Phylogenetic tree-building programs are the workhorses of evolutionary analysis. Thus it might be surprising that, given there are at least 1.7 million named species of plants and animals, output trees with over 1000 taxa are exceptional. The primary reason is computational–the number of possible arrangements rises logarithmically with input taxa (eg for 1000 taxa, ~10^2500 possible trees; Tamura et al 2004), such that standard algorithms, even those that sample a fraction of “tree space,” are too slow. As a result, so far the Tree of Life has been constructed by concatenating multitudes of trees each built with relatively small numbers of taxa. This is unsatisfying and possibly unreliable.
In May 2009 Cladistics researchers from Argentina and Sweden report on the largest tree to date–73,060 eukaryotic taxa, essentially everything Goloboff and colleagues could find in GenBank, ranging from algae and protozoans to flowering plants and vertebrates. In addition to size, there were several remarkable features. The tree was constructed from just 13 genes, each of which was sequenced for a subset of the total (750 to ~20,000 taxa), plus 604 morphologic characters that applied across most of the data set. Nearly all (92%) of the cells in the resulting data matrix (73,060 taxa x 9535 characters) were empty due to lack of data. Nonetheless, the parsimony analysis recovered most eukaryotic groups down to the level of order as monophyletic taxa. The analysis utilized TNT software previously developed (and made publicly available) by Goloboff and colleagues and took 2.5 months on 3 desktop computers (total 96 GB RAM, 16 x 3 Ghz processors). To manage the flow of data, nearly all steps were automated from extracting, labeling, and aligning GenBank sequences to analyzing monophyly of groups at various taxonomic levels.
Looking ahead, the authors see biggest challenges not in tree-building, but in alignment software and “that the sequence information required is simply non-existent, and the morphological information is scanty and fragmentary.” I know that a short segment of a single mitochondrial gene is considered insufficient for phylogeny, but it would be interesting to see what TNT could do with 40,777 COI sequences from 6,506 fish species (FishBOL), for example. I imagine that even TNT might have trouble analyzing all 603,002 COI sequences of the 57,159 species represented in BOLD (with many more to come). Phylogenetic trees are established as the goal of evolutionary analysis, but we may need alternate methods for analyzing differences and similarities in very large data sets.