Table 3. Fitting parameters in the duplication-divergence model for all organisms.

Species
			prNOG	roNOG	maNOG	veNOG	inNOG	meNOG	fuNOG	KOG/euNOG	COG/NOG
eco	0.7	0.0008									0.007
sce	0.7	0.0002							0.0008	0.0007	0.001
ath	0.7	0.0001								0.003	0.008
cel	0.5	0.0004						0.002		0.001	0.005
dme	0.5	0.0004					0.003	0.004		0.004	0.004
mmu	0.7	0.0002		0.001	0.001	0.001		0.001		0.001	0.003
hsa	0.7	0.0002	0.0002		0.0004	0.0005		0.0005		0.0003	0.0004

and are time-independent and describe the probability that an interaction is retained after a duplication and the probability that an interaction is created de novo, respectively. The fraction of interacting pairs in the ancestral network at time is represented by . There are in total nine ancestral time levels for the organisms investigated: the ancestral primates (prNOG), the ancestral rodents (roNOG), the ancestral mammals (maNOG), the ancestral vertebrates (veNOG), the ancestral insects (inNOG), the ancestral animals (meNOG), the ancestral fungi (fuNOG), the ancestral eukaryotes (KOG/euNOG), and the LUCA (COG/NOG). Existing time levels are specific for every species depending on its lineage.