Identity by descent

Allele copies are identical by descent if they derive from the same specified ancestral copy. Identical observed states need not imply this ancestry. Two diploid individuals are 2-IBD when both of their allele copies can be paired as identical by descent; autozygous individuals carrying two copies of the same ancestral copy are mutually 2-IBD when that ancestor is shared.

For full siblings in an outbred pedigree, condition on both being affected under multiplicative diallelic penetrance and on residual disease outcomes being independent given their genotypes. The usual Mendelian IBD sharing of full siblings probabilities $(1/4,1/2,1/4)$ are weighted by $p^2{\alpha }^4,p^2{\alpha }^2\beta ,p^2{\beta }^2$, respectively, giving the displayed conditional sharing probabilities. Since $\beta -{\alpha }^2=\varphi (1-\varphi )(\theta -1{)}^2\ge 0$, $z_1\le 1/2$, strictly for a polymorphic locus with a nontrivial effect.

For two individuals carrying labelled copies $(a,b)$ and $(c,d)$, condensed identity coefficients give the probabilities of nine identity by descent patterns, identifying states that differ only by exchanging the two homologues within either individual. They retain within-individual autozygosity, which three ordinary outbred sharing coefficients omit. One convention isEach block consists of copies identical by descent, and different blocks have distinct ancestral origins. For siblings whose parents are otherwise outbred first cousins, these coefficients are $(1,0,2,1,2,1,15,30,12)/64$. This follows by conditioning on whether the parents share one ancestral copy and enumerating the four independent Mendelian segregation choices to their two children. The kinship coefficient is ${\Delta }_1+({\Delta }_3+{\Delta }_5+{\Delta }_7)/2+{\Delta }_8/4$, here $9/32$. Weir's discussion of identity states uses this convention.

Let $J$ be the largest number of chromosome copies that can be paired across the two full siblings as identical by descent, counting repeated copies when a child is autozygous. For offspring of otherwise outbred first cousins, with probability $3/4$ the parental copies have no common ancestral origin, giving ordinary sibling sharing $(1/4,1/2,1/4)$. With probability $1/4$, write the parental copies as $(A,B)$ and $(A,C)$ with three distinct origins. Each child independently has one of $AA,AB,AC,BC$, equally likely. Among sixteen ordered child pairs, two share no copy, ten share one, and four share two. The mixture gives the displayed probabilities. These three numbers do not determine all Jacquard identity coefficients; the formula $\varphi =\mathbb{E}[J]/4$ is restricted to noninbred individuals and fails here.

For first cousins in an otherwise outbred pedigree, compare the copies transmitted from their related parents, who are full siblings. These transmissions trace to the same shared grandparent with probability $1/2$ and then to the same homologous copy of that grandparent with probability $1/2$, giving $k_1=1/4$. The unrelated parental contributions cannot match, so two shared copies have probability zero. Selecting one random copy from each cousin chooses those two potentially shared copies with probability $1/4$, giving kinship coefficient $k_1/4=1/16$.

An identical-by-descent segment is a chromosomal tract inherited from the same ancestral chromosome without an intervening breakpoint in the tracked ancestry. With a specified total number $m$ of independent meioses and a uniform recombination map, the probability that a fixed tract of genetic length $d$ survives without genetic recombination is approximately $e^{-md}$. Recent common ancestry therefore tends to give longer shared tracts. Lengths of tracts selected by covering a random point are length-biased relative to tracts sampled by their boundaries.

The kinship coefficient ${\varphi }_{XY}$ is the probability that one randomly selected allele copy from each of $X,Y$ is identical by descent. For a noninbred individual, ${\varphi }_{XX}=1/2$, and more generally ${\varphi }_{XX}=(1+F_X)/2$. For distinct individuals with parents $M_X,P_X$, Mendelian segregation gives ${\varphi }_{XY}=[{\varphi }_{M_{X}Y}+{\varphi }_{P_{X}Y}]/2$. The offspring's inbreeding coefficient equals the parents' kinship coefficient.

// Target: biology.bigb

For $N$ individuals in monogamous families of exactly two offspring, let ${\Phi }_G$ be mean pairwise kinship coefficient, $F_G$ mean inbreeding and ${\Phi }_{m,G}$ mean kinship of mates. A random distinct offspring pair are siblings with probability $1/(N-1)$. Accounting separately for within-family and cross-family pairs gives the displayed recurrence, while $F_{G+1}={\Phi }_{m,G}$. Random mating makes ${\Phi }_{m,G}={\Phi }_G$. Sibling avoidance changes the mating-pair mean; it does not create unrelated founders or stop eventual drift to ancestral identity in a closed finite population.

For otherwise outbred opposite-sex first cousins, the probability that the mother's randomly transmitted X copy matches the father's X by descent depends on which of their parents are siblings. It is zero when the male cousin is related through his father, $1/8$ when the female cousin is related through her father and the male through his mother, and $3/16$ when their mothers are sisters. Daughters can be X-autozygous; sons have one X and a Y and are not homozygous for a paired X chromosome. Recombination and pseudoautosomal regions require a locus-based formulation instead of whole-chromosome blocks.

In an outbred pedigree, the two full siblings receive the same paternal copy with probability $1/2$, and independently the same maternal copy with probability $1/2$. Thus the number $J$ of shared copies has a binomial distribution with probabilities $(1/4,1/2,1/4)$, and $E[J/2]=1/2$.

// Target: biology.bigb

Autozygosity is homozygosity by descent: the maternal and paternal copies in one individual derive from the same ancestral copy. Unlike ordinary homozygosity, it concerns the ancestry of chromosome copies rather than only their observed states. In a pedigree with one ancestral disease-allele copy and fully penetrant recessive inheritance, every affected individual is autozygous for that copy.

Two allele copies are identical by state when their observed states agree, regardless of whether they derive from one recent ancestral copy. Equal marker haplotypes can therefore reflect either identity by descent or matching founder haplotypes.