Chapter 16, Problem 16P

Consider the phylogenetic tree below with three related species (A, B, C) that share a common ancestor (last common ancestor, or LCA). The lineage leading to species A diverges before the divergence of species B and C.

For gene X, no gene duplications have occurred in any lineage, and each gene X is derived from the ancestral gene X via speciation events. Are genes AX, BX, and CX orthologous, paralogous, or homologous?

For gene Y, a gene duplication occurred in the lineage leading to A after it diverged from that leading to B and C. Are genes $\text{AY1}$ and $\text{AY2}$ orthologous or paralogous? Are genes $\text{AY1}$ and BY orthologous or paralogous? Are genes BY and CY orthologous or paralogous?

For gene Z, gene duplications have occurred in all species. Define orthology and paralogy relationships for the different Z genes.