Nodes, Branches, and Phylogenetic Definitions
نویسندگان
چکیده
منابع مشابه
Nodes, branches, and phylogenetic definitions.
Adopting the perspective of graph theory, Martin et al. (2010) described two kinds of phylogenetic trees, which they termed node-based and stem-or branch-based, that differ with respect to the biological interpretations of their component nodes and branches. After establishing equivalency between the two different kinds of trees in terms of encoded information regarding taxa and their phylogene...
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A general rationale for the formulation and placement of taxonomic definitions in phylogenetic taxonomy is proposed, and commonly used terms such as "crown taxon" or "node-based definition" are more precisely defined. In the formulation of phylogenetic definitions, nested reference taxa stabilize taxonomic content. A definitional configuration termed a node-stem triplet also stabilizes the rela...
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Three main codes currently govern biological nomenclature: (i) The International Code of Botanical Nomenclature (ICBN), (ii) The International Code of Zoological Nomenclature (ICZN), and (iii) The International Code of Nomenclature of Bacteria (ICNB). Recently, the PhyloCode – a code based on phylogenetic nomenclature, has been presented as an alternative. To facilitate a comparison between the...
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In molecular systematics, evolutionary trees are reconstructed from sequences at the tips under simple models of site substitution. A central question is how much sequence data is required to reconstruct a tree accurately? The answer depends on the lengths of the branches (edges) of the tree, with very short and very long edges requiring long sequences for accurate tree inference, particularly ...
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Long-branch attraction is a well-known source of systematic error that can mislead phylogenetic methods; it is frequently invoked post hoc, upon recovering a different tree from the one expected based on prior evidence. We demonstrate that methods that do not force the data onto a single tree, such as spectral analysis, Neighbor-Net, and consensus networks, can be used to detect conflicting sig...
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ژورنال
عنوان ژورنال: Systematic Biology
سال: 2013
ISSN: 1076-836X,1063-5157
DOI: 10.1093/sysbio/syt027