Phylogenetic Trees: Applications, Construction, and Assessment

Abstract

Molecular phylogeny is used to study the relationships among the set of objects by generating phylogenetic or evolutionary tree. The objects in the study can be organisms or biomolecules such as gene or protein. The evolutionary history hidden in the biomolecules establishes the evolutionary patterns in the form of a tree when a suitable data, data substitution models, and tree construction methods are used. These evolutionary patterns are used to study the relationships among the objects. These patterns sometimes make it difficult to infer the relationship among the objects. In addition, different tree construction methods like unweighted pair group method with arithmetic mean (UPGMA), neighbor joining, minimum evolution, Fitch-Margoliash, maximum parsimony, maximum likelihood, Monte Carlo’s simulation, Bayes, and so on and types of data used in the analysis make it much more complicated to infer the relationships. The above tree construction methods follow different principles to construct a phylogenetic tree. Most often, the tree topologies generated by different methods for the same data will be the same, whereas in some cases the tree topologies may be different in their internal branching. These differences in the tree topologies may make it difficult to assess the confidence of the phylogenetic tree. Further, combination of the tree construction methods and data used by phylogeny program packages such as MEGA, Molphy, Phylip, PAML, and PAUP also make it difficult to assess the confidence of the phylogenetic tree. Molecular phylogeny has a wide range of applications such as affiliating taxonomy of an organism, studying reproductive biology in lower organisms, assessing the process of cryptic speciation in a species, understanding the history of life, resolving controversial history of life, reconstructing the paths of infection in an epidemiology, classifying proteins or genes into families, and many more. If the interpretation of the evolutionary patterns is not appropriate, then the inference of the study may be misleading. Thus, interpretation of the tree and relationships among the organisms is always dependent on assessing the confidence of the phylogenetic tree. Literature review shows that sampling methods such as bootstrapping, jackknifing, and Bayesian simulation and statistical methods such as Kishino-Hasegawa test and Shimodaira-Hasegawa test are used to assess the confidence of the phylogenetic tree. Thus, this chapter reviews the applications, construction, and assessment of phylogenetic tree.