Pruning the Tree of Life

by | Nov 14, 2018

For as long as humans have noticed that life on Earth is phenomenally diverse, we’ve been trying to group living things into categories. Taxonomy (from the Greek taxis, meaning “arrangement,” and nomos, meaning “law”) is the study of how living things should be formally given scientific names. The modern basis for putting organisms into scientifically named groups is based on our most current knowledge of how organisms are related to one another. This is a way of knowing the natural world and our place in it.

Aristotle wrote the seminal text on the topic, History of Animals, in which he grouped organisms by shared characteristics. If an animal has wings, for example, it must be a bird. He used his own observations to make distinctions, the best tool available at the time. How organisms are similar, how they differ and what that says about their relationship to one another is still at the heart of taxonomy, though now scientists have much better tools at their disposal.

Photo of Fred Spiegel


“Since the late 1990s, we can look at genes organisms have in common to make classifications,” said Fred Spiegel, Distinguished Professor of biology and the director of the Office of Undergraduate Research. “We compare single, universally present genes to establish ideas of relationship. We can also make comparisons among the whole genomes of organisms.”

Put those relationships into graphic form that emphasizes common ancestry – an idea popularized by Charles Darwin ­– and you have a phylogenetic tree, or “tree of life.”

Spiegel is one of about 40 experts worldwide, and one of three affiliated with the University of Arkansas, tasked with periodically updating one such phylogenetic tree. Matthew Brown, now an assistant professor of biology at Mississippi State University, earned his bachelor’s and Ph.D. here; and Laura Shadwick, an instructor in the Department of Biological Sciences who also earned her Ph.D. here, are also contributors.

The collection of scientists works out the phylogenetic tree for eukaryotes. (Relatively painless bit of biology background: All living things can be broadly classified into two categories: eukaryotes and prokaryotes. The former have a complex cellular structure and include plants, animals, most algae, some fungi and protozoa. You are eukaryote. Prokaryotes, with a much simpler cell structure, are everything else, for example bacteria and archaea.)

Genetics brought such a wealth of discoveries to the classification field that scientists needed a new way of doing things. In 2005, the International Society of Protistologists provided it with paper titled The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists. The paper combined traditional research that emphasized an organisms’ structure with genetics, ultimately creating new groups, new relationships among organisms, and a new vocabulary to describe those relationships.

“We came up with a classification that was a big improvement,” said Spiegel, an expert in amoebae. “It was a big difference from what came before. We could now say, ‘Wow, these things that look so different from each other really aren’t.’ But there was a long way to go.”

The Society built on their findings in 2012 with a second paper, The Revised Classification of Eukaryotes, which moved groups around, found a home for lineages that didn’t fit in the prior version, and predicted that new and surprising findings in the future would come from relatively under sampled areas of the world such as the deep sea. Indeed, that turned out to be the case.


The 2012 version of the phylogenetic tree of life will be updated in January with new discoveries from remote locations such as the deep ocean. Image courtesy of Wiley Publishing. 

And in January, after another seven years of discovery and massive new amounts of genetic information, the Society will publish a third version, once again refining the existing picture of the phylogenetic tree and uncovering new layers of diversity. “Sampling soils, deeper marine waters, and the deep sea will continue to fill us with surprises,” the paper states.

The papers are among the most influential and cited in all of biology, Spiegel said. “It’s the authoritative classification people go to. We do it as a community, so we don’t necessarily agree about everything, but we agree this is the best we can do at this time.”

That’s important for scientists who study evolution and biological diversity, and it’s also key to research involving organisms as models to study processes or disease. “If you are going to use something as a model, you need to know how good of a model it is,” said Spiegel.

All graphic representations of the interconnectedness of life are hypotheses, and the family tree will undoubtedly need to be revised again in the future. But the big picture is clearer than ever before, Spiegel said.  

“There are probably a few more iterations needed, there are still some big questions still open. But I wouldn’t be surprised if it were unnecessary to do something on this scale in 20 years.”

About The Author

Bob Whitby writes about bioscience, geoscience, physics, space and planetary sciences, psychology and sociology. Reach him at 479-575-4737, or

University Relations Science and Research Team

University Relations Science and Research Team

Matt McGowan
science and research writer

Robert Whitby
science and research writer

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