politically is part of Papua New Guinea but geographically is part of the main Solomon Islands chain.

Austronesian

The most geographically widespread family of languages, extending from Taiwan through mainland and island southeast Asia, Near Oceania, Remote Oceania and even Madagascar.

Near Oceania

Refers to New Guinea and nearby offshore islands, including the main Solomon Islands chain (excluding Santa Cruz); Near Oceania was first colonized by humans at least 40,000 years ago, whereas Remote Oceania (Santa Cruz and all islands to the east) was only colonized by humans beginning about 3,200 years ago.

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Stoneking, M., Krause, J. Learning about human population history from ancient and modern genomes. Nat Rev Genet 12, 603–614 (2011). https://doi.org/10.1038/nrg3029

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