Phylogenetics and Systematics in a Nutshell
During the last 50 years, phylogenetic systematics has suffered a substantial transformation in philosophy and methods. Systematics has gone from been a merely descriptive discipline to a scientific theory encompassing solid evolutionary principles capabl
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Phylogenetics and Systematics in a Nutshell Alejandro Espinosa de los Monteros
Abstract During the last 50 years, phylogenetic systematics has suffered a substantial transformation in philosophy and methods. Systematics has gone from been a merely descriptive discipline to a scientific theory encompassing solid evolutionary principles capable of inferring robust and replicable historical hypothesis about the interrelationships of taxa. This chapter provides the basic concepts in the field of systematic biology (e.g., terminology, characters codification, tree description) and phylogenetic reconstructions (e.g., alignments, reconstruction methods, support measurements). A particular emphasis is given to nucleotide data. It will provide a guide on how sequences can be used to detect natural selection, adaptation, recombination, and to evaluate substitution saturation. In particular, this chapter seeks to provide the novice with all basic concepts necessary to understand and interpret phylogenetic hypotheses: for instance, to understand nucleotide substitution models, what a molecular clock is, tree selection methods (e.g., Maximum Parsimony, Maximum Likelihood, Bayesian), how to interpret node support values, and testing tree topologies (e.g., Kishino-Hasegawa). Finally, a short review is presented on the current phylogenetic knowledge of avian Haemosporida. Keywords Avian Haemosporida phylogeny · Bayesian inference · Maximum Likelihood · Molecular clock · Parsimony · Phylogenetic reconstruction
3.1 Introduction It is possible that taxonomy and systematics are the earliest biological subjects developed by mankind. The need to organize and classify natural resources was indubitably an essential issue for the survival of human populations. In 1735, the Swedish naturalist Carl von Linné published Systema Naturae formalizing the rules
A. Espinosa de los Monteros (*) Laboratorio de Sistematica Filogenetica. Departamento de Biología Evolutiva, Instituto de Ecología, Xalapa, Veracruz, Mexico © Springer Nature Switzerland AG 2020 D. Santiago-Alarcon, A. Marzal (eds.), Avian Malaria and Related Parasites in the Tropics, https://doi.org/10.1007/978-3-030-51633-8_3
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for binomial nomenclature. Although Linné’s system has been challenged, he is still considered as the father of modern taxonomy. The domain of taxonomy (i.e., naming taxa and classification) is different from that of systematics. Systematics is the basis to understand the evolutionary interrelationships of taxa in an attempt to generate historical scenarios for how lineages have changed and diversified throughout time. In other words, systematics is the method that scientists used for reconstructing the pattern of events that have assembled the current biodiversity on Earth. Phylogenetic systematics is the way that biologists infer hypotheses that explain the evolutionary history of life, both living and extinct. During the last 50 years, this discipline has suffered radical changes due mainly to the consolidation of evo
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