Table 1.

Comparison of the Four Alternative Orthology Inference Methods Used in This Study.

High-Quality Outgroups	Genome Duplications	Examples	MI	RT	MO	1to1
Present	Absent	HYM, MIL	Good	Good	Good if only interested in low-copy genes	OK with a small number of taxa
Absent	Absent	Deep metazoan phylogeny; GRP	Good	Bad	Bad	OK with a small number of taxa
Present	Present	Many plant groups	Bad	Good	Good if only interested in low-copy genes	OK with a small number of taxa
Absent	Present	Many plant groups	Bad	Bad	Bad	May be the only choice