Population and quantitative genetics theory is built with parameters that describe relatedness, and estimation of these parameters from genetic markers enables progress in fields as disparate as plant breeding, human disease gene mapping and forensic science.
Relatedness can be described by the probabilities that two individuals share zero, one or two pairs of alleles that are identical-by-descent. More probabilities are needed if the individuals are inbred, meaning that their parents were related.
Alternative hypotheses about the relationship between two individuals can be evaluated by dividing the probability of the observed genotypes of the individuals under one hypothesis by the probability of the genotypes under the other. The ratio of probabilities is called the likelihood ratio. In paternity testing, it is called the paternity index.
The probabilities of patterns of identity-by-descent can be estimated by the method of maximum likelihood.
Even for individuals whose parents are not related, and who are therefore not inbred, account needs to be taken of 'background relatedness' that is due to evolutionary history in a population.
Even though the probabilities of identity-by-descent are defined by the family and population relatedness of two individuals, there is variation in actual identity-by-descent along the genome. This reflects the differences in actual genealogies at different loci, and it is influenced by recombination along with mutation and natural selection.
Relationship is best estimated by highly polymorphic markers, to minimize the ambiguity between identity-in-state and identity-by-descent. However, reliable estimates can be obtained with a sufficiently large number of biallelic SNPs.
Individuals who belong to the same family or the same population are related because of their shared ancestry. Population and quantitative genetics theory is built with parameters that describe relatedness, and the estimation of these parameters from genetic markers enables progress in fields as disparate as plant breeding, human disease gene mapping and forensic science. The large number of multiallelic microsatellite loci and biallelic SNPs that are now available have markedly increased the precision with which relationships can be estimated, although they have also revealed unexpected levels of genomic heterogeneity of relationship measures.
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This work was supported in part by grants from the National Institutes of Health, the National Institute of Justice and the National Science Foundation. We are grateful to W.G. Hill and the reviewers for helpful comments.
The authors declare no competing financial interests.
- Additive variance
The portion of the variance of a quantitative trait that is due to the single effects of alleles at the loci that influence the trait.
- Dominance variance
The portion of the variance of a quantitative trait that is due to the interaction of the two alleles that an individual carries at the loci that influence the trait.
- Affected-relative linkage studies
Studies that aim to estimate the degree of linkage between a disease and a marker locus on the basis of the marker genotypes of relatives who have the disease.
Also known as a short tandem repeat. A class of repetitive DNA that is made up of repeats that are 2–5 nucleotides in length. The number of these repeats is usually extremely variable in a population.
- Linkage disequilibrium
The non-random association of alleles at different loci, whether or not the loci are linked.
A region of DNA in which repeat units of 10–50 bp are tandemly arranged in arrays that are 0.5–30 kb in length.
- Association study
A study that aims to identify the joint occurrence of two genetically encoded characteristics in a population. Often, an association between a genetic marker and a phenotype (for example, a disease) is assessed.
- Inbreeding coefficient
The probability that an individual carries two identical-by-descent alleles at a locus.
- Coancestry coefficient
The probability that two alleles at a locus, one taken at random from two individuals, are identical-by-descent. It is also called the coefficient of parentage or coefficient of consanguinity.
- Unordered genotypes
The probability of unordered genotypes does not require specifying which genotype belongs to which individual (for example, which is for the parent and which is for the child). By contrast, the probability of ordered genotypes requires this information.
- Likelihood ratio
The ratio of two probabilities for the same observations, calculated under alternative hypotheses. In the context of relatedness analysis, the likelihood ratio is formed by dividing the probability of the observed pair of genotypes using the identical-by-descent probabilities for one possible relationship by the probability of the genotypes using identical-by-descent probabilities for the other possible relationship. The likelihood ratio is a continuous variable that can take any non-negative value, and values greater than one support the relationship used for the numerator.
- CODIS forensic set
A set of 13 highly polymorphic and essentially unlinked microsatellite markers that were developed by the US Federal Bureau of Investigations for human identification purposes.
- Bayesian (framework)
An inference framework in which the posterior probability of a parameter depends explicitly on its prior probability, reflecting some previous belief about this parameter.
- Maximum likelihood (method)
The process of estimating parameters by choosing their values to maximize the probability of some observed data.
- Bayes theorem
The means of going from a probability of one event, given another, to the probability of the second event, given the first. It is often used to express the (posterior) probability of a hypothesis, given some data, as being proportional to the probability of the data, given the hypothesis, multiplied by the (prior) probability of the hypothesis.
- Prior probability
The probability of an event or hypothesis before consideration of some data that will alter the probability of that event or hypothesis.
- Posterior probability
The probability of an event or hypothesis after consideration of some data that have altered the probability of that event or hypothesis.
- Population substructure
The existence of groups of individuals within a population that have some degree of reproductive isolation from the rest of the population, and for which the allele frequencies are likely to be different from the population as a whole.
- Kin selection
William D. Hamilton's theory to explain the evolution of the hallmark of social life: altruistic cooperation (carrying out functions that are costly to the individual but that benefit others). By helping a relative, an individual increases its fitness by increasing the number of copies of its genes in the population.
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Weir, B., Anderson, A. & Hepler, A. Genetic relatedness analysis: modern data and new challenges. Nat Rev Genet 7, 771–780 (2006). https://doi.org/10.1038/nrg1960
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