In addition to using phylogenetic methods to infer evolutionary relationships, biologists can use these techniques to reconstruct the morphology, behavior, or nucleotide and amino acid sequences of ancestral species (as was demonstrated for the ancestral sequence of bacteriophage T7 in Investigating Life: Testing the Accuracy of Phylogenetic Analysis). In the opening of this chapter, we described how Mikhail Matz used phylogenetic analysis to reconstruct the sequence of changes in fluorescent proteins of corals to understand how red fluorescent proteins could be produced.
Reconstruction of ancient DNA sequences can also provide information about the biology of long-extinct organisms. For example, phylogenetic analysis was used to reconstruct an opsin protein in the ancestral archosaur (the most recent common ancestor of birds, dinosaurs, and crocodiles). Opsins are pigment proteins involved in vision; different opsins (with different amino acid sequences) are excited by different wavelengths of light. Knowledge of the opsin sequence in the ancestral archosaur would provide clues about the animal’s visual capabilities and therefore about some of its probable behaviors. Investigators used phylogenetic analysis of opsin from living vertebrates to estimate the amino acid sequence of the pigment that existed in the ancestral archosaur. A protein with this same sequence was then constructed in the laboratory. The investigators tested the reconstructed opsin and found a significant shift toward the red end of the spectrum in the light sensitivity of this protein compared with that of most modern opsins. Modern species that exhibit similar sensitivity are adapted for nocturnal vision, so the investigators inferred that the ancestral archosaur might have been active at night. Thus, reminiscent of the movies Jurassic Park and Jurassic World, phylogenetic analyses are being used to reconstruct extinct species, one protein at a time.