Linkage Disequilibrium in Natural Populations

Linkage disequilibrium (LD) describes the non-random association of alleles at different genetic loci within natural populations. It arises through the interplay of forces such as recombination, genetic drift, mutation and selection, and is shaped by population history, mating system and demographic events. Patterns of LD vary across taxa and genomic regions, reflecting life-history traits and ecological pressures. In large, outcrossing populations recombination tends to erode LD rapidly over short distances, while small or structured populations often retain extended haplotypes. Measuring LD is central to mapping adaptive variants, reconstructing demographic history and designing conservation strategies. Empirical surveys across humans, wildlife and plant populations have revealed both conserved and unique LD landscapes, highlighting how selection for local adaptation or admixture can produce unexpected blocks of association. The global significance of LD extends from tracing ancient migrations in human populations to guiding marker choices in breeding programmes and identifying regions under selection in threatened species.

Research from Nature Portfolio

Recent simulation work has assessed the ability of multi-locus statistics to detect divergent epistatic selection in subdivided populations. By applying D’IS2 and FST metrics, researchers showed that additive-by-additive interactions generate pronounced departures from neutrality in diverged subpopulations, while other forms of epistasis are more challenging to distinguish. The study highlights both the promise and limitations of genome-wide scans in identifying pairs of loci under epistatic selection and underscores the need for careful threshold setting and frequency filtering when interpreting signal peaks.

Linkage Disequilibrium in Natural Populations publication trend

The graph below shows the total number of articles in linkage disequilibrium in natural populations across all publications each year (not limited to Nature Index journals).

Technical terms

Linkage disequilibrium: non-random association of alleles at different loci in a population.

Haplotype: combination of alleles at adjacent loci that are inherited together as a block.

Recombination: process by which genetic material is reshuffled during meiosis, breaking down associations among loci over generations.

Epistasis: interaction between genes in which the effect of one locus depends on the genotype at another locus.

r2 statistic: squared correlation coefficient measuring the strength of linkage disequilibrium between two loci.

References

1. Screening for epistatic selection signatures: A simulation study. Scientific Reports (2019).
2. Negative linkage disequilibrium between amino acid changing variants reveals interference among deleterious mutations in the human genome. PLOS Genetics (2021).
3. On the Distribution of Tract Lengths During Adaptive Introgression. G3: Genes, Genomes, Genetics (2020).
4. Exact Distribution of Linkage Disequilibrium in the Presence of Mutation, Selection, or Minor Allele Frequency Filtering. Frontiers in Genetics (2020).