Dataset Information

Sound Colless-like balance indices for multifurcating trees.

ABSTRACT: The Colless index is one of the most popular and natural balance indices for bifurcating phylogenetic trees, but it makes no sense for multifurcating trees. In this paper we propose a family of Colless-like balance indices [Formula: see text] that generalize the Colless index to multifurcating phylogenetic trees. Each [Formula: see text] is determined by the choice of a dissimilarity D and a weight function [Formula: see text]. A balance index is sound when the most balanced phylogenetic trees according to it are exactly the fully symmetric ones. Unfortunately, not every Colless-like balance index is sound in this sense. We prove then that taking f(n) = ln(n + e) or f(n) = en as weight functions, the resulting index [Formula: see text] is sound for every dissimilarity D. Next, for each one of these two functions f and for three popular dissimilarities D (the variance, the standard deviation, and the mean deviation from the median), we find the most unbalanced phylogenetic trees according to [Formula: see text] with any given number n of leaves. The results show that the growth pace of the function f influences the notion of "balance" measured by the indices it defines. Finally, we introduce our R package "CollessLike," which, among other functionalities, allows the computation of Colless-like indices of trees and their comparison to their distribution under Chen-Ford-Winkel's ?-?-model for multifurcating phylogenetic trees. As an application, we show that the trees in TreeBASE do not seem to follow either the uniform model for multifurcating trees or the ?-?-model, for any values of ? and ?.

SUBMITTER: Mir A

PROVIDER: S-EPMC6155497 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Sound Colless-like balance indices for multifurcating trees.

Mir Arnau A Rotger Lucía L Rosselló Francesc F

PloS one 20180925 9

The Colless index is one of the most popular and natural balance indices for bifurcating phylogenetic trees, but it makes no sense for multifurcating trees. In this paper we propose a family of Colless-like balance indices [Formula: see text] that generalize the Colless index to multifurcating phylogenetic trees. Each [Formula: see text] is determined by the choice of a dissimilarity D and a weight function [Formula: see text]. A balance index is sound when the most balanced phylogenetic trees a ...[more]

PMID: 30252858

Similar Datasets

Project description:For trees in tropical forests, competition for light is thought to be a central process that offers opportunities for niche differentiation through light gradient partitioning. In previous studies, a canopy index based on three-dimensional canopy census data has been shown to be a good predictor of species-specific demographic rates across the entire tree community on Barro Colorado Island, Panama, and has allowed quantifying between-species variation in light response. However, almost all other forest census plots lack data on the canopy structure. Hence, this study aims at assessing whether position-based neighborhood competition indices can replace information from canopy census data and produce similar estimates of the interspecific variation of light responses. We used inventory data from the census plot at Barro Colorado Island and calculated neighborhood competition indices with varying relative effects of the size and distance of neighboring trees. Among these indices, we selected the one that was most strongly correlated with the canopy index. We then compared outcomes of hierarchical Bayesian models for species-specific recruitment and growth rates including either the canopy index or the selected neighborhood competition index as predictor. Mean posterior estimates of light response parameters were highly correlated between models (r>0.85) and indicated that most species regenerate and grow better in higher light. Both light estimation approaches consistently found that the interspecific variation of light response was larger for recruitment than for growth rates. However, the classification of species into different groups of light response, e.g. weaker than linear (decelerating) vs. stronger than linear (accelerating) differed between approaches. These results imply that while the classification into light response groups might be biased when using neighborhood competition indices, they may be useful for determining species rankings and between-species variation of light response and therefore enable large comparative studies between different forest census plots.

Project description:BackgroundClinicians are routinely required to make decisions about fall risk among lower limb prosthesis (LLP) users. These decisions can be guided by standardized clinical balance tests but require population- and test-specific cutoff scores and validity indices to categorize individuals as probable fallers or nonfallers on the basis of test performance. Despite the importance of cutoff scores and validity indices to clinical interpretation of clinical balance test scores, they are rarely reported for LLP users. In their absence, clinicians cannot use results from clinical balance tests to assess the likelihood of a fall by any one patient.ObjectiveDerive cutoff scores, and associated validity indices, for clinical balance tests administered to established unilateral LLP users.DesignCross-sectional study.SettingOutpatient clinic and research laboratory.ParticipantsEstablished ambulatory unilateral transtibial and transfemoral prosthesis users (n?=?40).InterventionNot applicable.Main outcome measure(s)Optimal cutoff scores and related validity indices (ie, area under the curve, sensitivity, specificity, likelihood ratios) were computed for five balance tests, the activities-specific balance confidence scale (ABC), timed up and go (TUG), four square step test (FSST), Berg balance scale (BBS), and narrowing-beam walking test (NBWT).ResultsCutoff scores were identified for the NBWT (?.43/1.0), TUG (?8.17?seconds], FSST (?8.49 seconds), BBS (?50.5/56), and ABC (?80.2/100). Validity indices (ie, area under the curve, sensitivity, specificity, and likelihood ratios) for the NBWT, TUG, and FSST had greater diagnostic accuracy and provided more information about the probability of a fall than those for the BBS or ABC.ConclusionPerformance above or below identified cutoff scores for the NBWT, FSST, and TUG provides information about potentially important shifts in the probability of falling among established unilateral LLP users. These results can serve as initial benchmarks to reduce uncertainty surrounding fall risk assessment in established unilateral LLP users but require future prospective evaluation.Level of evidenceIII.

Dataset Information

Sound Colless-like balance indices for multifurcating trees.

Publications

Sound Colless-like balance indices for multifurcating trees.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure