Literature Review For Partitioned Bayesian Analyses

Construction of a Phylogenetic Tree

Discuss about the Literature Review for Partitioned Bayesian Analyses.

In the paper by Ciccarelli, the problems associated with the construction of the phylogenetic tree of life are presented. Although the evolutionary relationships of many organisms have been successfully placed in the tree of life, there have been numerous debates on this issue (Brandley et al., 2005). The author indicates that even after the advent of generation of genomic data through molecular biology techniques, there are increasing debates on the tree of life. These debates are as a result of lack of proper theoretical and practical limits that are set out during the construction of a phylogenetic tree. In other cases, there are concerns on the lack of sufficient characters (Kremp et al., 2014). In the computing resources so as to be able to cope up with increasing number of species. In essence, there can a rise in biasness in terms of sampling of species as well as the dilution of the horizontal gene transfer in bacteria.

In figure one, of this article, the process of developing a phylogenetic tree by use of bootstrap is presented. In this figure, the major steps are presented alongside the parts that can be automated (Chao et al., 2014). As a result of evolution which takes place, the construction of a phylogenetic tree involves the collection of data which is representative of the ancestral relationship (Ciccarelli et al., 2006). Then the universal families are identified, followed by the removal of the families that may contain several gene transfers. The next step is to construct the tree by use of concatenated alignment. This step involves the removal of pseudo genes, paralogs and copies of the organelles. The remaining genetic materials are aligned in a way that they cover all the three domains of life. The next step is to perform the detection of any horizontal gene transfers and removing them. In this case, the randomly chosen samples consisting of eight families are subjected to jack knife tests (Yilmaz et al., 2014). The final step involves the reconstruction of the phylogenetic tree by use maximum likelihood approaches which is aided by use of bootstraps, gamma 4 and the phyml protocols. Bootstrap is the use of the already obtained data to make inferences of uncertain data. This method improves statistics because it pulls on its bootstraps by sampling the input data. In this case, bootstrapping gives an indication on the number of times, out of 100, a certain branch of the phylogenetic tree is observed when the construction of a phylogenetic tree is repeated on a set of resampled data (Schreiber et al., 2014).

Problems with the Phylogenetic Tree

From the caption, the official title for figure2 is on ‘the global phylogeny of fully sequenced organisms showing the alignment of 31 universal proteins in bacteria, archaea and eukaryote. However, the decoded title from this figure is ‘the representation of the evolutionary relationship of bacteria, archaea and eukaryotes on the basis of 31 proteins alignment.’ The specific questions being answered in the experiment which yielded figure 2 is, ‘how are evolutionary trends determined in bacteria by the use of protein families?’ The data which was used for the reconstruction of the phylogenetic tree presented in Figure 2 was derived from 31 concarnated genes that occur universally and had undisputable orthologs. From around 91 species whose genomes were already annotated. The 31 genes used are important in transduction and hence were based on the non-translational genes which are domain-specific. In general, from figure 2, it is evident that the proteins used to construct an evolutionary tree should be based on protein families that are universally expressed by all species. As the branching of the tree continues, more specific proteins are put into consideration in order to determine the length of the branches which corresponds with the level of relatedness (Ciccarelli et al., 2006).. Moreover, from this figure, it can be noted that when constructing the phylogenetic tree, it is important to ensure that all the three domains of life are considered.

Although much information has been presented in these articles, there are some concerns which can be raised. For instance, the accuracy of the phylogenetic tree, the recommended tools for use in bootstrapping and the ways to choose the closely related family problems. These questions can be structured in this manner; how can the accuracy of a phylogenetic tree be determined? What are the recommended tools to be used to generate a phylogenetic tree? What are the recommended methods of choosing the family proteins for use in the construction of a phylogenetic tree?

Dagon and Martin calls the tree which was generated by Ciccarelli et al., as ‘the tree of one percent’ because its construction was based on the assumption that all genes are linked by a single bifurcating tree in terms of evolutionary relatedness (Dagan and Martin, 2006). For instance, since the genome of prokaryotes have about 3,000 genes that code for proteins use of 31 proteins by Ciccarelli et al., indicates that these proteins were representative of only 1 % of the prokaryotic genome, which is not fully representative. Based on the comparison between the prokaryotic proteome and the proteins used, the Ciccarelli et al., tree is thus an insufficient model. The origin of these genes is very important because it offers a clear indication of the nature of the evolutionary relatedness between organisms. The authors of this article argue that the origin of the genes used to construct this tree was based on endosymbiosis. In this case, it is argued that the eukaryotes acquired many genes from the endosymbionts (Baum and Smith, 2013).

Recommended Tools for Use in Bootstrapping

The process that Dagan and Martin argue that was neglected by Ciccarelli et al., is the lack of consideration of whether the genes could make a phylogenetic tree. This analysis is important because it gives a biologist an opportunity to study he patterns and level of genetic relatedness of various species. From figure 2 in the article by Ciccarelli et al., it is evident that within each of the levels of taxonomy between the eukaryotes, archaea and bacteria the length of the branches is different. On the other hand, there is a strong discrepancy between the divisions in prokaryotes and eukaryotes (Winter et al., 2013). For instance, there are some animals which have been assigned to make a separation in a certain phylain eukaryotes is able to be classified in the same phyla as in the prokaryotes too.

In figure 2 by Dagon and Martin, the symbiotic tree model is similar to Ciccarelli et al., model of evolutionary relationship is the symbiotic tree which proposes that the common ancestor in eukaryotes was from the endosymbiotic process of one prokaryote, say X, in another prokaryote host, say Y (Dagan and Martin, 2006).. this process led to the development of a nucleated eukaryote which gave rise to several other eukaryotes from a common lineage.

Although the work by Ciccareli et al was published in a prestigious journal, Science, the immediate criticism by Dogon and Martins, despite the comments given by the reviewers and editors indicate that through intensive research, other researchers determined a gap in construction of a phylogenetic tree. It is the paper by Ciccareli et al which supports the fact that some computer programs assume that the history of life is best depicted by use of a tree. This is true because some of these computer programs use the bootstrap method so as to determine the relatedness of unknown proteins based on the known proteins from various species. The article by Koonin ends the controversy in the initial two articles by indicating that there are numerous gene exchange processes which take place in organisms. In this case, the reliability of phylogenetics becomes an issue of concern because viruses and plasmids re the major agents of horizontal gene transfer. The arguments of Koonin as presented in this article are convincing because when there is increased cases of gene transfers and recombination, then the evolutionary tree of life might not be relevant (Koonin, 2016). However, Koonin advices that endosymbiosis blocks the horizontal gene transfers and thus phylogenies should be used with caution.

Reference List

Ciccarelli, F.D., Doerks, T., Von Mering, C., Creevey, C.J., Snel, B. and Bork, P., 2006. Toward automatic reconstruction of a highly resolved tree of life. science, 311(5765), pp.1283-1287.

Koonin, E.V., 2016. Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions. F1000Research, 5.

Dagan, T. and Martin, W., 2006. The tree of one percent. Genome biology, 7(10), p.118.

Brandley, M.C., Schmitz, A. and Reeder, T.W., 2005. Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Systematic biology, 54(3), pp.373-390.

Kremp, A., Tahvanainen, P., Litaker, W., Krock, B., Suikkanen, S., Leaw, C.P. and Tomas, C., 2014. Phylogenetic relationships, morphological variation, and toxin patterns in the Alexandrium ostenfeldii (Dinophyceae) complex: implications for species boundaries and identities. Journal of phycology, 50(1), pp.81-100.

Baum, D.A. and Smith, S.D., 2013. Tree thinking: an introduction to phylogenetic biology. Roberts.

Yilmaz, P., Parfrey, L.W., Yarza, P., Gerken, J., Pruesse, E., Quast, C., Schweer, T., Peplies, J., Ludwig, W. and Glöckner, F.O., 2014. The SILVA and “all-species living tree project (LTP)” taxonomic frameworks. Nucleic acids research, 42(D1), pp.D643-D648.

Winter, M., Devictor, V. and Schweiger, O., 2013. Phylogenetic diversity and nature conservation: where are we?. Trends in Ecology & Evolution, 28(4), pp.199-204.

Schreiber, F., Patricio, M., Muffato, M., Pignatelli, M. and Bateman, A., 2014. TreeFam v9: a new website, more species and orthology-on-the-fly. Nucleic acids research, 42(D1), pp.D922-D925.

Chao, A., Chiu, C.H. and Jost, L., 2014. Unifying species diversity, phylogenetic diversity, functional diversity, and related similarity and differentiation measures through Hill numbers. Annual Review of Ecology, Evolution, and Systematics, 45, pp.297-324.