hapoprocesses

Hapoprocesses refer to the suite of biological and evolutionary processes that determine the fate of haplotypes—the sets of genetic variants inherited together on a chromosome—across generations. The concept emphasizes how combinations of alleles are created, maintained, or broken apart over time, rather than focusing solely on individual variants.

Key components include mutation, recombination, and gene conversion that generate and reshuffle haplotypic structure; genetic drift and demographic factors that change haplotype frequencies; selection that acts on haplotypes as units; gene flow through migration or admixture that introduces new haplotypes into populations; and the formation of haplotype blocks shaped by linkage disequilibrium and regional recombination landscapes.

Methodologically, hapoprocesses are studied with population-genetic models such as coalescent theory, diffusion approximations, and ancestral recombination graphs. Practical analysis relies on phasing to infer haplotypes from genotype data, haplotype networks, and statistical methods that exploit haplotype information for demographic inference, selection scans, or disease association studies.

Applications include elucidating population history and migrations, improving imputation and association tests by accounting for haplotype structure, and detecting natural selection on haplotype backgrounds. Hapoprocesses help study the genetic architecture of complex traits and understand how recombination and mutation interact with demography to shape genomic diversity.

Limitations include phasing inaccuracies, especially in populations with complex structure; joint modeling of recombination and selection remains computationally intensive; and distinguishing selection signals from demographic history requires careful statistical design.