The Applications of the Tree of Life

“As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever-branching and beautiful ramifications.”

Charles Darwin, 1872

The Tree of Life.

It is a term that naturalist Charles Darwin used in his book The Origin of Species, which served as a metaphor for how the world’s species are evolutionary related. In the Tree of Life, each branch connects organisms to a common ancestor.

What started as a metaphor introduced in the 19^th century, is now an inspiration to many of today’s biologists.

One of them is David Hillis, Professor in Natural Sciences at the University of Texas. He visited Ohio University’s lecture last Thursday to speak about the application of phylogenetics, which is the study of evolutionary relationships among species, and therefore is based on the Tree of Life.

Hillis started his lecture using Darwin’s almost poetic quotation about the Tree of Life, mentioning: “when was the last time you read a scientific paper that has something as beautiful as this written in it?”

For most of the twentieth century, phylogenetics had very little impact on evolutionary thinking. However, since 1990, there has been an enormous growth in applications of phylogenetics in scientific papers.

According to Scott Moody, professor in phylogenetics and systematics at Ohio University, there have been three major reasons for this. First, the invention of very fast computers in order to analyze the data and calculate phylogenetic hypotheses. Second, the discovery of an thermostable enzyme in a bacterial species (Thermus aquaticus) which is capable of repeated copying of DNA in the laboratory. And third, the development of laboratory devices, which can sequence genomes quickly and inexpensively.

“When I began doing phylogenetic analyses in the early 1970’s,” Moody said, “I would crunch the data by hand calculation of the algorithms and by the mid 1970’s I would batch punch cards through huge IBM computers. Sometimes it would take hours to retrieve phylogenetic trees.  Today, high speed computers, even a laptop with sufficient computational power, can generate thousands of trees very quickly.”

According to Joseph Bielwaski, Professor in Biology at Dalhousie University in Halifax, Canada, there is a practical value of phylogenetics in almost every branch of biology. In what practical cases, then, can phylogenetics be applied?

“Perhaps the most traditional application of phylogenetics is classification and systematics”, Bielwaski wrote in his article Applications of Phylogenetics. “Biological classifications are systems that organize the diversity of life, and systematics is the study of that diversity relative to some kind of specified relationship.” The ultimate goal of phylogenetic systematics is to create the ultimate “Tree of Life,” a database of all life on earth, accessible to everybody, or at least to all scientists.

In his lecture, Hillis used the example of the tricorder, a device used in the fictional Star Trek universe for scouting unfamiliar lands and making detailed examination of living things. “Wouldn’t it be great to have such a tricorder in real life?”, Hillis mentioned, “and to be able to examine every plant or animal, to look up the descendence of any species you find?”

Creating a database of all life on earth is, according to Professor Moody, a laudable goal. “But I am afraid that I will have to be pessimistic about this”, he said. “Even though the molecular methodology has been incredibly cheaper, just do the math to realize that it will still cost a lot of money and the US and European countries are financially broken. Trillions of dollars are spent on unwise military adventures without flinching, but for the hundreds of millions to be spent on something that benefits everybody, not.”

Hillis also mentioned that today, the world is in the midst of a significant extinction, because of human environmental degradation and disturbance and habitat destruction. “A huge number of species will be completely lost before they can even be scientifically “discovered” and entered into the database,” Hillis said.

Another application of phylogenetics is comparative biology, where biologists try to discover evolutionary patterns and to understand the causes of those patterns. Then there is the application of Biogeography, the study of the distribution of biological diversity in time and space.

“With recent advances in DNA sequencing technology,” Bielwaski wrote, “phylogenetic analysis of genes has developed into an important tool for tracking the evolution and spread of diseases.”

According to Professor Moody, you can create many viruses in the laboratory by changing the genome and therefore the proteins. Consequently, you can study the impact of a predicted hypothetical virus that may very well arise in the future.

As an example, Science published a paper this past week describing how researchers were able to find a variant protein working in the immune system of 1 of every 300 HIV-positive patients that recognizes HIV infections and prevents viral replication that would overwhelm the immune system. Part of the procedure of discovery involved phylogenetic analyses.

One of Professor Moody’s teaching areas is Forensic Science. “There are tens of thousands of cold and unsolved cases even with DNA evidence from the victims and/or crime scenes,” Moody said. “This past summer the “Grim Sleeper” was finally arrested after a 20 year period of at least 10 rapes and murders of women in Los Angeles. Although they had a DNA profile since the suspect was not in the DNA registry, the crime labs could not identify him until they found a close match with another older man who turned out to be his father.” Phylogenetic analysis is the same as genealogical analysis of individuals and useful not only for solving violent crimes but also for paternity cases.

During Hillis’ lecture, also visited by Professor Moody, Moody thought several times of the “sad irony” that 47 to 60% of adult US citizens reject evolution as the cause of diversity of all living organisms and viruses.

“They reject evolution as the organizing principle of biology in that knowing the evolutionary relationships of organisms allows us to make predictions of the various physiological, biochemical, heritance and other functional mechanisms and adaptations,” Moody said. “Science is exponentially jumping forward by leaps and bounds, the public is reaping lots of benefits from this research using phylogenetics, and at the same time is rejecting the methodology and principles in favor of fairy tales.”

Moody mentioned that many of the “tea party” Republicans are evolution deniers and have stated on record that they will cut research funding to the National Science Foundation (NSF) and the National Institutes of Health (NIH). “ It doesn’t require much imagination as to which disciplines will be targeted for reduction in funds,” Moody said.

Moody finds it striking that there is such low acceptance of the Tree of Life, which he calls the unifying principle of all biology.

“This is why it is so important to have the annual Darwin lectures like Hillis’ at Ohio University,” Moody said.

---