The species should form an evolutionary tree

Ever since Darwin the universal evolutionary tree has been a unifying principle in biology. Evolution predicted that this universal tree can be derived by arranging the species according to their similarities and differences. And as more data became available, particularly from the dramatic breakthroughs in molecular biology in the latter half of the twentieth century, expectations were high for the determination of this tree. As one paper explains, “Once universal characters were available for all organisms, the Darwinian vision of a universal representation of all life and its evolutionary history suddenly became a realistic possibility. Increasing reference was made to this universal, molecule-based phylogeny as the ‘comprehensive’ tree of the “entire spectrum of life” (O’Malley and Koonin) But those expectations were dashed: “By the mid-1980s there was great optimism that molecular techniques would finally reveal the universal tree of life in all its glory. Ironically, the opposite happened.” (Lawton)
 
As one study explained, the problem is so confusing that results “can lead to high confidence in incorrect hypotheses.” And although evolutionists thought that more data would solve their problems, the opposite has occurred. With the ever increasing volumes of data, incongruence between trees “has become pervasive.” (Dávalos) As another researcher explained, “Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.” (Woese) These incongruities are not minor statistical variations and the general failure to converge on a single topology has some researchers calling for a relaxation from “tree-thinking.” (Bapteste, et. al.) Nor are these incongruities limited to protein-coding genes. As one research commented, “I’ve looked at thousands of microRNA genes, and I can’t find a single example that would support the traditional tree.” (Dolgin)
 
These incongruities have forced evolutionists to filter the data carefully in order to obtain evolutionary trees. As one paper explains, “selecting genes with strong phylogenetic signals and demonstrating the absence of significant incongruence are essential for accurately reconstructing ancient divergences.” (Salichos and Rokas) But this raises the question of whether the resulting tree is real: “Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL [tree of life] rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true.” (Doolittle and Bapteste).
 
References
 
Bapteste E., et. al. 2005. “Do orthologous gene phylogenies really support tree-thinking?.” BMC Evolutionary Biology 5:33.
 
Dávalos L., et. al. 2012. “Understanding phylogenetic incongruence: lessons from phyllostomid bats.” Biological Reviews Cambridge Philosophical Society 87:991-1024.
 
Dolgin, E. 2012. “Phylogeny: Rewriting evolution.” Nature 486:460-462.
 
Doolittle, W., E. Bapteste. 2007. “Pattern pluralism and the Tree of Life hypothesis.” Proceedings of the National Academy of Sciences 104:2043-2049.
 
Lawton, G. 2009. “Why Darwin was wrong about the tree of life.” New Scientist January 21.
 
O’Malley, M., E. Koonin. 2011. “How stands the Tree of Life a century and a half after The Origin?.” Biology Direct 6:32.
 
Salichos L., A. Rokas. 2013. “Inferring ancient divergences requires genes with strong phylogenetic signals.” Nature 497:327-331.

Woese C. 1998. “The universal ancestor.” Proceedings of the National Academy of Sciences 95:6854-6859.