Eliane Barbosa Evanovich dos Santos

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http://dx.doi.org/10.5772/intechopen.79422

#### **Abstract**

Describing the diversity of living beings has always instigated man. The classification proposed by Aristotle today seems naïve and unnatural, but it lasted from ancient Greece until the publication of the Linnaeus *Systema Naturae* in 1758. Although quite accurate, the taxonomic classification proposed by naturalist Carl Linnaeus did not consider the evolutionary relationships between living beings. This view, although prior to Charles Darwin, only gained deserved prominence after *On the Origin of Species*. Only in the twentieth century, a new area founded by Hennig, phylogenetic systematics was implemented, and with this, a series of useful methods in the construction of phylogenetic trees arose, as maximum parsimony, neighbor joining, UPGMA, maximum likelihood, and Bayesian inference. With the advancement of information technology, phylogenetic analyses have become more sophisticated and faster. The algorithms used in the analysis programs have become more complex and realistic, favoring the addition of substitution models. The application of these data and the greater facility in generating nucleotide and amino acid sequences allowed the comparison previously unimaginable, for example, between bacteria and eukaryotes. In this way, the history of the advances of phylogenetic knowledge is confused with the greater knowledge about the origin of life.

**Keywords:** evolution, phylogenetic systematics, phylogenetic tree, taxonomy, phylogenetic methods

#### **1. Introduction**

Different criteria of biological classification were created throughout history. Some are arbitrary and do little to reflect the evolutionary relationship between species, for example, the- Aristotelian system. But not always reflecting the relations of relatives was a concern. Even- the iconic classification suggested by Linnaeus was not intended to reflect this relationship- (although it is very consistent with current taxonomic classification). Only with Darwin and-

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his successors did common ancestry gain prominence and was accepted as a fundamental tool in taxonomic analysis through Hennig. The systematic phylogenetic title of the book of the German entomologist opened the door to a new way of looking at taxonomy through kinship relations. The proposal of this new taxonomy would, therefore, be an unequivocal way of understanding the evolutionary history of the species. We now know the various phylogenetic artifacts that may mask or hinder a robust phylogenetic hypothesis. But, computational advancement and new phylogenetic approaches are emerging, reducing the effects of these- artifacts. This chapter makes a narrative review of the history and current advances in phylogeny. The analysis was conducted using PubMed (https://www.ncbi.nlm.nih.gov/pubmed/),- Scopus (https://www.scopus.com), and Google Scholar (https://scholar.google.com/). The first- part of the review describes succinctly the work of Anaximander, Aristotle, Carl Linnaeus,- Peter Simon Pallas, Charles Darwin, and Willi Hennig; the second aspect is showing the phylogenetic methods and phylogenetic analysis programs, and the third focus presents the difference between gene tree and species and shows the criteria used in building of tree of life.
