Identity by Descent: Variation in Meiosis, Across Genomes, and in Populations

Abstract

Gene identity by descent (IBD) is a fundamental concept that underlies genetically mediated similarities among relatives. Gene IBD is traced through ancestral meioses and is defined relative to founders of a pedigree, or to some time point or mutational origin in the coalescent of a set of extant genes in a population. The random process underlying changes in the patterns of IBD across the genome is recombination, so the natural context for defining IBD is the ancestral recombination graph (ARG), which specifies the complete ancestry of a collection of chromosomes. The ARG determines both the sequence of coalescent ancestries across the chromosome and the extant segments of DNA descending unbroken by recombination from their most recent common ancestor (MRCA). DNA segments IBD from a recent common ancestor have high probability of being of the same allelic type. Non-IBD DNA is modeled as of independent allelic type, but the population frame of reference for defining allelic independence can vary. Whether of IBD, allelic similarity, or phenotypic covariance, comparisons may be made to other genomic regions of the same gametes, or to the same genomic regions in other sets of gametes or diploid individuals. In this review, I present IBD as the framework connecting evolutionary and coalescent theory with the analysis of genetic data observed on individuals. I focus on the high variance of the processes that determine IBD, its changes across the genome, and its impact on observable data.The descent and ancestry of DNA At a given location in the genome, the descent of DNA as described by Mendel's first law (Mendel 1866) provides the framework for analyses of the genetic consequences of coancestry among individuals. This fundamental law of inheritance is phrased in probabilistic terms. In a diploid individual, at each location in the genome, a random one of the two homologous copies of the DNA at that location is the DNA copied to the offspring gamete. Additionally, all meioses are independent; the random choice is made independently for each offspring, independently in the two parents of an individual, and independently from generation to generation in an ancestral lineage.DNA in different current gametes that is a copy of a single piece of DNA in some ancestral individual is said to be identical by descent or IBD from that ancestor. There is no absolute measure of IBD; IBD is always relative to some ancestral reference population. Many experimental or agricultural populations have a natural founding stock, as do some natural populations, and IBD may be measured relative to this founder population. More generally, IBD may be measured relative to the population at some past time point, with the implication that more remote coancestry of current gametes is ignored. In pedigrees, IBD is well defined relative to the specified founders of the pedigree. The fact of IBD does not depend on whether pedigree relationships are known. Specification of a pedigree relationship merely imposes a specific prior distribution o...

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