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Title:

Peer Review #2 of "Fast and accurate estimation of the covariance between pairwise maximum likelihood distances (v0.1)"

Publisher:

PeerJ

Year of Publication:

2014

Document Type:

Text

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doi:10.7717/peerj.583

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Title:

Preface

Description:

May they live long and prosper.

May they live long and prosper. Minimize

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The Pennsylvania State University CiteSeerX Archives

Year of Publication:

2008-07-01

Source:

http://edoc.ub.uni-muenchen.de/3992/1/Klaere_Steffen.pdf

http://edoc.ub.uni-muenchen.de/3992/1/Klaere_Steffen.pdf Minimize

Document Type:

text

Language:

en

Subjects:

Zusammenfassung

Zusammenfassung Minimize

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Metadata may be used without restrictions as long as the oai identifier remains attached to it.

Metadata may be used without restrictions as long as the oai identifier remains attached to it. Minimize

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Title:

Phylogenetic Diversity on Split Networks

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In biodiversity conservation, one is interested in selecting a subset of taxa for preservation priority. Phylogenetic diversity (PD) provides a quantitative measure for taxon selection on phylogenetic trees. In particular, PD is the total length of the minimal subtree induced by the selected taxa. Recently, it has been shown that on trees the ma...

In biodiversity conservation, one is interested in selecting a subset of taxa for preservation priority. Phylogenetic diversity (PD) provides a quantitative measure for taxon selection on phylogenetic trees. In particular, PD is the total length of the minimal subtree induced by the selected taxa. Recently, it has been shown that on trees the maximal PD score and the corresponding subset of taxa can be computed by a greedy algorithm. However, if evolution is not treelike and networks are a more appropriate illustration of phylogenetic relationships, then the greedy strategy no longer works. Here, we will extend the notion of PD to phylogenetic networks. To this end, we suggest a dynamic programming algorithm (PD-NET) which guarantees the computation of optimal PD scores and PD sets for circular networks, a commonly encountered category of networks. PD-NET has polynomial time complexity. Finally we apply PD-NET to biological data and compare the resulting PD sets to the selection of taxa derived from a tree. The outcome indicates that it is advisable to include also non-treelike effects when dealing with conservation questions. Minimize

Contributors:

The Pennsylvania State University CiteSeerX Archives

Year of Publication:

2011-06-20

Source:

http://www.newton.cam.ac.uk/preprints/NI07090.pdf

http://www.newton.cam.ac.uk/preprints/NI07090.pdf Minimize

Document Type:

text

Language:

en

Subjects:

phylogenetic diversity ; dynamic programming ; phylogenetic network

phylogenetic diversity ; dynamic programming ; phylogenetic network Minimize

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Metadata may be used without restrictions as long as the oai identifier remains attached to it.

Metadata may be used without restrictions as long as the oai identifier remains attached to it. Minimize

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Title:

Phylogenetic diversity within seconds

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Abstract.—We consider a (phylogenetic) tree with n labeled leaves, the taxa, and a length for each branch in the tree. For any subset of k taxa, the phylogenetic diversity is defined as the sum of the branch-lengths of the minimal subtree connecting the taxa in the subset. We introduce two time-efficient algorithms (greedy and pruning) to comput...

Abstract.—We consider a (phylogenetic) tree with n labeled leaves, the taxa, and a length for each branch in the tree. For any subset of k taxa, the phylogenetic diversity is defined as the sum of the branch-lengths of the minimal subtree connecting the taxa in the subset. We introduce two time-efficient algorithms (greedy and pruning) to compute a subset of size k with maximal phylogenetic diversity in O(«log/c) and O[n + (n- k) login- k)] time, respectively. The greedy algorithm is an efficient implementation of the so-called greedy strategy (Steel, 2005; Pardi and Goldman, 2005), whereas the pruning algorithm provides an alternative description of the same problem. Both algorithms compute within seconds a subtree with maximal phylogenetic diversity for trees with 100,000 taxa or more. [Biodiversity conservation; Comparative genomics; Greedy algorithm; Phylogenetic diversity; Phylogenetic tree; Pruning algorithm.] Minimize

Contributors:

The Pennsylvania State University CiteSeerX Archives

Year of Publication:

2013-08-18

Source:

http://sysbio.oxfordjournals.org/content/55/5/769.full.pdf

http://sysbio.oxfordjournals.org/content/55/5/769.full.pdf Minimize

Document Type:

text

Language:

en

Subjects:

Recently ; Steel (2005) and Pardi and Goldman (2005

Recently ; Steel (2005) and Pardi and Goldman (2005 Minimize

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Metadata may be used without restrictions as long as the oai identifier remains attached to it.

Metadata may be used without restrictions as long as the oai identifier remains attached to it. Minimize

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Title:

Stochastic Models of Molecular Evolution

Publisher:

Ludwig-Maximilians-Universität München

Year of Publication:

2005-07-08

Document Type:

Dissertation ; NonPeerReviewed

Subjects:

Fakultät für Mathematik ; Informatik und Statistik

Fakultät für Mathematik ; Informatik und Statistik Minimize

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http://edoc.ub.uni-muenchen.de/3992/

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Title:

Extinction in a branching process: why some of the fittest strategies cannot guarantee survival

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Abstract Biological fitness is typically measured by the expected rate of reproduction, but strategies with high fitness can also have high probabilities of extinction. Likewise, gambling strategies with a high expected payoff can also have a high risk of ruin. We take inspiration from the gambler’s ruin problem to examine how extinction is rela...

