How are phylogenetic methods used to resurrect protein sequences from extinct organisms?

Most genes and proteins of organisms that lived millions of years ago have decomposed in the fossil remains of these species. Nonetheless, the sequences of many ancient genes and proteins can be reconstructed by the methods described in this chapter. As we saw in Investigating Life: Testing the Accuracy of Phylogenetic Analysis, we can reconstruct ancestral DNA sequences—if we have enough information about the genomes of their descendants. Biologists have reconstructed gene sequences from species that have been extinct for millions of years. Using this information, a laboratory can reconstruct real proteins that correspond to those gene sequences. This is how Mikhail Matz and his colleagues were able to resurrect fluorescent proteins from the extinct ancestors of modern corals, then visualize the colors produced by these proteins in the laboratory (Figure 21.15).

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Future directions

Biologists are now using phylogenetic analysis to reconstruct many ancient protein sequences. These reconstructed protein sequences are then made into actual proteins in the laboratory. For example, when biologists measured the temperature optima for resurrected proteins that were present in the common ancestor of all life, they found that the proteins functioned best in the range of 55°C–65°C. This result is consistent with hypotheses that life evolved in a high-temperature environment.

To reconstruct protein sequences from species that have been extinct for millions or even billions of years, biologists use detailed mathematical models that take into account much of what we have learned about molecular evolution, as described in Key Concept 21.2. These models incorporate information on rates of replacement among different amino acids in proteins, information on different substitution rates among nucleotides, and changes in the rate of molecular evolution among the major lineages of life. These studies are opening up opportunities to see how proteins have evolved through time and how extinct species once functioned.