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Concatabominations: identifying unstable taxa in morphological phylogenetics using a heuristic extension to safe taxonomic reduction.

Siu-Ting K, Pisani D, Creevey CJ, Wilkinson M - Syst. Biol. (2014)

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, National University of Ireland, Maynooth, Co. Kildare, Ireland; School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK; Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK; and Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Aberystwyth SY23 3FG, UK Department of Biology, National University of Ireland, Maynooth, Co. Kildare, Ireland; School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK; Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK; and Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Aberystwyth SY23 3FG, UK Department of Biology, National University of Ireland, Maynooth, Co. Kildare, Ireland; School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK; Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK; and Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Aberystwyth SY23 3FG, UK agalychnica@gmail.com.

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Perhaps less controversial is that individual taxa may sometimes be relatively phylogenetically unstable by virtue of limited data and extensive missing data (e.g., ; ; ; ). developed an approach for diagnosing taxon instability due to missing data a priori termed safe taxonomic reduction (STR)... STR allows the identification of “rogue” taxa that can be removed from a data set safe in the knowledge that their removal will not impact upon the interrelationships that will be inferred among the remaining taxa under the parsimony criterion... The potential benefits of such deletion are reductions in numbers of optimal trees and run times and better resolved consensus summaries... In such cases there may be many pairs of leaves with p-distances of zero but, because of the distribution of missing entries, the character states of neither are a proper subset of those of the other (category D, Fig. 1). called such pairs of leaves “potential taxonomic equivalents that are asymmetric both ways” (we will call them pairs) and recognized that, in contrast to the other categories of taxonomic equivalence, the deletion of either member of the pair cannot be guaranteed to be safe a priori... We also define, for each leaf, ABC as the number of taxonomic equivalents of that leaf in the STR categories, , or (each of which identifies scope for a priori safe deletion)... Note however that this improvement of the strict consensus can be obtained through the deletion of just Hulsanpes and Saurornitholestes... Although deletions of Liliensternus and/or, Procompsognathus are both safe and reduce the number of MPTs they are not effective at increasing the resolution of the corresponding strict consensus... The two leaves with the highest * (Hulsanpes and Sauronitholestes) scores are also identified by traditional STR as taxa that can be safely deleted... Deletion of Hulsanpes alone reduces the number of MPTs for the remaining data to 45,654 without affecting tree length but does not improve (increase the number of splits in) the corresponding strict consensus... Whereas STR identifies two additional taxa (Procompsognathus and Liliensternus) that can also be safely deleted, ranking based on * scores prompts the experimental deletion of Coelurus... As already noted, the deletion of Procompsognathus and Liliensternus reduces the number of MPTs (to 197) but does not further improve the strict consensus... One undoubted attraction of STR is that a taxon is deleted a priori only if we are certain that this deletion cannot impact upon the relationships inferred among the remaining taxa... In any particular case there may be useful safe taxon deletions that are not identified a priori using STR... As highly connected, potentially unstable, taxa are deleted any changes in the degree of the remaining vertices and of their relative rankings will be apparent... Natural stopping points for experimental deletion are when formerly connected clusters of taxa completely separate or when connected taxa cannot be safely deleted or their safe deletion does not improve the consensus.

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Taxonomic equivalents inferred from the concatabominations pipeline visualized in a network with all taxa (a) and with the successive deletions of Hulsanpes (Hul) (b), Saurornitholestes (Sas) (c) and Coelurus (Coe) (d). Vertices represent taxa and the edges represent a taxonomic equivalence relation existing between the taxa they connect. Vertex size is scaled to represent the number of taxonomic equivalents a taxon has, where the bigger the vertex the more equivalences it has, hence more unstable (see scale at the bottom of figure). Types of equivalences found between taxa are represented by dashed lines (types C and E) and solid lines (type D). For a complete list of abbreviations used for the taxa names refer to Table 1.
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Figure 4: Taxonomic equivalents inferred from the concatabominations pipeline visualized in a network with all taxa (a) and with the successive deletions of Hulsanpes (Hul) (b), Saurornitholestes (Sas) (c) and Coelurus (Coe) (d). Vertices represent taxa and the edges represent a taxonomic equivalence relation existing between the taxa they connect. Vertex size is scaled to represent the number of taxonomic equivalents a taxon has, where the bigger the vertex the more equivalences it has, hence more unstable (see scale at the bottom of figure). Types of equivalences found between taxa are represented by dashed lines (types C and E) and solid lines (type D). For a complete list of abbreviations used for the taxa names refer to Table 1.

Mentions: Table 1 shows the data obtained from the concatabominations pipeline and Figure 4a provides a graphical representation of the same in Cytoscape with vertices representing leaves and edges connecting pairs that are either (i) taxonomic equivalents in categories , , or (which support safe deletion rules) or (ii) concatabominations that do not increase the pairwise incompatibility of the data. The two leaves with the highest * (Hulsanpes and Sauronitholestes) scores are also identified by traditional STR as taxa that can be safely deleted. Deletion of Hulsanpes alone reduces the number of MPTs for the remaining data to 45,654 without affecting tree length but does not improve (increase the number of splits in) the corresponding strict consensus. The further deletion of Saurornitholestes further reduces the number of MPTs to 2758 and is sufficient to produce all the increased resolution of the consensus (from three to five splits) that can be achieved using traditional STR alone.


