"The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species. (...)
The only illustration in Charles Darwin's seminal work The Origin of Species, published in 1859
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."
To reconstruct the Tree of Life - or fragments of it (e.g. Bininda-Emonds et al., 2007) - is one of the goals of the field of phylogenetics, not just because of its intrinsic beauty, but also because the phylogenetic context allows us to test hypotheses and make inferences on the origin and generation of biological diversity from the molecular level up to the biotic.
Although large numbers of phylogenies have been and are being published, they still cover only a small fraction of all the diversity of life, and each of these phylogenies usually describes the evolutionary relationship of few taxa from a relatively narrow taxonomic range. Our knowledge of 'the' tree of life is fragmented.
The challenges to overcome are wide-ranging: inferring large phylogenies poses great computational difficulties, some of which I have discussed in my dissertation. In my ongoing research I have contributed to the development of new tools, programming libraries, data standards, databases and reporting standards to integrate the ever-growing amount of comparative data from molecular, morphological and other sources in more and more detailed and comprehensive estimates of phylogeny. I also am part of various collaborations, standards bodies and recurrent meetings to develop and promote interoperability in evolutionary informatics and I organize courses and mentor students to train young scientists in the application of these technologies.