Kristen Ruth Bleazard Summary of Search for a Tree of Life in the thicket of the phylogenetic forest In the Search

for a Tree of Life in the thicket of the phylogenetic forest the authors explored the tree of life concept employed by Darwin to represent the evolution of life. However comparative genomics had revealed extensive horizontal gene transfer (the transfer of genes between organisms in a way other than the accepted traditional reproduction concept) which seriously undermined Darwins original concept. There is a possibility though that a central trend may still exist in a greatly modified form. A consistent phylogenetic signal was found when a comparative analysis of nearly 7,000 phylogenetic trees for prokaryotic genes was performed. This proved true even though there were high levels of inconsistency between the signals on a superficial level. Horizontal gene transfers (HGTs) were random in nature leaving this central trend intact. Conversely topological consistency appeared at shallower tree depths but drop radically at the levels of archaeal and bacterial phyla. This find seemed to indicate that at the very roots of evolution there may be many individual pieces. It is possibly due to the extensive HGT between prokaryotes that Darwins original tree of life theory may be somewhat obsolete. For more than 100 years the predominant metaphor representing the theory of evolution has been the tree of life. In order to perpetuate that idea trees were constructed based on species or organismal traits. A new domain of life the Archaea fostered the idea that a conclusive, single tree of life model would soon be realized. However it became obvious due to multiple HGTs a more correct picture of a net of life might better represent the evolution process. Due to advances in comparative genomics, distinct tree topologies were observed for different trees.

This discovery discredited the single tree of life concept since HGTs disallow any one particular tree from being an accurate model of the evolution of whole genomes. The tree of life was chopped down due to the discovery of pervasive HGT in prokaryotes, resulting in a foundational shift in evolutionary biology. Current research dictated that all life forms on a cellular level are firmly connected by a tree of cell divisions. This concept added to the complexity of a single tree concept, nearly causing it to be divided into two separate trunks; one which dealt with the phylogenetic analysis of genes and genomes and the second which dealt with cells. Through phylogenomic studies it had become evident that genes are tied to set biological connotations. This idea must be expressly understood as it was the bases for the article. Biologists are continually pruning and grafting on to the idea of the tree of life. Three camps had emerged as scientists have continued to study the importance of HGT between gene phylogenies. The first group was in complete denial of the significance of HGT for evolutionary biology. The second subscribed to a somewhat more liberal view of the concept of the tree of life. The third, by far the most radical, tossed away the entire concept stating that it was meaningless. If the middle ground was chosen, some sense of the tree of life concept still held true; it was argued that a central trend could be derived by in-depth studies of tree topologies. The most radical view argued that due to the observed high levels of HGT, the tree of life hypothesis should be dismissed all together and replaced with a net of evolution. In an attempt to blaze a trail into the forest of life nearly seven thousand phylogenetic trees which sprung from a group of proteins were analyzed. It was discovered in most of these trees only a small number of species were involved. In this small collection the attempt was made to

pick out patterns in search of the existence of a central trend. If this could be accomplished it would result in something similar to the concept of the tree of life. The primary focus in this research was a thorough study of the topological differences between the trees. This was depicted more as a network while also being subjected to classical multidimensional scaling (CMDS) which allowed for distinction between various groups of trees. Furthermore an inconsistency score (IS) was also presented which provided a measurement of how typical a particular tree related to the rest of the forest. It was discovered there were many different subsets of trees in a variety of species; these occurred mostly in small numbers. This caused the need for the addition of a pruning step which would cut back on any overlay within the subsets. In an effort to escape any grey area that might come as a result of the pruning procedure, a subset of nearly universal trees (NUTs) was also considered. For most of the information that followed, the NUTs were analyzed in tandem with a full set of trees in the forest of life. This investigation resulted in findings that showed the topologies of NUTs (were for the most part) highly coherent. Among the NUTs however there was an inconsistency in which the mean value ranged from just over 1% to about the 4% level. This result pointed to the idea that the NUTs were extremely consistent. It must be noted using a gap statistics analysis there was of a lack of any real clustering of the NUTs within the trees. This discovery suggested all the NUTs belonged to a solitary cluster surrounding a single point; this could be due to the result of HGT. Different bootstrap support thresholds used in an analysis of the observed inconsistencies between the trees found low IS levels but the inconsistency could never be completely removed.

The NUTs were based on heavily documented genes whose phylogenies had been well studied. Through research the deduction was made that a high level of HGT took place in the genes that encoded the aminoacyl-tRNA synthetases bits of the translation machinery but none was expected for the ribosomal proteins. A fair level of topological agreement was found in the supertree and a goodly number of the NUTs when a chain of universal proteins were scrutinized. This conclusion seemed to indicate that the original universal tree of life as in envisioned by Ciccarelli and others was nearly identical to the NUTs. The makeup of the forest of life was analyzed using the CMDS procedure. Through an analysis using gap statistics, distinct clusters of trees were found in the forest. This sparked the idea there may be distinct groves existing within the greater forest. After analysis it was found the trees strongly indicated there had been numerous HGT events. An additional exploration looking at the distribution of ISs revealed a high percentage had either a consistency level that was very high or alternatively very low. This discovery pointed to bimodal distribution of the amounts of HGT. This unexpected result did not match the predicted outcomes of the original hypothesis. Inconsistency between the trees greatly increased with phylogenetic depth. This fact could perhaps crack the possibility of the NUTs as a reflection of the central trend in the forest of life. Further studies suggested that many of the edges tying the network of trees together were rooted on the similarities of the topologies in the tops of the trees. These surprising results made detecting a central trend within the forest difficult at best, making the possible identification of a single tree of life remote.

At the deeper levels within the forest of life there was a sharp increase in the inconsistency between trees. This may indicate there was a separate evolutionary process which directed this portion of the forest as compared with that which worked in lesser depths. This dual concept of early evolution presented the idea of compressed cladogenesis (CC) and the Biological Big Bang (BBB). This research, in conjunction with other recent studies, topples the original concept of a single tree of life. Two central themes emerged in the end. The first dealt with the high levels of inconsistency within the tree of the forest of life. The second centered around a clear signal of a consensus topology between the NUTs. Many trees of the forest were similar to the topology of the NUTs, so while NUTs do not completely represent the forest they were contenders for embodying a central trend. Conversely this high consistency was only present at shallow depths. This clouded the notion of the existence of a central trend. It further caused the possibility that early on in evolution development may have been non-tree like. In an attempt to understand this problem more completely evolution was simulated using both the CC model and BBB model. Results were inconclusive. It is clear through this research the original hypothesis was no longer valid. Even so without that representation there seemed to be a measureable amount of consistency within the forest of life. Convenience dictated the picture represented by a single tree of life may be valuable in metaphor only. The nature of the central trend hypothesis had only been scratched at the surface and warranted further research. The results presented in this study were derived through analysis of representatives of nearly 7000 clusters of orthologous of phylogenetic genes. Alignments of the protein sequences along

with tree construction were created using the Muscle and the Gblocks programs. Additionally the Multiphyl program was used as a substitute model for the phylogenetic trees. To create a super network of phylogenetic material methods instituted by Huson and others were employed. Tree comprises were based on fairly new methods judged reliable by the authors.