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Phylogenetic Trees: Applications, Construction, and Assessment

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Essentials of Bioinformatics, Volume III

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.

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Acknowledgment

The authors are grateful to Gandhi Institute of Technology and Management (GITAM) Deemed-to-be-University, for providing necessary facilities to carry out the research work and for extending constant support in writing this review.

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Authors and Affiliations

  1. Department of Biochemistry and Bioinformatics, Institute of Science, Gandhi Institute of Technology and Management (GITAM) (Deemed to be University), Visakhapatnam, Andhra Pradesh, India

    Surekha Challa & Nageswara Rao Reddy Neelapu

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  1. Surekha Challa
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  2. Nageswara Rao Reddy Neelapu
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Editors and Affiliations

  1. Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia

    Khalid Rehman Hakeem

  2. Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia

    Noor Ahmad Shaik

  3. Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia

    Babajan Banaganapalli

  4. Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia

    Ramu Elango

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Challa, S., Neelapu, N.R.R. (2019). Phylogenetic Trees: Applications, Construction, and Assessment. In: Hakeem, K., Shaik, N., Banaganapalli, B., Elango, R. (eds) Essentials of Bioinformatics, Volume III. Springer, Cham. https://doi.org/10.1007/978-3-030-19318-8_10

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