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The X chromosome in population genetics

Nature Reviews Genetics volume 5, pages 43–51 (2004)Cite this article

Key Points

  • The X chromosome is unique as a population-genetics tool because it combines the desirable features of other commonly used genetic markers: it recombines and has a deep history, similar to the autosomes; and it has accessible haplotypes and a sex-biased mode of inheritance, similar to mtDNA and the Y chromosome.

  • Haplotype-based phylogenetic studies of the X chromosome, among others that have used this chromosome, have contributed greatly to the debate between the Out of Africa and multiregional models of the origin of modern humans.

  • So far, the X chromosome has made almost no contribution to finer-scale historical studies, which are dominated by mtDNA and the Y chromosome. Its potential for contributing to these studies is great, however, because of the independent historical records that are preserved by different loci on this chromosome.

  • The X chromosome probably contains hundreds of independent loci, each informative enough to allow detailed historical studies without the complications that are created by an excessive amount of recombination.

  • Comparisons of X and Y chromosomes, and autosomes are the basis for the continuing study of differences between male and female mutation rates.

  • Linkage disequilibrium on the X chromosome will provide the only practical route to understanding differences between male and female recombination patterns.

  • Comparison of the X chromosome and autosomes might contribute significantly to understanding a complex set of anthropological and historical questions about the different roles of males and females in human history.

Abstract

Genetic variation records a large amount of information about the history of a species and about the processes that create and shape that variation. Owing to the way in which it is inherited, the X chromosome is a rich resource of easily accessible genetic data, and therefore provides a unique tool for population-genetic studies. The potential of the human X chromosome, which rivals that of the more traditional mtDNA and Y chromosome, has only just begun to be tapped.

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Figure 1: Signal for selection?

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Acknowledgements

I wish to thank D. Reich, M. Daly and two anonymous reviewers for helpful comments on the manuscript, and G. Thorisson for providing remapped TSC data.

Author information

Authors and Affiliations

  1. Whitehead/MIT Center for Genome Research, Cambridge, 02139, Massachusetts, USA

    Stephen F. Schaffner

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  1. Stephen F. Schaffner
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FURTHER INFORMATION

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Glossary

PHYLOGENETIC TREE

A graph that depicts the ancestor–descendant relationships between organisms or gene sequences. The sequences are the tips of the tree. Branches of the tree connect the tips to their (unobservable) ancestral sequences.

MICROSATELLITE

A class of repetitive DNA that is made up of repeats that are 2 to 8 nucleotides in length. They can be highly polymorphic and are frequently used as molecular markers in population-genetic studies.

LINKAGE DISEQUILIBRIUM

A nonrandom correlation between alleles of physically linked loci.

SYNTENY

Collinearity in the order of genes (or of other DNA sequences) in a chromosomal region of two species.

EFFECTIVE POPULATION SIZE

(Ne). The size of the ideal population in which the effects of random drift would be the same as those seen in the actual population.

HETEROZYGOSITY

A measure of the genetic variation in a population: the mean number of differences found when comparing two copies of a sequence. Usually expressed as the number of differences per base pair.

THE SNP CONSORTIUM

(TSC). A public–private effort that mapped approximately 1 million SNPs across the human genome.

POPULATION STRUCTURE

A departure from random mating as a consequence of factors such as inbreeding, overlapping generations, finite population size and geographical subdivision.

GENETIC DISTANCE

The degree of genetic differentiation between two populations. It is measured by comparing allele frequencies (and in the case of microsatellite markers, by comparing allele sizes) between populations.

OUT OF AFRICA MODELS

Models for the origin of modern human populations in which anatomically modern Homo sapiens evolved ∼100,000–150,000 years ago in Africa and expanded from there to the rest of the world.

BOTTLENECK

A marked reduction in population size followed by the survival and expansion of a small random sample of the original population.

SELECTIVE SWEEP

The process by which new, favourable mutations become fixed so quickly that physically linked alleles also become fixed by 'hitchhiking'.

SUMMARY STATISTIC

A single number that summarizes complex data; examples include mean and variance.

MULTIREGIONAL MODELS

Models for the origin of modern human populations in which anatomically modern Homo sapiens evolved simultaneously throughout Africa, Europe and Asia.

PATRILOCALITY

A residential pattern in which a married couple settles in the husband's home or community.

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Schaffner, S. The X chromosome in population genetics. Nat Rev Genet 5, 43–51 (2004). https://doi.org/10.1038/nrg1247

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