Phylogenies in flux

Phylogenetics is the study of the relationships among living things — the shape of the tree of life. The most fundamental things to understand about phylogenetics are (1) that our understanding of the relationships among different organisms is constantly changing and will continue to do so for the foreseeable future, and (2) that this ongoing process of revising what we think we know is not a weakness, but a strength. Let's examine those two points in a bit more detail.

Critics of phylogenetic approaches to understanding evolution and biodiversity sometimes quip that cladistics might be good for something, someday — just as soon as the trees are all done. Even some evolutionary biologists look forward eagerly to the day when our understanding of the tree of life is complete. There is a sense that we'll be able to start the serious work as soon as we get all of these pesky critters squared away in our classifications. In this view, biology is sort of like building a car. It will be a lot of fun to drive around in, but we have to have all the pieces in place first and know exactly how they go together before we can do any useful work. But in fact biology is more like exploration — we're discovering new things all the time, and trying to figure out how they relate to our existing knowledge. And there are several reasons why this process of exploration is going to go on for a long time to come:

1. We are constantly discovering new kinds of living organisms. This includes not only the hundreds of species of insects and thousands of species of invertebrate animals that are discovered and named each year, but also fish, amphibians, reptiles, birds, and mammals. Even large mammals — the past decade has seen the discovery of a new species of manatee and at least two new species of big cats from the Amazon basin alone. Southeast Asia is another hotbed of discovery of large animals, including big hoofed mammals. As new species with previously unknown specializations and new combinations of characters are discovered, parts of the tree of life have to be revised to take them into account, just as Renaissance mapmakers had to regularly redraw their charts based on new information flowing back to Europe from the Americas.

2. We are constantly discovering new kinds of fossil organisms. These newly-discovered extinct forms can radically affect our understanding of evolutionary history, even more than living organisms, because our knowledge of the past is so spotty compared to our knowledge of the present. In the present day we are discovering new species of otherwise familiar animals, like monkeys and kangaroos. In the fossil record we are discovering entirely new branches of the tree of life, organisms that are sometimes so bizarre that they defy classification for years or decades until better fossil material is discovered. And the process of discovery is accelerating — half of all of the known species of dinosaurs have been described in the last thirty years.

3. We are discovering new sources of data that provide new information on the relationships among living things. Half a century ago it was becoming possible to classify organisms based on their protein sequences. Then in recent decades we added DNA sequences to our scientific toolbox. And now in the past decade we have gained the ability to compare the entire genomes of organisms. Development, physiology, biochemistry, ecology, and behavior are all sources of information that can be incorporated into our understanding of evolutionary history.

4. We are developing new methods for analyzing the many kinds of data that are now at our disposal, and new statistical techniques for evaluating our results. This is not a trivial concern — analyzing gene sequence data requires different assumptions and different algorithms than analyses based on skeletal anatomy or behavioral traits. An active area of research right now concerns the best way to combine different kinds of data into a single analysis. Discovering the pattern of the tree of life requires the skills of mathematicians and computer scientists, in addition to classically trained biologists.

In almost all of these areas, the pace of discovery and innovation is actually accelerating. So where does this leave the researcher, student, or interested lay person who just wants to know how species X is related to species Y? How is all of this frantic work doing us any good if it isn't giving us solid answers?

These questions get to the heart of what science is. Science is a process of continually refining our view of the world by generating new ideas, testing them against reality, and discarding or modifying ideas that no longer match what we know to be true. This ongoing process of revision can be a two-edged sword. On one hand, our picture of the universe is constantly growing in its breadth, depth, and accuracy. On the other hand, it can be frustrating for people who are not intimately involved in the process of science to keep up with the pace of discovery — especially when those discoveries overturn something that we previously thought to be true. But the universe is a big, complex place, and the number of things that we understand is small compared to the amount of knowledge still to be gained. Scientists engage in vigorous debates, long-held ideas are overturned, and our perception of the world shifts in bizarre and unpredictable ways — and these are all signs that science is healthy, that it is keeping pace with our intellectual and technological reach, and that no hypothesis or theory is beyond revision when contradictory information comes to light. Phylogenetics is no different from the rest of science in this way.

Keep all of these things in mind as you navigate this site. All of our pages represent the best available understanding at the time that they were written. Inevitably, some of what you find written here will already be outdated by the time you read it. Hopefully the mismatch between the latest information and what you find here will be small, but sometimes it may not be. We'll do our best to keep updating and revising our content as new information flows in from students and researchers around the world. That's okay; that's how science works.
 

Text by Matt Wedel, 6/2010.