Distributions of Tree Comparison Metrics-Some New Results

Steel, Mike; Penny, David

doi:10.2307/2992536

Cited by 136 publications

(150 citation statements)

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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%

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

Nyakatura

Bininda-Emonds²

2012

BMC Biology

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Background: Although 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.

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Section: Resultsmentioning

confidence: 99%

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

Nyakatura

Bininda-Emonds²

2012

BMC Biology

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“…Table 2 lists the relative similarity of different topologies as measured by the normalised partition metric [55,56] and 'explicitly agree' triplets. It indicates that both the application of the source tree selection protocol of Bininda-Emonds et al [32] and the inclusion of more recent source trees are important in explaining the differences between our updated supertree topology and the original LEA supertree.…”

Section: Resultsmentioning

confidence: 99%

“…We used the normalised partition metric (also known as the Robinson-Foulds topological distance [55,56]) and 'explicitly agree' triplets to quantify the topological differences between: 1) the full supertree (Figure 1), 2) the subsidiary analysis of the LEA references alone, using the 4:1 weighting scheme (Figure 2), 3) the subsidiary analysis, using 1:1 equal weighting (topology not shown), 4) the original LEA combined supertree, 5) the topology of Murphy et al ([17]; their Figure 1; this is the taxonomically most comprehensive molecular phylogeny of placental mammals currently available), and 6) the combined molecular and morphological topology of Gatesy et al ([11]; their Figure 4). The normalised partition metric scores were calculated using the perl script partitionMetric, whilst the 'explicitly agree' triplet scores were calculated using COMPONENT [74]; for both metrics, trees pruned to have identical taxon sets for each pairwise comparison.…”

Section: Methodsmentioning

confidence: 99%

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et al. 2006

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Background:The higher-level phylogeny of placental mammals has long been a phylogenetic Gordian knot, with disagreement about both the precise contents of, and relationships between, the extant orders. A recent MRP supertree that favoured 'outdated' hypotheses (notably, monophyly of both Artiodactyla and Lipotyphla) has been heavily criticised for including low-quality and redundant data. We apply a stringent data selection protocol designed to minimise these problems to a much-expanded data set of morphological, molecular and combined source trees, to produce a supertree that includes every family of extant placental mammals.

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“…To compare the estimated topologies with the input trees, we used the quartet distance metric (Day 1986;Steel & Penny 1993), as implemented in the program QUARTETDIST (Christiansen et al 2006). This calculates the number of different combinations of four taxa (languages) in both trees and is normalized by dividing by the total number of quartets for the tree.…”

Section: Methodsmentioning

confidence: 99%

Does horizontal transmission invalidate cultural phylogenies?

2009

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Phylogenetic methods have recently been applied to studies of cultural evolution. However, it has been claimed that the large amount of horizontal transmission that sometimes occurs between cultural groups invalidates the use of these methods. Here, we use a natural model of linguistic evolution to simulate borrowing between languages. The results show that tree topologies constructed with Bayesian phylogenetic methods are robust to realistic levels of borrowing. Inferences about divergence dates are slightly less robust and show a tendency to underestimate dates. Our results demonstrate that realistic levels of reticulation between cultures do not invalidate a phylogenetic approach to cultural and linguistic evolution.

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Distributions of Tree Comparison Metrics-Some New Results

Cited by 136 publications

References 0 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

Untitled

Does horizontal transmission invalidate cultural phylogenies?

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