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Phylogenetic Studies

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Leishmania

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1971))

Abstract

Phylogenetics is an important component of the systems biology approach. Knowledge about evolution of the genus Leishmania is essential to understand various aspects of basic biology of these parasites, such as parasite–host or parasite–vector relationships, biogeography, or epidemiology. Here, we present a comprehensive guideline for performing phylogenetic studies based on DNA sequence data, but with principles that can be adapted to protein sequences or other molecular markers. It is presented as a compilation of the most commonly used genetic targets for phylogenetic studies of Leishmania, including their respective primers for amplification and references, as well as details of PCR assays. Guidelines are, then, presented to choose the best targets in relation to the types of samples under study. Finally, and importantly, instructions are given to obtain optimal sequences, alignments, and datasets for the subsequent data analysis and phylogenetic inference. Different bioinformatics methods and software for phylogenetic inference are presented and explained. This chapter aims to provide a compilation of methods and generic guidelines to conduct phylogenetics of Leishmania for nonspecialists.

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Notes

  1. 1.

    Long branch attraction is a phenomenon in phylogenetics that can alter tree topology. It can occur when the mutation rate is higher along a lineage, or in the presence of a single more distantly related branch. This longer branch tends to be pushed toward the root, or toward shorter branches. It is a problem for most methods, although more for some (Maximum Parsimony, UPGMA) than for others (Maximum Likelihood, Neighbor-Joining), but it is still a problem for those considered as the best methods, such as maximum likelihood, even for long (>100,000 positions) sequences [118]. Reviewed by [119].

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Authors and Affiliations

  1. Molekulare Biotechnologie und Funktionelle Genomik, Technische Hochschule Wildau, Wildau, Germany

    Katrin Kuhls

  2. Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugal

    Isabel Mauricio

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  1. Katrin Kuhls
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  1. Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany

    Joachim Clos

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Kuhls, K., Mauricio, I. (2019). Phylogenetic Studies. In: Clos, J. (eds) Leishmania. Methods in Molecular Biology, vol 1971. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9210-2_2

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