Assembling, Visualizing, and Analyzing 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.

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One response

  1. Shouldn’t bioinformatic refer as well to the behavioral strategies that contributed to the evolution of divergent species? Hierarchies of behaviors certainly played their part, no?

    October 17, 2013 at 7:14 pm

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