Fig. 3.

Allele and paralog constraints. a Genes are sampled at two loci 1 and 2 from two individuals i and ii in a single species A. Within this species, genes at the same locus (across multiple individuals) must be alleles, and genes at different loci (regardless of individual) must be paralogs. b A valid reconciliation must not include a duplication along the path between alleles (left, each color corresponds to one locus, and no colored branch can have a duplication). At the same time, a valid reconciliation must include a duplication along the path between paralogs (right, every colored path must have a duplication on at least one branch of the path). There is no way to simultaneously satisfy these constraints, so this gene tree is not reconcilable