Linkageiga

Linkageiga is a term used in theoretical discussions of population genetics to describe a proposed framework for the joint analysis of genetic linkage information and the inferred ages of genetic variants. The name combines linkage analysis, which tracks the co-segregation of markers within families, with age inference methods that attempt to date alleles and lineages. The concept is not an established methodology but a model used to illustrate how combining recombination-based maps with allele-age estimates might improve historical reconstructions of genomes.

Definition and scope: Linkageiga envisions models that simultaneously estimate locus order and allele ages from dense genotype data, using coalescent-inspired priors and recombination rate information. The approach aims to resolve questions about when and where recombination events shaped haplotype blocks, and how demographic events affected allele ages.

Methodology and data: It would require high-density genotype or sequencing data, accurate recombination maps, and robust statistical inference, typically Bayesian or maximum likelihood frameworks. Computation would be intensive due to the joint estimation of many parameters and the need to integrate over complex recombination histories.

Applications and challenges: Potential applications include inference of population split times, detection of selection on variants, and improved haplotype-based disease mapping. Limitations include sensitivity to model assumptions, data quality, and confounding factors such as gene conversion, phasing errors, and selection.

Status: As a formal method, linkageiga remains speculative and not widely implemented; it is mainly discussed in theoretical contexts or as a target for future methodological development. See also genetic linkage analysis, coalescent theory, and haplotype-based age estimation.