Concatabominations: identifying unstable taxa in morphological phylogenetics using a heuristic extension to safe taxonomic reduction.

Siu-Ting K, Pisani D, Creevey CJ, Wilkinson M - Syst. Biol. (2014)

Taxonomic equivalents inferred from the concatabominations pipeline visualized in a network with all taxa (a) and with the successive deletions of Hulsanpes (Hul) (b), Saurornitholestes (Sas) (c) and Coelurus (Coe) (d). Vertices represent taxa and the edges represent a taxonomic equivalence relation existing between the taxa they connect. Vertex size is scaled to represent the number of taxonomic equivalents a taxon has, where the bigger the vertex the more equivalences it has, hence more unstable (see scale at the bottom of figure). Types of equivalences found between taxa are represented by dashed lines (types C and E) and solid lines (type D). For a complete list of abbreviations used for the taxa names refer to Table 1.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4265141&req=5

Figure 4: Taxonomic equivalents inferred from the concatabominations pipeline visualized in a network with all taxa (a) and with the successive deletions of Hulsanpes (Hul) (b), Saurornitholestes (Sas) (c) and Coelurus (Coe) (d). Vertices represent taxa and the edges represent a taxonomic equivalence relation existing between the taxa they connect. Vertex size is scaled to represent the number of taxonomic equivalents a taxon has, where the bigger the vertex the more equivalences it has, hence more unstable (see scale at the bottom of figure). Types of equivalences found between taxa are represented by dashed lines (types C and E) and solid lines (type D). For a complete list of abbreviations used for the taxa names refer to Table 1.
Mentions: Table 1 shows the data obtained from the concatabominations pipeline and Figure 4a provides a graphical representation of the same in Cytoscape with vertices representing leaves and edges connecting pairs that are either (i) taxonomic equivalents in categories , , or (which support safe deletion rules) or (ii) concatabominations that do not increase the pairwise incompatibility of the data. The two leaves with the highest * (Hulsanpes and Sauronitholestes) scores are also identified by traditional STR as taxa that can be safely deleted. Deletion of Hulsanpes alone reduces the number of MPTs for the remaining data to 45,654 without affecting tree length but does not improve (increase the number of splits in) the corresponding strict consensus. The further deletion of Saurornitholestes further reduces the number of MPTs to 2758 and is sufficient to produce all the increased resolution of the consensus (from three to five splits) that can be achieved using traditional STR alone.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, National University of Ireland, Maynooth, Co. Kildare, Ireland; School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK; Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK; and Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Aberystwyth SY23 3FG, UK Department of Biology, National University of Ireland, Maynooth, Co. Kildare, Ireland; School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK; Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK; and Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Aberystwyth SY23 3FG, UK Department of Biology, National University of Ireland, Maynooth, Co. Kildare, Ireland; School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK; Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK; and Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Aberystwyth SY23 3FG, UK agalychnica@gmail.com.

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

Perhaps less controversial is that individual taxa may sometimes be relatively phylogenetically unstable by virtue of limited data and extensive missing data (e.g., ; ; ; ). developed an approach for diagnosing taxon instability due to missing data a priori termed safe taxonomic reduction (STR)... STR allows the identification of “rogue” taxa that can be removed from a data set safe in the knowledge that their removal will not impact upon the interrelationships that will be inferred among the remaining taxa under the parsimony criterion... The potential benefits of such deletion are reductions in numbers of optimal trees and run times and better resolved consensus summaries... In such cases there may be many pairs of leaves with p-distances of zero but, because of the distribution of missing entries, the character states of neither are a proper subset of those of the other (category D, Fig. 1). called such pairs of leaves “potential taxonomic equivalents that are asymmetric both ways” (we will call them pairs) and recognized that, in contrast to the other categories of taxonomic equivalence, the deletion of either member of the pair cannot be guaranteed to be safe a priori... We also define, for each leaf, ABC as the number of taxonomic equivalents of that leaf in the STR categories, , or (each of which identifies scope for a priori safe deletion)... Note however that this improvement of the strict consensus can be obtained through the deletion of just Hulsanpes and Saurornitholestes... Although deletions of Liliensternus and/or, Procompsognathus are both safe and reduce the number of MPTs they are not effective at increasing the resolution of the corresponding strict consensus... The two leaves with the highest * (Hulsanpes and Sauronitholestes) scores are also identified by traditional STR as taxa that can be safely deleted... Deletion of Hulsanpes alone reduces the number of MPTs for the remaining data to 45,654 without affecting tree length but does not improve (increase the number of splits in) the corresponding strict consensus... Whereas STR identifies two additional taxa (Procompsognathus and Liliensternus) that can also be safely deleted, ranking based on * scores prompts the experimental deletion of Coelurus... As already noted, the deletion of Procompsognathus and Liliensternus reduces the number of MPTs (to 197) but does not further improve the strict consensus... One undoubted attraction of STR is that a taxon is deleted a priori only if we are certain that this deletion cannot impact upon the relationships inferred among the remaining taxa... In any particular case there may be useful safe taxon deletions that are not identified a priori using STR... As highly connected, potentially unstable, taxa are deleted any changes in the degree of the remaining vertices and of their relative rankings will be apparent... Natural stopping points for experimental deletion are when formerly connected clusters of taxa completely separate or when connected taxa cannot be safely deleted or their safe deletion does not improve the consensus.

Show MeSH
Related in: MedlinePlus