  Gene gains and losses have shaped the gene repertoire of species since the
universal last common ancestor to species today. Genes in extant species were
gained at different historical times via de novo creation of new genes,
duplication of existing genes or transfer from genes of another species (HGT),
and get lost gradually. With the increasing number of sequenced genomes, some
comparative analyses have been done to quantify the evolutionary history of
gene gains and losses in restricted lineages like vertebrates, insects, fungi,
plants and so on. Here, we have constructed and analyzed over 10,000 gene
family trees to reconstruct the gene content of ancestral genomes at an
unprecedented scale, covering hundreds of genomes across all domains of life.
This is the most comprehensive genome-wide analysis of all events in gene
evolutionary histories. We find that our results are largely consistent with
earlier, less complete comparative studies on specific lineages such as the
vertebrates, but find significant differences especially in recent evolutionary
histories. We find that the rate of gene gain varies widely among branches of
the species tree, and find that some periods of rapid gene duplication are
associated with great extinctions in geological history.
