- Ongoing updates to faulty links and functions.
- Updated basal land-plant [Embryophyta] trees.
- Added new albuliform fish, †Baugeichthys caeruleus Filleul, 2000.
- Added new fossil cichlid genus †Mahengechromis Murray, 2000 and possible phylogenetic treatment of cichlids.
- Added new ophidiiform fish, †Genypterus valdensensis Riva Rossi et al., 2000 and recent species of Genypterus.
- Lungfish-trees updated.
- Added new species of lungfish, †Chirodipterus potteri Kemp, 2000
- A new preferred phylogeny added to tetrapods and pro-amniotes.
- Updated Mosasauroidea [Squamata: Pythonomorpha] after Caldwell, 2000
- Added alternative phylogeny of basal crocodylomorphs after Clark, Sues & Berman, 2000.
- Added †Sunosuchus -species [Crocodyliformes, Goniopholididae]
- Added new ?hesperornithiform bird, †Potamornis skutchi Elzanowski, Paul & Stidham, 2000
- Updated pampatheriids [Mammalia: Xenarthra: Pampatheriidae].
- Added new bat [Mammalia: Microchiroptera], †Karstala silva Czaplewski & Morgan, 2000
- Added new anthracotheriid mammal, †Siamotherium pondaungensis Ducrocq et al., 2000.