Single Nucleotide Polymorphisms in Human Disease and Evolution: Phylogenies and Genealogies

Abstract

Single nucleotide polymorphisms (SNPs) are common genetic variants within a population. Several SNPs have been implicated directly in human diseases, but their biggest promise lies in their potential as genetic markers for discovering genetic factors in a wide variety of human diseases and other traits. There are two methods for modeling the processes by which population genetic variation has evolved: genealogy, the actual family tree in which genetic variants arose and were inherited from parents to children and phylogeny, a compressed history of how these genetic variants accumulated in lineages of successive copies of deoxyribonucleic acid (DNA) sequences. Genealogies and phylogenies are two ways to view the same evolutionary process, and each has specific applications to the discovery of genetic factors in human disease, especially relevant in the genomic era.

Keywords: population genetics; polymorphism; disease; evolution; phylogenetics

Figure 1.

Genetic differences between two homologous chromosome regions. Three single‐nucleotide differences are shown: an A/G difference (transition), a C/T difference (transition) and a G/T difference (transversion). Each of these three differences may appear at a different frequency in the population.

Figure 2.

Probability that an allele will change in frequency to 100%, given its current frequency. When the selection pressure is small (|s|<∼0.01% in an effective population of Ne=10 000), the allele behaves as if neutral (diagonal line). When negative selection is strong (s<–0.1%), it becomes very improbable that the allele will increase in frequency enough to result in polymorphism. Each curve represents a different coefficient of selection, s, conferred by the allele. Positive values of s indicate positive selection, negative values represent negative selection. Probability is calculated according to Kimura (1983) as y=[1−exp(−Sx)]/[1−exp(−S)], where S=4Nes. Therefore we are assuming the effective population size as 10 000, the estimated value during most of human evolution.

Figure 3.

A toy example illustrating the evolution of SNPs, seen from (a) the genealogical view and (b) the phylogenetic view. The starting population is genetically homogeneous and the population size is constant. (a) Individuals are shown as large open circles, with two chromosomes (grey bars). Mutations (copying errors) are shown as closed circles on the chromosomes. When variants arising from mutation are faithfully copied into following generations, they are shown as open circles. When a variant reaches 1% in the population, it is shown as a star. In this example, allele a (arising from an erroneous substitution of the parental allele A) is created by a mutation when an individual from the first generation copies its chromosomes and passes allele a to its children. After N generations, allele a has drifted to 1% frequency. In this example, allele b has already arisen as a mutation of allele B on a chromosome with allele a, sometime during the N generations. After an additional M generations, b reaches 1% frequency. The frequency of allele a must be greater than the frequency of allele b, since allele a can be found with both alleles B and b, but allele b is only found with allele a (because it was created on a chromosome with allele a, and is so close to a that it has not been separated by recombination). (b) Each unique DNA sequence is represented by an oval, with branches in the SNP phylogeny represented by arrows. Before N generations have passed, the AB allele is the only unique high‐frequency variant. After N generations, allele a reaches 1% frequency, represented as the aB allele (with the mutation labelled Aa on the branch). After M additional generations, the ab allele reaches 1% frequency as a phylogenetic ‘child’ of the aB allele. To help illustrate how phylogenies are represented, we also show an alternate tree that does not correspond to the genealogy shown in (a). This is the tree that would have resulted if allele b had arisen by mutation on an AB chromosome, instead of an aB chromosome.

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Further Reading

Felsenstein J (2004) Inferring Phylogenies. New York: Sinauer, Inc.

Kimura M (1983) The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.

Reich DE and Lander ES (2001) On the allelic spectrum of human disease. Trends in Genetics 17: 502–510.

Rosenberg NA and Nordborg M (2002) Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nature Reviews. Genetics 3: 380–390.

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Thomas, Paul D(Jul 2008) Single Nucleotide Polymorphisms in Human Disease and Evolution: Phylogenies and Genealogies. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020763]