Grafting together “the great Tree of Life”
Richard ReeSunday, February 8th, 2009
At the Biodiversity Synthesis Center, one of our core interests is phylogeny, especially how to incorporate it into the EOL. This post is about phylogenetic synthesis, and highlights in particular a new BioSynC tool in development called Phylografter. But first some background.
The modern concept of phylogeny (genealogical history tracing the common ancestry of species) was one of Darwin’s most significant contributions to science. In On the Origin of Species, he described how species have proliferated using wonderful botanical imagery:
“As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications.”[1]
Since then, great strides have been made in reconstructing the Tree of Life, using DNA sequences, morphological traits, and other evidence observed in both living and fossilized organisms. But these strides have necessarily been piecemeal. Individual studies in the primary literature are inherently limited in scope to resolving local “ramifications”: the branch holding the lemurs, for example, or the deepest splits near the root. This is because for any given problem, representative organisms and data must be sampled very judiciously. As a result, even with continuing advances in data acquisition, analytical methods, and computational power, our understanding of the whole Tree depends fundamentally on focused, hierarchically nested research efforts. I think it is even safe to say that it will never be practical or worthwhile to try and estimate the phylogeny of all known species in a single analysis, from scratch.
At the same time, mounting interest in phylogeny as a means of understanding broad-scale patterns in biodiversity has heightened the need to synthesize primary research — to effectively link together published results, forming ever more inclusive phylogenetic “megatrees.” Synthetic phylogenies of this sort can be powerful tools for testing hypotheses about the tempo and mode of evolution. So, how does one go about doing this — “grafting” together published trees into a greater whole, while keeping track of the sources of the parts?