Abstract Biological fitness is typically measured by the expected rate of reproduction, but strategies with high fitness can also have high probabilities of extinction. Likewise, gambling strategies with a high expected payoff can also have a high risk of ruin. We take inspiration from the gambler’s ruin problem to examine how extinction is related to population growth. Using moment theory we demonstrate how higher moments can impact the probability of extinction and how the first few moments can be used to find bounds on the extinction probability, focusing on s -convex ordering of random variables. This approach generates “best case” and “worst case” scenarios to provide upper and lower bounds on the probability of extinction. MSC Codes 92D15, 60J80, 60E15 Minimize

Publisher:

BioMed Central Ltd.

Year of Publication:

2014-06-16

Document Type:

Research

Language:

en

Subjects:

Extinction ; Branching process ; S-convex

Extinction ; Branching process ; S-convex Minimize

Rights:

Copyright 2014 Sawaya and Klaere; licensee Springer.

Copyright 2014 Sawaya and Klaere; licensee Springer. Minimize

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Title:

An algebraic analysis of the two state Markov model on tripod trees

Description:

Methods of phylogenetic inference use more and more complex models to generate trees from data. However, even simple models and their implications are not fully understood. Here, we investigate the two-state Markov model on a tripod tree, inferring conditions under which a given set of observations gives rise to such a model. This type of invest...

Methods of phylogenetic inference use more and more complex models to generate trees from data. However, even simple models and their implications are not fully understood. Here, we investigate the two-state Markov model on a tripod tree, inferring conditions under which a given set of observations gives rise to such a model. This type of investigation has been undertaken before by several scientists from different fields of research. In contrast to other work we fully analyse the model, presenting conditions under which one can infer a model from the observation or at least get support for the tree-shaped interdependence of the leaves considered. We also present all conditions under which the results can be extended from tripod trees to quartet trees, a step necessary to reconstruct at least a topology. Apart from finding conditions under which such an extension works we discuss example cases for which such an extension does not work. ; Comment: 32 pages, four figures Minimize

Year of Publication:

2010-11-30

Document Type:

text

Subjects:

Quantitative Biology - Populations and Evolution ; Mathematics - Algebraic Geometry

Quantitative Biology - Populations and Evolution ; Mathematics - Algebraic Geometry Minimize

DDC:

519 Probabilities & applied mathematics *(computed)*

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Title:

Extinction in a branching process: Why some of the fittest strategies cannot guarantee survival

Description:

The fitness of a biological strategy is typically measured by its expected reproductive rate, the first moment of its offspring distribution. However, strategies with high expected rates can also have high probabilities of extinction. A similar situation is found in gambling and investment, where strategies with a high expected payoff can also h...

The fitness of a biological strategy is typically measured by its expected reproductive rate, the first moment of its offspring distribution. However, strategies with high expected rates can also have high probabilities of extinction. A similar situation is found in gambling and investment, where strategies with a high expected payoff can also have a high risk of ruin. We take inspiration from the gambler's ruin problem to examine how extinction is related to population growth. Using moment theory we demonstrate how higher moments can impact the probability of extinction. We discuss how moments can be used to find bounds on the extinction probability, focusing on s-convex ordering of random variables, a method developed in actuarial science. This approach generates "best case" and "worst case" scenarios to provide upper and lower bounds on the probability of extinction. Our results demonstrate that even the most fit strategies can have high probabilities of extinction. ; Comment: Best case extrema added Minimize

Year of Publication:

2012-09-10

Document Type:

text

Subjects:

Quantitative Biology - Populations and Evolution ; Statistics - Applications

Quantitative Biology - Populations and Evolution ; Statistics - Applications Minimize

DDC:

519 Probabilities & applied mathematics *(computed)*

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Title:

The link between segregation and phylogenetic diversity

Description:

We derive an invertible transform linking two widely used measures of species diversity: phylogenetic diversity and the expected proportions of segregating (non-constant) sites. We assume a bi-allelic, symmetric, finite site model of substitution. Like the Hadamard transform of Hendy and Penny, the transform can be expressed completely independe...

We derive an invertible transform linking two widely used measures of species diversity: phylogenetic diversity and the expected proportions of segregating (non-constant) sites. We assume a bi-allelic, symmetric, finite site model of substitution. Like the Hadamard transform of Hendy and Penny, the transform can be expressed completely independent of the underlying phylogeny. Our results bridge work on diversity from two quite distinct scientific communities. ; Comment: 14 pages, 1 figure, 12 references Minimize

Year of Publication:

2010-08-26

Document Type:

text

Subjects:

Quantitative Biology - Populations and Evolution ; Mathematics - Probability

Quantitative Biology - Populations and Evolution ; Mathematics - Probability Minimize

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Title:

The impact of single substitutions on multiple sequence alignments

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We introduce another view of sequence evolution. Contrary to other approaches, we model the substitution process in two steps. First we assume (arbitrary) scaled branch lengths on a given phylogenetic tree. Second we allocate a Poisson distributed number of substitutions on the branches. The probability to place a mutation on a branch is proport...

We introduce another view of sequence evolution. Contrary to other approaches, we model the substitution process in two steps. First we assume (arbitrary) scaled branch lengths on a given phylogenetic tree. Second we allocate a Poisson distributed number of substitutions on the branches. The probability to place a mutation on a branch is proportional to its relative branch length. More importantly, the action of a single mutation on an alignment column is described by a doubly stochastic matrix, the so-called one-step mutation matrix. This matrix leads to analytical formulae for the posterior probability distribution of the number of substitutions for an alignment column. Minimize

Publisher:

The Royal Society

Year of Publication:

2008-10-07

Document Type:

Text

Language:

en

Subjects:

Research Article

Research Article Minimize

Rights:

© 2008 The Royal Society

© 2008 The Royal Society Minimize

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