Tree Balance

Shao, Kwang‐Tsao; Sokal, Robert R.

doi:10.2307/2992186

Cited by 144 publications

(236 citation statements)

References 0 publications

Supporting

Mentioning

234

Contrasting

Unclassified

Order By: Relevance

“…Equation (2.6) is a measure of tree imbalance, i.e. the degree to which subtrees are divided in groups of unequal size [47]. Here, the average path length is lower bounded by d min ¼ 121/N.…”

Section: Adaptive Radiations and Tree Imbalancementioning

confidence: 99%

“…Such asymmetric growth seems to be characteristic of evolution in living systems, where adaptive radiations and strong differences between clades are known to exist [46]. In order to measure this asymmetry, we use standard measures of tree imbalance [47,48]. Tree imbalance measures allows the study of how species diversity is arranged through different branches.…”

Section: Adaptive Radiations and Tree Imbalancementioning

confidence: 99%

See 1 more Smart Citation

Punctuated equilibrium in the large-scale evolution of programming languages

Valverde

Solé

2015

J. R. Soc. Interface.

View full text Add to dashboard Cite

The analogies and differences between biological and cultural evolution have been explored by evolutionary biologists, historians, engineers and linguists alike. Two well-known domains of cultural change are language and technology. Both share some traits relating the evolution of species, but technological change is very difficult to study. A major challenge in our way towards a scientific theory of technological evolution is how to properly define evolutionary trees or clades and how to weight the role played by horizontal transfer of information. Here, we study the large-scale historical development of programming languages, which have deeply marked social and technological advances in the last half century. We analyse their historical connections using network theory and reconstructed phylogenetic networks. Using both data analysis and network modelling, it is shown that their evolution is highly uneven, marked by innovation events where new languages are created out of improved combinations of different structural components belonging to previous languages. These radiation events occur in a bursty pattern and are tied to novel technological and social niches. The method can be extrapolated to other systems and consistently captures the major classes of languages and the widespread horizontal design exchanges, revealing a punctuated evolutionary path.

show abstract

Section: Adaptive Radiations and Tree Imbalancementioning

confidence: 99%

Section: Adaptive Radiations and Tree Imbalancementioning

confidence: 99%

Punctuated equilibrium in the large-scale evolution of programming languages

Valverde

Solé

2015

J. R. Soc. Interface.

View full text Add to dashboard Cite

show abstract

“…In fact, S(T ) for a rooted tree T is an equivalent to Sackin's index S ind (T ) used to measure the tree balance (Sackin, 1972;Shao and Sokal, 1990). Particularly, for a tree T ∈ R B n we have S(T ) = S ind (T ) + n. We use a strong result (Theorem 8) given by Blum et al (2006).…”

Section: Distances Of Random Treesmentioning

confidence: 99%

On a matching distance between rooted phylogenetic trees

Bogdanowicz¹,

Giaro²

2013

International Journal of Applied Mathematics and Computer Science

View full text Add to dashboard Cite

The Robinson-Foulds (RF) distance is the most popular method of evaluating the dissimilarity between phylogenetic trees. In this paper, we define and explore in detail properties of the Matching Cluster (MC) distance, which can be regarded as a refinement of the RF metric for rooted trees. Similarly to RF, MC operates on clusters of compared trees, but the distance evaluation is more complex. Using the graph theoretic approach based on a minimum-weight perfect matching in bipartite graphs, the values of similarity between clusters are transformed to the final MC-score of the dissimilarity of trees. The analyzed properties give insight into the structure of the metric space generated by MC, its relations with the Matching Split (MS) distance of unrooted trees and asymptotic behavior of the expected distance between binary n-leaf trees selected uniformly in both MC and MS (Θ(n 3/2 )).

show abstract

“…For our purposes here, we considered two axes of tree shape: imbalance and stemminess. 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

View full text Add to dashboard Cite

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.

show abstract

Tree Balance

Cited by 144 publications

References 0 publications

Punctuated equilibrium in the large-scale evolution of programming languages

Punctuated equilibrium in the large-scale evolution of programming languages

On a matching distance between rooted phylogenetic trees

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

Contact Info

Product

Resources

About