Changes from version 1.002
The taxonomy was revisited. For extant species the taxonomy was updated to match the most recent IUCN taxonomy. For extinct species the taxonomy was updated based on various sources (listed under each species). 
The phylogeny for a number of families totaling 1903 species were reanalyzed occasionally including information published since the original phylogeny was published.
For a number of families totaling 1443 species we let the relative ages be based directly on sequence data rather than just simulated data as before. 
We initially used the simulation approach (described in the paper) because it enabled us to be more flexible in the topological modifications of the tree. 
The simulation procedure enabled us to place un-sampled species without any constraints on the internal topology of species with data. 
For these 1443 species complex modifications was however not needed either because all species had data or the desired topological placement of the missing species could be proposed without influencing the placement of missing species. 
This is for instance the case if the missing species is supposed to be the combined sister to two species which are monophyletic with a posterior probability of 1.000, 
but not if the support for the monophyly of the two species in question is only partially supported (where we discuss how our placement of the missing species does not influence the placemnt of the two species with data in the paper). 
Due to increased data the number of species in the small tree has been increased to 4230. 

Changes from version 1.001

Different treatment of the five families of new world monkeys relative to original version.
All five have a posterior probability og 1.000 in our trees and we therefore chose to use external dating for their relationships,like we did for all other families,
 even though we did not enforce family monophyly for them. All dates for them were taken from Perelman et al 2011
Perelman P et al (2011) A molecular phylogeny of living primates. PLoS Genetics 7 e1001342.

Changes from version 1.000

Minor error causing an incomplete sampling of the posterior distribution in some clades fixed.

Some minor inconsistencies in the choice of species for the smaller tree changed so the new tree contain 4160 species instead of 4125

Topology within Camelidae modified based on the new study 
"Heintzman et al Genomic data from extinct North American Camelops revise camel evolutionary history
MBE Advance Access published June 2, 2015

Placement of Notoungulata and Lipoterma changed based on the new study 
http://www.nature.com/nature/journal/v522/n7554/abs/nature14249.html