Jacquard identity coefficients (${\Delta }_1,\dots ,{\Delta }_9$)

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.