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PhyloCode names are not useful for phylogenetic synthesis

Ok, the title is intentionally a bit provocative, but bear with me.

A primary aim of the Open Tree project is to synthesize increasingly comprehensive estimates of phylogeny from “source trees” — published phylogenies constructed to resolve relationships in disparate parts of the tree of life. The general idea is to combine these localized efforts into a unified whole, using clever bioinformatic algorithms.

In this context, a basic operational question is: how do we know if a clade in one source tree is the same as a clade in another source tree? This can be difficult to answer, because source trees are typically constructed from carefully selected samples of individual organisms and their characters (usually DNA sequences). If two source trees are inferred from completely non-overlapping samples of individual organisms, as is commonly the case, is it possible for them to have clades in common, or rather, is it possible for us to determine whether they have clades in common?

I would argue that the answer is yes, with a very important condition: that the organisms sampled for each tree are placed into a common taxonomic hierarchy that embodies a working hypothesis of named clades in the tree of life.

Note an important distinction here: a clade in a source tree depicts common ancestry of selected individual organisms, while a clade in the tree of life is a conceptual group defined by common ancestry that effectively divides all organisms, living and dead, into members and non-members. So a taxon in this sense is a name that refers to a particular tree-of-life clade whose membership is formalized by its position in the comprehensive taxonomic hierarchy.

By placing sampled organisms into a common taxonomic hierarchy, one can compute the relationships between source-tree clades and tree-of-life clades in terms of taxa, a process that I refer to as “taxonomic normalization.”

An idea that emerges from this line of thinking is that the central paradigm of systematics is (or should be) the reciprocal illumination of phylogeny and taxonomy. That is, phylogenetic research tests and refines taxonomic concepts, and those taxonomic concepts in turn guide the selection of individual organisms for future research. I would argue that this, in a nutshell, is “phylogenetic synthesis.”

Which brings me to the title of this post. In the PhyloCode, taxonomic names are not hypothetical concepts that can be refuted or refined by data-driven tests. Instead, they are definitions involving specifiers (designated specimens) that are simply applied to source trees that include those specifiers. This is problematic for synthesis because if two source trees differ in topology, and/or they fail to include the appropriate specifiers, it may be impossible to answer the basic question I began with: do the trees share any clades (taxa) in common? If taxa are functions of phylogenetic topology, then there can be no taxonomic basis for meaningfully comparing source trees that either differ in topology, or do not permit the application of taxon definitions.

So phylogenetic synthesis requires taxa that are explicitly not functions of phylogenetic topology. Instead, taxa should exist independently as hypotheses to be tested by phylogenetic evidence, and as systematists we should strive to construct comprehensive taxonomic hierarchies. I think this is going to be the real key to making progress in answering the question, “what do we know about the tree of life, and how do we know it?”

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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.