What is the Tree of Life?

Taxonomy and the tree of life

What’s in a name?

It is now widely accepted that taxonomy should reflect phylogeny — that the names we use in biological classifications should refer to branches on the tree of life. This was one of Darwin’s most revolutionary ideas, that common ancestry is the fundamental organizing principle for natural classification:

“… community of descent is the hidden bond which naturalists have been unconsciously seeking.”

Charles Darwin, On the Origin of Species

One of the main goals of the Open Tree of Life project is to facilitate phylogenetic “synthesis”. What does this mean? The general idea is to take disparate pieces of information — in this case, phylogenetic trees from the scientific literature, or the data sets on which they are based — and merge them together in ways that yield more comprehensive and (hopefully) more accurate inferences of the tree of life as a whole. Like a jigsaw puzzle, the assembled pieces reveal the big picture.

Taxonomy is central to this exercise, because names are the primary link between the products of phylogenetic research. Without taxonomy, a phylogenetic tree from a typical study would simply depict relationships among individual organisms. This would not, in general, be very useful. Imagine if someone told you: “I know of a red house and a blue house, and the road between them runs north-south for about 100 miles.” Without any additional information, this statement has little if any value. For it to make sense, you would ideally want to know the address of each house, and the name of the road connecting them; but even incomplete information (what cities and states are the houses in?) is better than nothing. Only then could you figure out that the route in question is, for example, Interstate 94 between Chicago, IL and Milwaukee, WI.

Similarly, the organisms used in a particular phylogenetic study must be taxonomically classified in order to establish, like pins on a map, how the branches of the inferred tree represent “real” branches in the tree of life. This allows common relationships across studies to be discovered. To continue the analogy, if you know of a yellow house in Chicago and a green house in Milwaukee, you also know that I-94 connects them just as it does the red and blue houses mentioned above. The phylogenetic tree relating a rose, pumpkin, and oak depicts the same relationships — that is, it traces essentially the same evolutionary history — as the tree relating an apple, cucumber, and walnut. In each case, different organisms were chosen to represent the angiosperm orders Rosales, Cucurbitales, and Fagales, respectively.

You might recognize something paradoxical here. I started off by stating that taxonomy should reflect phylogeny. But then, I proceeded to describe how taxonomy is needed to interpret the results of phylogenetic studies. If taxonomy reflects knowledge of phylogeny, and knowledge of phylogeny is derived from studies of organisms chosen for the taxa they represent, isn’t this a chicken-and-egg problem?

The short answer: yes, it is. Systematic biology is a science of reciprocal illumination between, on one hand, what we discover about the tree of life, and on the other, how we reflect and communicate that knowledge through taxonomy. One can view a taxonomic hierarchy — the arrangement of species within genera, genera within families, and so on — as a working hypothesis, subject to revision. Taxonomic names refer to branches on the tree of life that we believe to exist, but we are open to new information that may change our view. For example, we might discover that members of two genera, hypothesized to be exclusive groups based on their morphological differences, are in fact co-mingled on the same branch of the tree of life when DNA evidence is studied. The question then arises: what happens to the names of the original genera? How should we refer to their common branch? These are issues of nomenclature, a topic beyond the scope of this blog post, but the bottom line is that eventually, taxonomy should be updated to reflect this new knowledge.

The tension between taxonomy and phylogeny is at the heart of the basic question, “what do we know about the tree of life, and how do we know it?” While this question is somewhat metaphysical, it also has very practical implications of immediate concern to the Open Tree project. Most importantly, it has been necessary for us to cobble together a comprehensive taxonomic hierarchy that includes all of life, since none existed previously that were reasonably up-to-date. This “Open Tree Taxonomy” serves a critical purpose — basically, it is what allows us to wrangle herds of phylogenetic trees into a common bioinformatic corral. The challenge we face moving forward is how our synthesis efforts can be leveraged to improve and refine our working taxonomy, closing the loop of reciprocal illumination that is central to the discipline of systematics.

Richard Ree is a curator at the Field Museum of Natural History and a faculty member of the Committee on Evolutionary Biology at the University of Chicago.


Presentation slides from Evolution 2013 available

Open Tree of Life at meetings

The Open Tree of Life project is one of the many phylogeny projects that are featured during the Evolution 2013 meeting that currently takes place in Snowbird (UT). The presentation slides from Karen Cranston, the principal investigator of Open Tree of Life, are available online (LINK). Presentation slides from other investigators are added here in the upcoming days.

Evolution 2013 is the joint annual meeting of the Society for the Study of Evolution (SSE), the Society of Systematic Biologists (SSB), and the American Society of Naturalists (ASN). The conference meets jointly with the iEvoBio conference. Open Tree of Life is represented at both events. About 1400 participants are expected to share their research in evolution, systematics, biodiversity, software, and mathematics.


Across disciplinary boundaries

The interdisciplinary team of the Open Tree of Life project

What do a fungal evolutionary biologist and a computer scientist have in common?

It is usually easier to name a long list of differences, but that does not mean that those scholars are investigating different issues all the time. They may be very much interested in the same problems, yet apply different perspectives and methods in search for answers.

Those scientists could continuously work on their individual research projects for may years. However, in some cases only an interdisciplinary collaboration leads to a solution. The investigators of the Open Tree of Life project hope this will be the case for them as well. Their goal: creating a tree of life that includes all 1.9 million known species. (more…)

A ‘Social’ Tree

Our group is faced with the challenge of gathering scattered research on some two million known species, placing them and their associated data on a single evolutionary tree of life and then providing a way for new species to be added by researchers around the world. (hence the “Open” in our name). Traditional data storage and software are simply not up to the task. With any number of scientists and researchers contributing their work to the Open Tree, standardization is key. The largest existing evolutionary trees (for example the trees in Price et al, 2010) contain around 100,000 species. Creating a system to include twenty times that amount means redefining how and what types of data storage are used.

This is no simple task. For instance, what are the criteria that should be used to distinguish species? Is it genetic material? Is it a variation in certain features? For species that are extinct, like early mammals or dinosaurs, we don’t have enough genetic material to say for certain where those species fit in the tree. Does morphology (the animal’s form or shape) then come into play? Terminology must be standardized. One research team might store their data under one scientific name, while another might use a completely different one.


Audio interview: What is the Tree of Life project?

The incredibly wonderful thing about audio is that you can continue doing what you’re doing while listening and learning. Here, biologist and leader of our Open Tree of Life project, Dr Karen Cranston (from the National Evolutionary Synthesis Center at Duke University), explains our evolutionary  to Bryan Crump from Radio New Zealand. The Open Tree of Life is the first real attempt to draw a single tree of life (as envisioned by evolutionary scientist Charles Darwin) that includes every known species on Earth.

Link to audio

(about 20 minutes)

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