Phylogenetic reconstruction methods: An overview

De Bruyn Alexandre, Martin Darren Patrick, Lefeuvre Pierre. 2014. Phylogenetic reconstruction methods: An overview. In : Molecular Plant Taxonomy. by Pascale Besse (ed.). New York : Humana Press, 257-277. (Mehtods in Molecular Biology, 1115) ISBN 978-1-62703-766-2

Résumé : Initially designed to infer evolutionary relationships based on morphological and physiological characters, phylogenetic reconstruction methods have greatly benefited from recent developments in molecular biology and sequencing technologies with a number of powerful methods having been developed specifically to infer phylogenies from macromolecular data. This chapter, while presenting an overview of basic concepts and methods used in phylogenetic reconstruction, is primarily intended as a simplified step-by-step guide to the construction of phylogenetic trees from nucleotide sequences using fairly up-to-date maximum likelihood methods implemented in freely available computer programs. While the analysis of chloroplast sequences from various Vanilla species is used as an illustrative example, the techniques covered here are relevant to the comparative analysis of homologous sequences datasets sampled from any group of organisms.

Mots-clés Agrovoc : organisme, phylogénie, évolution, séquence nucléotidique, adn, méthodologie, génie génétique, biologie moléculaire, chloroplaste, étude de cas, Vanilla planifolia, statistiques, bioinformatique

Mots-clés géographiques Agrovoc : La Réunion, France

Mots-clés complémentaires : Séquencage

Classification Agris : F70 - Taxonomie végétale et phytogéographie
U10 - Informatique, mathématiques et statistiques
F30 - Génétique et amélioration des plantes

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

• De Bruyn Alexandre, CIRAD-BIOS-UMR PVBMT (REU)
• Martin Darren Patrick, Institute of Infectious Diseases and Molecular Medicine (ZAF)
• Lefeuvre Pierre, CIRAD-BIOS-UMR PVBMT (REU) ORCID: 0000-0003-2645-8098

Source : Cirad - Agritrop (https://agritrop.cirad.fr/572399/)

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