Distributions of Tree Comparison Metrics--Some New Results

Steel, Mike; Penny, David

doi:10.1093/sysbio/42.2.126

Cited by 194 publications

(216 citation statements)

References 16 publications

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“…Comparison of the supertree topology with the supertree obtained only from the molecular gene trees reveals a difference of only 1.1% (with 229 species in common) as measured by a normalized partition metric [79,80] (Table 3; Additional file 3). This stands in sharp contrast to the value of 43.7% (for 265 species) in comparison to the supertree derived from the literature trees only.…”

Section: Resultsmentioning

confidence: 99%

“…Differences were quantified by the normalized partition metric [79,80]. Number of shared taxa and partition metric values appear above and below the diagonal, respectively.…”

Section: Resultsmentioning

confidence: 99%

“…The remaining supertrees and supermatrix tree (Additional file 3) are instead only compared generally to the main supertree, highlighting key areas of disagreement. Differences between all pairs of trees (pruned to the same taxon set as needed) were quantified using a normalized partition metric [79,80] as implemented in the Perl script partitionMetric v1.2.2. The first supertree and associated data matrix can be downloaded from TreeBASE at http://purl.org/phylo/treebase/phylows/study/TB2:S11954; dated versions of the supertree are also available in Additional file 5; all remaining trees are available in Additional file 3.…”

Section: Methodsmentioning

confidence: 99%

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Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

2012

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BackgroundAlthough it has proven to be an important foundation for investigations of carnivoran ecology, biology and evolution, the complete species-level supertree for Carnivora of Bininda-Emonds et al. is showing its age. Additional, largely molecular sequence data are now available for many species and the advancement of computer technology means that many of the limitations of the original analysis can now be avoided. We therefore sought to provide an updated estimate of the phylogenetic relationships within all extant Carnivora, again using supertree analysis to be able to analyze as much of the global phylogenetic database for the group as possible.ResultsIn total, 188 source trees were combined, representing 114 trees from the literature together with 74 newly constructed gene trees derived from nearly 45,000 bp of sequence data from GenBank. The greater availability of sequence data means that the new supertree is almost completely resolved and also better reflects current phylogenetic opinion (for example, supporting a monophyletic Mephitidae, Eupleridae and Prionodontidae; placing Nandinia binotata as sister to the remaining Feliformia). Following an initial rapid radiation, diversification rate analyses indicate a downturn in the net speciation rate within the past three million years as well as a possible increase some 18.0 million years ago; numerous diversification rate shifts within the order were also identified.ConclusionsTogether, the two carnivore supertrees remain the only complete phylogenetic estimates for all extant species and the new supertree, like the old one, will form a key tool in helping us to further understand the biology of this charismatic group of carnivores.

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Section: Resultsmentioning

confidence: 99%

“…Differences were quantified by the normalized partition metric [79,80]. Number of shared taxa and partition metric values appear above and below the diagonal, respectively.…”

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

2012

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“…S1b) but not in the three nuclear gene trees. Thus, to quantitatively examine the impact of each locus to the concatenated gene tree, we compared the similarity of the concatenated gene tree with the gene tree of each locus by calculating Robinson-Foulds (RF) distance (Steel and Penny, 1993) using package Phangorn (Schliep, 2011) in the statistical program R (R Development Core Team, 2012). These results indicate that the concatenated gene tree is most similar to the cyt-b gene tree (RF distance = 16; Appendix Fig.…”

Section: Phylogenetic Inferencementioning

confidence: 99%

Assessing species boundaries and the phylogenetic position of the rare Szechwan ratsnake, Euprepiophis perlaceus (Serpentes: Colubridae), using coalescent-based methods

Jiang

Guo

Huang

et al. 2014

Molecular Phylogenetics and Evolution

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“…One could perform a similar analysis for the path distance metric of Steel and Penny (1993), although we have not done so.…”

Section: Proof Of Theorem 32mentioning

confidence: 99%

Polyhedral Geometry of Phylogenetic Rogue Taxa

Cueto

Matsen

2010

Bull Math Biol

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It is well known among phylogeneticists that adding an extra taxon (e.g. species) to a data set can alter the structure of the optimal phylogenetic tree in surprising ways. However, little is known about this "rogue taxon" effect. In this paper we characterize the behavior of balanced minimum evolution (BME) phylogenetics on data sets of this type using tools from polyhedral geometry. First we show that for any distance matrix there exist distances to a "rogue taxon" such that the BME-optimal tree for the data set with the new taxon does not contain any nontrivial splits (bipartitions) of the optimal tree for the original data. Second, we prove a theorem which restricts the topology of BME-optimal trees for data sets of this type, thus showing that a rogue taxon cannot have an arbitrary effect on the optimal tree. Third, we computationally construct polyhedral cones that give complete answers for BME rogue taxon behavior when our original data fits a tree on four, five, and six taxa. We use these cones to derive sufficient conditions for rogue taxon behavior for four taxa, and to understand the frequency of the rogue taxon effect via simulation.

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Distributions of Tree Comparison Metrics--Some New Results

Cited by 194 publications

References 16 publications

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

Assessing species boundaries and the phylogenetic position of the rare Szechwan ratsnake, Euprepiophis perlaceus (Serpentes: Colubridae), using coalescent-based methods

Polyhedral Geometry of Phylogenetic Rogue Taxa

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