This study  is inspired from a quote by Max Delbruck: ”Any living cell carries with it the experience of a billion years of experimentation by its ancestors”. In this direction, it is possible to find evidence in the genomes of living organisms for ancient environmental changes with large biological impacts. For instance, the oxygen that most organisms currently use would have been extremely toxic to almost all life on earth before the accumulation of oxygen via oxygenic photosynthesis. It is known that this event happened approximately 2.4 billion years ago and it caused a dramatic transformation of life on earth.
A dynamic programming algorithm was developed in order to infer gene birth, duplication, loss and horizontal gene transfer events given the phylogeny of species and phylogeny of different genes. Horizontal gene transfer is the event in which bacteria transfer a portion of their genome to other bacteria from different taxonomic groups.
Figure 6.1 shows an overview of these inferred events in a phylogenetic tree focusing on prokaryote life. In each node, the size of the pie chart represents the amount of genetic change between two branches and each colored slice stands for the rate of a particular genetic modification event. Starting from the root of the tree, we see that almost the entire pie chart is represented by newly born genes represented by red. However, around 2.5 billion years ago green and blue slices become more prevalent, which represent rate of horizontal gene transfer and gene duplication events.
In Figure 6.2, a large spike can be seen during Archean eon representing large amount of genetic change on earth occurring during this particular time period. This study looked for enzymatic activity of genes that were born in this eon different from the genes that were already present. On the right hand side of Figure 6.2, logarithmic enrichment levels of different metabolites are displayed. Most enriched metabolites produced by these genes were discovered to be functional in oxidation reduction and electron transport. Overall, this study suggests that life invented modern electron transport chain around 3.3 billion years ago and around 2.8 billion years ago organisms evolved to use the same proteins that are used for producing oxygen also to breathe oxygen.