期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 35, 期 9, 页码 2327-2333出版社
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msy118
关键词
statistical confidence; phylogenetic trees; bootstrap; rogue taxa
资金
- Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES) [1668367]
- Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (Brazilian Education Ministry)
- Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq) [308387/2015-5]
- Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (Brazilian Science, Tecnology and Communications Ministry)
Most phylogenetic tree-generating programs produce a fully dichotomous phylogenetic tree. However, as different markers may produce distinct topologies for the same set of organisms, topological tests are used to estimate the statistical reliability of the clades. In this protocol, we provide step-by-step instructions on how to perform the widely used bootstrap test using MEGA. However, a single unstable lineage, also known as a rogue lineage, may decrease the bootstrap proportions in many branches of the tree. This occurs because rogue taxa tend to bounce between clades from one pseudo-replicate to the next, lowering bootstrap proportions for many correct Glades. Thus, it is important to identify and exclude rogue taxa before initiating a final phylogenetic analysis; here, we provide this protocol using the RogueNaRok platform.
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