How does population growth affect linkage disequilibrium?
When a population expands in size, the LD curve grows steeper, and this effect is especially pronounced following a bottleneck in population size. When a population shrinks, the LD curve rises but remains relatively flat. As LD converges toward a new equilibrium, its time path may not be monotonic.
What causes linkage disequilibrium within a population?
If selection favors individuals with particular combinations of alleles, then it produces linkage disequilibrium. Random processes can cause persistent linkage disequilibrium. If random sampling produces by chance an excess of a haplotype in a generation, linkage disequilibrium will have arisen.
What depends on linkage disequilibrium?
In population genetics, linkage disequilibrium (LD) is the non-random association of alleles at different loci in a given population. As a result, the pattern of linkage disequilibrium in a genome is a powerful signal of the population genetic processes that are structuring it.
What is admixture in population genetics?
Genetic admixture occurs when individuals from two or more genetically distinguishable groups have children together. This might happen when individuals from one part of the world settle into a new geographic region already inhabited by other people, e.g. due to invasions or large-scale migrations.
What does linkage disequilibrium tell us?
Linkage disequilibrium — the nonrandom association of alleles at different loci — is a sensitive indicator of the population genetic forces that structure a genome.
What does linkage disequilibrium refer to?
Linkage disequilibrium (LD) is the correlation between nearby variants such that the alleles at neighboring polymorphisms (observed on the same chromosome) are associated within a population more often than if they were unlinked.
How do you identify linkage disequilibrium?
Positive linkage disequilibrium exists when two alleles occur together on the same haplotype more often than expected, and negative LD exists when alleles occur together on the same haplotype less often than expected (Barnes, 2007). LD is a property of two loci, not their alleles.
What is admixture population?
Admixed populations are populations that possess ancestry from multiple source groups. They result from the fusion of populations that have long been separated, in processes such as long-distance migration and hybrid-zone formation at population boundaries.
What is population substructure?
Most discussions of the genetics of populations starts with the simplest description of a population as a very large, single collection of randomly mating individuals. The collection of genetically differentiated subpopulations is referred to as population substructure.
How is LD based inference used to investigate admixture?
An emerging new approach harnesses the exponential decay of admixture-induced linkage disequilibrium (LD) as a function of genetic distance. Here, we comprehensively develop LD-based inference into a versatile tool for investigating admixture.
Why is admixture an important force shaping genetic diversity?
Abstract (excerpt): Long-range migrations and the resulting admixture between populations have been an important force shaping human genetic diversity. Most existing methods for detecting and reconstructing historical admixture events are based on allele frequency divergences or patterns of ancestry segments in chromosomes of admixed individuals.
Which is admixture analysis uses weighted LD decay curves?
Admixture analysis using weighted LD decay curves was first proposed by Moorjani et al. (PLoS Genetics, 2011), whose ROLLOFF software package, described more fully in Patterson et al. (Genetics, 2012) , infers admixture dates from weighted LD curves. ALDER extends the general methodology of ROLLOFF, the most notable advances being: