Fig. 1.

Description of the methods used to build relationship matrices. a Haplotypes of five SNPs for two individuals. b Method DW, ${\mathbf{H}}_{1,2}$. Each haplotype segment has the same length ($\text{j}=2$, $\text{k}/\text{j}=5/2=3$, $\text{k}$ SNPs and window of size $\text{j}$), with the last window potentially using SNPs that may have been used in the penultimate segment. ${\mathbf{\Gamma }}_{\text{i}}$ is the relationship matrix for each window and $\mathbf{\Gamma }$ is the final relationship matrix. c Method SW, ${\mathbf{H}}_{2,2}$. Haplotypes that are two SNPs long are constructed from adjacent pairs of SNPs with SNPs present in more than one segment ($\text{j}=2$, $\text{k}-\text{j}+1=5-2+1=4$). d Method TMS, ${\mathbf{H}}_{3,2}$. The total number of SNPs in contiguous segments that are identical in pairs of haplotypes. The segment size 2 defines the minimum number of SNPs in two contiguous haplotype segments to be considered as identical by descent (IBD)