A Short History of Phylogenetic Trees

Who's related to whom and how? If you've ever sat around with your family and tried to figure out who's a second cousin once removed and who's a first cousin twice removed, you've dabbled a bit in the mechanics of phylogenetic trees. According to Dr. David Baum at the University of Wisconsin, Madison, a phylogenetic tree is a diagram that depicts the lines of evolutionary descent of different species, organisms, or genes from a common ancestor. In essence, a phylogenetic tree organizes the natural world into familial and evolutionary relationships. 

Charles Darwin is credited with the first phylogenetic trees based on an understanding of evolution. Scientists prior to him constructed trees according to their observations of the anatomical traits of species. Without understanding evolution and the concept of a common ancestor, however, their trees were flawed. Darwin drew many trees in his notebooks, including the one shown on the right. His trees are quick sketches, often scribbled over, that helped him organize his thoughts on evolution (American Museum of Natural History) The root of a phylogenetic tree represents the oldest or ancestral lineage and the branches represent the youngest. Branching indicates speciation, that is, the splitting of an ancestral lineage into multiple descendant lineages. Tracing two branches back to the node that joins them identifies the evolutionary point in time when the two had a common ancestor. A phylogenetic tree can represent only a few species, proteins, or other characteristics, or it can represent all of the natural world, in which case it is referred to as a 'tree of life.'

 

 

 

 

Throughout most of the 20th century, morphology and metabolic characteristics (chemotaxonomy) continued to drive phylogenetic tree construction. In the latter part of the century, however, more precise molecular techniques based on DNA differences between species were used to completely redraw the tree of life. Carl Woese is credited with the now standard method of comparing species based on the DNA sequence of their small subunit ribosomal RNA (SSU rRNA). Since all life forms must synthesize proteins, all have ribosomes and all have SSU rRNA.  These analyses have revealed three major branches of the tree of life: bacteria, archaea and eukarya. Prior to Woese's molecular taxonomy work, the archaea were considered part of the bacterial kingdom. Sequence analysis revealed, however, that archaea are different enough from bacteria that they correctly belong in a separate kingdom despite their morphological similarity to bacteria.

In 2016, Jillian Banfield's group at UC Berkeley published the most inclusive phylogenetic tree to date (A new view of the tree of life, Nature Microbiology 1:16048). In addition to using over 30,000 publicly available sequenced genomes, her tree incorporates data from over 1000 new genomes reconstructed by her group. Many of her prokaryotic DNA data were acquired from unusual sources, i.e., a shallow aquifer system, a deep subsurface research site in Japan, a salt crust in the Atacama Desert of Chile, grassland meadow soil in northern California, a CO₂-rich geyser system, and two dolphin mouths. Her tree is illustrated as a starburst diagram. As it is not known which lineage is oldest, a starburst evolutionary tree has no root. Furthermore, the length of the branches corresponds to the amount of evolutionary change in that lineage based on the amount of difference in DNA sequences. For more information on the different shapes of phylogenetic trees, visit the Field Guide to Evolutionary Trees. The Understanding Evolution website maintained by the University of California Museum of Paleontology is a rich source of information on evolution and phylogenetic trees.

I came across Banfield's new tree of life when I decided to add a phylogenetic tree design to my collections. I was instantly smitten with the shape and the colors. To me, it resembles a tropical bird in flight. If you look at the tail feathers of the bird, the long green feathers on the right side of the tail in the Banfield diagram represent the eukarya (you, your cat, your house plant, the fungus growing on your bread). All of the rest of the tree represents bacterial and archaeal species. I have recreated the shape of Jillian Banfield's tree as a pendant design: Phylogenetic Tree Pendant. I think it is currently the most accurate phylogenetic tree jewelry available.