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iteRates: An R Package for Implementing a Parametric Rate Comparison on Phylogenetic Trees.

Fordyce JA, Shah P, Fitzpatrick BM - Evol. Bioinform. Online (2014)

Bottom Line: Patterns of diversification rate variation detected in phylogenetic hypotheses are frequently used to infer historical, ecological, and evolutionary processes.The parametric rate comparison (PRC) is a method for detecting rate variation in trees that models branch lengths as random variables drawn from familiar statistical distributions. iteRates is a library of functions for the R statistical computing environment for implementing PRC on phylogenetic trees.Here, we describe some of the functions in iteRates for subtree identification, tree manipulation, applying the PRC and K-clades PRC analyses, and conducting a whole-tree randomization test.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA. ; National Institute for Mathematical and Biological Synthesis, Knoxville, TN, USA.

ABSTRACT
Patterns of diversification rate variation detected in phylogenetic hypotheses are frequently used to infer historical, ecological, and evolutionary processes. The parametric rate comparison (PRC) is a method for detecting rate variation in trees that models branch lengths as random variables drawn from familiar statistical distributions. iteRates is a library of functions for the R statistical computing environment for implementing PRC on phylogenetic trees. Here, we describe some of the functions in iteRates for subtree identification, tree manipulation, applying the PRC and K-clades PRC analyses, and conducting a whole-tree randomization test.

No MeSH data available.


Related in: MedlinePlus

A phylogenetic tree showing regions of rate variation identified by the function comp.subs using the function color.tree.plot.Notes: The colored circles range from hot (red) indicating a relative rate increase to cold (blue) indicating a relative rate decrease. The size of each of the colored circles is scaled to the statistical support for a rate shift at that branch.
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f1-ebo-10-2014-127: A phylogenetic tree showing regions of rate variation identified by the function comp.subs using the function color.tree.plot.Notes: The colored circles range from hot (red) indicating a relative rate increase to cold (blue) indicating a relative rate decrease. The size of each of the colored circles is scaled to the statistical support for a rate shift at that branch.

Mentions: Here, we present the R library iteRates, which implements the parametric rate comparison (PRC) test,13 a new method and approach for identifying rate variation in phylogenetic trees. An in-depth description of the PRC, as well as an examination of its statistical power and false positive rates, can be found in the study by Shah et al.13 Briefly, the PRC examines the fit of a distribution of branch lengths extracted from a phylogenetic tree to standard statistical distributions.14 The lengths of terminal branches are treated as censored at the time of sampling. Internal branch lengths and terminal branch lengths are jointly modeled using the censored form of a given distribution. This approach differs from other approaches aimed at identifying rate heterogeneity in a phylogenetic tree in that it does not attempt to estimate the parameters of a particular model of diversification, rather it simply examines the statistical properties of the distribution of branch lengths. By iterating through subtrees in a tree, the PRC can be used to identify subclades where diversification rate differs from the remainder of the tree (see Fig. 1 in Shah et al.13). The PRC can also be used to compare a priori defined groups, and does not require that these groups be monophyletic. The PRC can be used both as a hypothesis testing tool and for exploratory data analysis using functions in iteRates library.


iteRates: An R Package for Implementing a Parametric Rate Comparison on Phylogenetic Trees.

Fordyce JA, Shah P, Fitzpatrick BM - Evol. Bioinform. Online (2014)

A phylogenetic tree showing regions of rate variation identified by the function comp.subs using the function color.tree.plot.Notes: The colored circles range from hot (red) indicating a relative rate increase to cold (blue) indicating a relative rate decrease. The size of each of the colored circles is scaled to the statistical support for a rate shift at that branch.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4125422&req=5

f1-ebo-10-2014-127: A phylogenetic tree showing regions of rate variation identified by the function comp.subs using the function color.tree.plot.Notes: The colored circles range from hot (red) indicating a relative rate increase to cold (blue) indicating a relative rate decrease. The size of each of the colored circles is scaled to the statistical support for a rate shift at that branch.
Mentions: Here, we present the R library iteRates, which implements the parametric rate comparison (PRC) test,13 a new method and approach for identifying rate variation in phylogenetic trees. An in-depth description of the PRC, as well as an examination of its statistical power and false positive rates, can be found in the study by Shah et al.13 Briefly, the PRC examines the fit of a distribution of branch lengths extracted from a phylogenetic tree to standard statistical distributions.14 The lengths of terminal branches are treated as censored at the time of sampling. Internal branch lengths and terminal branch lengths are jointly modeled using the censored form of a given distribution. This approach differs from other approaches aimed at identifying rate heterogeneity in a phylogenetic tree in that it does not attempt to estimate the parameters of a particular model of diversification, rather it simply examines the statistical properties of the distribution of branch lengths. By iterating through subtrees in a tree, the PRC can be used to identify subclades where diversification rate differs from the remainder of the tree (see Fig. 1 in Shah et al.13). The PRC can also be used to compare a priori defined groups, and does not require that these groups be monophyletic. The PRC can be used both as a hypothesis testing tool and for exploratory data analysis using functions in iteRates library.

Bottom Line: Patterns of diversification rate variation detected in phylogenetic hypotheses are frequently used to infer historical, ecological, and evolutionary processes.The parametric rate comparison (PRC) is a method for detecting rate variation in trees that models branch lengths as random variables drawn from familiar statistical distributions. iteRates is a library of functions for the R statistical computing environment for implementing PRC on phylogenetic trees.Here, we describe some of the functions in iteRates for subtree identification, tree manipulation, applying the PRC and K-clades PRC analyses, and conducting a whole-tree randomization test.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA. ; National Institute for Mathematical and Biological Synthesis, Knoxville, TN, USA.

ABSTRACT
Patterns of diversification rate variation detected in phylogenetic hypotheses are frequently used to infer historical, ecological, and evolutionary processes. The parametric rate comparison (PRC) is a method for detecting rate variation in trees that models branch lengths as random variables drawn from familiar statistical distributions. iteRates is a library of functions for the R statistical computing environment for implementing PRC on phylogenetic trees. Here, we describe some of the functions in iteRates for subtree identification, tree manipulation, applying the PRC and K-clades PRC analyses, and conducting a whole-tree randomization test.

No MeSH data available.


Related in: MedlinePlus