Factors Determining the Accuracy of Cladogram Estimation: Evaluation Using Computer Simulation

Fiala, Kent L.; Sokal, Robert R.

doi:10.1111/j.1558-5646.1985.tb00398.x

Cited by 81 publications

(70 citation statements)

References 18 publications

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“…One explanation for the contrasting resolution observed in the metazoan and fungal trees may be differences in ''stemminess: (32): a measure of the relative length of internal versus external branches. Theoretical work indicates that the accuracy of reconstruction is higher for trees exhibiting high stemminess (that is, trees with longer internodes and shorter terminal branches) (32). In agreement with these studies, phylogenetic resolution is higher in the fungal tree, which is characterized by long internodes (Fiala and Sokal's stemminess index F 0 0.201), and poorer in the metazoan clade, where internodes are much shorter (F 0 0.121) (15).…”

Section: Animal Evolution and The Molecular Signature Of Radiations Csupporting

confidence: 69%

Animal Evolution and the Molecular Signature of Radiations Compressed in Time

Rokas

Krüger

Carroll

2005

Science

353

192

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model or whether there are other mechanisms for producing such echoes. Possible mechanisms are wind-driven atmospheric waves excited by topographic features and various types of wavelike structures in the ionosphere driven by interactions with the solar wind.Conclusion. The MARSIS ionospheric soundings have shown that the ionosphere of Mars is in good agreement with the expectations of Chapman's 1931 photoequilibrium theory for the origin of planetary ionospheres. The soundings have also revealed a number of unexpected features. These include echoes that reoccur at the electron cyclotron period, large variations in the absorption apparently caused by energetic solar events, oblique echoes caused by ionospheric structures associated with the crustal magnetic fields of Mars, diffuse echoes apparently caused by scattering from ionospheric irregularities, and ionospheric holes. Because the subsurface soundings must occur at frequencies well above the maximum electron plasma frequency in the ionosphere and under conditions of low ionospheric absorption, these measurements have already proved to be quite useful for planning subsurface sounding operations. The electron cyclotron echoes also provide a new method of measuring the local magnetic field strength, which is useful because Mars Express does not have a magnetometer. Animal Evolution and the Molecular Signature of Radiations Compressed in TimeAntonis Rokas,* Dirk Krüger,. Sean B. Carroll-The phylogenetic relationships among most metazoan phyla remain uncertain.We obtained large numbers of gene sequences from metazoans, including key understudied taxa. Despite the amount of data and breadth of taxa analyzed, relationships among most metazoan phyla remained unresolved. In contrast, the same genes robustly resolved phylogenetic relationships within a major clade of Fungi of approximately the same age as the Metazoa. The differences in resolution within the two kingdoms suggest that the early history of metazoans was a radiation compressed in time, a finding that is in agreement with paleontological inferences. Furthermore, simulation analyses as well as studies of other radiations in deep time indicate that, given adequate sequence data, the lack of resolution in phylogenetic trees is a signature of closely spaced series of cladogenetic events.Detailed knowledge of the phylogenetic relationships among Metazoa and their eukaryotic relatives is critical for understanding the history of life and the evolution of molecules, phenotypes, and developmental mechanisms.Currently, with the exception of the well-resolved phylogenetic history of the deuterostomes (1), the relationships between and within protostome and diploblastic metazoan phyla remain unresolved (2-5). The uncertainty surrounding metazoan relationships may result from analytical and biological factors such as insufficient amounts of available sequence data, mutational saturation, the occurrence of unequal rates of evolution between lineages, or the rapidity with which metazoan phyla diversified (3-7). Recen...

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Section: Animal Evolution and The Molecular Signature Of Radiations Csupporting

confidence: 69%

Animal Evolution and the Molecular Signature of Radiations Compressed in Time

Rokas

Krüger

Carroll

2005

Science

353

192

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“…But several studies also furnish some information about the factors influencing accuracy. Fiala and Sokal (1985) and Lynch (1989) focused on the various factors contributing to the accuracy of a given method-rather than just finding the best method. Rohlfand Wooten (1988) compared the restricted maximum-likelihood, MP, and UPGMA (applied to a variety of genetic distance coefficients).…”

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confidence: 99%

“…There is also an extensive series of papers by Nei and his associates (e.g., Nei et al, 1983;Tateno et al, 1982;Saitou and Nei, 1987), which we review in the discussion section below. The current study is a direct outgrowth ofthe work ofFiala and Sokal (1985). We investigate two factors related to the topology of phylogenetic trees: noncumulative stemminess and tree imbalance (lack of symmetry).…”

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confidence: 99%

Accuracy of Estimated Phylogenies: Effects of Tree Topology and Evolutionary Model

et al. 1990

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A simulation study was carried out to investigate the relative importance of tree topology (both balance and stemminess), evolutionary rates (constant, varying among characters, and varying among lineages), and evolutionary models in determining the accuracy with which phylogenetic trees can be estimated. The three evolutionary context models were phyletic (characters can change at each simulated time step), speciational (changes are possible only at the time of speciation into two daughter lineages), and punctuational (changes occur at the time of speciation but only in one of the daughter lineages). UPGMA clustering and maximum parsimony (“Wagner trees”) methods for estimating phylogenies were compared. All trees were based on eight recent OTUs. The three evolutionary context models were found to have the largest influence on accuracy of estimates by both methods. The next most important effect was that of the stemminess × context interaction. Maximum parsimony and UPGMA performed worst under the punctuational models. Under the phyletic model, trees with high stemminess values could be estimated more accurately and balanced trees were slightly easier to estimate than unbalanced ones. Overall, maximum parsimony yielded more accurate trees than UPGMA—but that was expected for these simulations since many more characters than OTUs were used. Our results suggest that the great majority of estimated phylogenetic trees are likely to be quite inaccurate; they underscore the inappropriateness of characterizing current phylogenetic methods as being for reconstruction rather than for estimation.

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“…Imbalance expresses the variation in the number of lineages between sister taxa (Shao and Sokal 1990). Stemminess captures the relative difference in internodal distances between divergences toward the tips of a phylogenetic tree and those toward its root (Fiala andSokal 1985, Mooers andHeard 1997): Trees with longer branches toward the root are ''stemmy,'' whereas trees with longer branches toward the tips are ''tippy. ''…”

Section: Trait Distributions and Phylogenetic Topologymentioning

confidence: 99%

Using phylogenetic trees to test for character displacement: a model and an example from a desert mammal community

Davies

Cooper

Diniz‐Filho

et al. 2012

Ecology

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Abstract. The distribution of traits within communities is thought to provide information on the evolutionary and ecological forces that structure community composition. Ecological character displacement (evolutionary divergence among populations of interacting species within a community), as well as community-wide character displacement (even dispersion of species traits within a community via species sorting), have been widely reported and are typically interpreted as evidence for interspecific competition. However, defining an appropriate null distribution with which to assess the observed distribution of traits within a community has proved controversial. Phylogenetic methods provide an alternative approach to evaluating community structure, but such methods also require an appropriate null and have typically overlooked the potential for evolutionary dynamics within communities. Here, we present a novel phylogenetic framework that uses evolutionary expectations to generate a simple null model of the expected distribution of traits among co-occurring species. Using a stochastic Brownian motion model of trait change, we illustrate that the expected communitywide dispersion of traits varies with phylogenetic tree shape. We then use data on body mass for mammals to evaluate the accuracy with which phylogeny can predict the empirical distribution of traits and find a strong correlation between predicted and observed trait distributions. We suggest that deviations from phylogenetic expectations may therefore provide a useful tool for evaluating the role of competition in shaping community structure. Finally, we demonstrate the utility of our approach using empirical data on body mass and a phylogeny for a small community of terrestrial mammals in Yotvata, Israel, and reveal evidence consistent with ecological and community-wide character displacement. Our method unites ecological and evolutionary approaches, and it provides a novel framework for exploring community structure.

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Factors Determining the Accuracy of Cladogram Estimation: Evaluation Using Computer Simulation

Cited by 81 publications

References 18 publications

Animal Evolution and the Molecular Signature of Radiations Compressed in Time

Animal Evolution and the Molecular Signature of Radiations Compressed in Time

Accuracy of Estimated Phylogenies: Effects of Tree Topology and Evolutionary Model

Using phylogenetic trees to test for character displacement: a model and an example from a desert mammal community

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