TABLE 1.

A glossary of key terms

Term	Definition
Ancestral recombination graph (ARG)	A graphical representation of the complete ancestry of a sample of genomes through a series of coalescence and recombination events. The ARG can be decomposed into a series of marginal trees that give the relationships between samples within each nonrecombining region
Branch	A part of a genealogical tree at a single locus, which connects two coalescence events
Coalescence	The merging of lineages in a common ancestor, as one traces lineages backward in time
Edge	A set of genomic regions that are the immediate ancestors of a specific coalescence event, and that are ancestral to a specific set of sampled genomes. An edge has two dimensions (generations × map length). Any SNP that falls on an edge will be shared by the set of descendant genomes, and only by those genomes
Haplotype	A haploid genotype. A diploid genotype consists of a pair of haplotypes
Haplotype block	The set of genomic regions that descend from a particular edge in the ARG, which is defined by a unique coalescence event, and by the set of descendant samples
Identity by descent (IBD)	Segments of the genome are identical by descent if they descend from the same common ancestor
Lineage	A chain of genes that descends from parent to offspring, or (tracing backwards) from offspring to parent
Linkage disequilibrium (LD)	Nonrandom association of alleles at different loci
Phasing	The process of assigning alleles to the maternal and paternal chromosomes in a diploid individual
Time to most recent common ancestor (TMRCA)	The time of the most recent coalescence event from which a focal set of samples descends