The molecular chaperone DnaK accelerates protein evolution

The molecular chaperone DnaK accelerates protein evolution

Jose Aguilar-Rodriguez, Beatriz Sabater-Munoz, Victor Berlanga, David Alvarez-Ponce, Andreas Wagner, Mario A. Fares

Explaining Missing Heritability Using Gaussian Process Regression

Explaining Missing Heritability Using Gaussian Process Regression

Kevin Sharp, Wim Wiegerinck, Alejandro Arias-Vasquez, Barbara Franke, Jonathan Marchini, Cornelis A Albers, Hilbert J Kappen

Experimental evolution of modern Escherichia coli harboring an ancient Elongation Factor gene

Experimental evolution of modern Escherichia coli harboring an ancient Elongation Factor gene

Betul Kacar, Lily I Tran, Xueliang Ge, Suparna Sanyal, Eric A. Gaucher

Analytical results for directional and quadratic selection gradients for log-linear models of fitness functions

Analytical results for directional and quadratic selection gradients for log-linear models of fitness functions

Michael Morrissey, Ian B. J. Goudie

Genome-culture coevolution promotes rapid divergence in the killer whale

Genome-culture coevolution promotes rapid divergence in the killer whale

Andrew Foote, Nagarjun Vijay, Maria Avila-Arcos, Robin Baird, John Durban, Phillip Morin, Matteo Fumagalli, Richard Gibbs, Bradley Hanson, Thorfinn Korneliussen, Michael Martin, Kelly Robertson, Vitor Sousa, Filipe Vieira, Tomas Vinar, Paul Wade, Kim Worley, Laurent Excoffier, Thomas Gilbert, Jochen Wolf

BuddySuite: Command-line toolkits for manipulating sequences, alignments, and phylogenetic trees

BuddySuite: Command-line toolkits for manipulating sequences, alignments, and phylogenetic trees

Stephen R Bond, Karl E Keat, Andreas D Baxevanis

Family-joining: A fast distance-based method for constructing generally labeled trees

Family-joining: A fast distance-based method for constructing generally labeled trees
Prabhav Kalaghatgi, Nico Pfeifer, Thomas Lengauer

The widely used model for evolutionary relationships is a bifurcating tree with all taxa/observations placed at the leaves. This is not appropriate for taxa that have been densely sampled across evolutionary time and may be in a direct ancestral relationship. In this paper, we present a fast distance-based agglomeration method called family-joining (FJ) for constructing so-called generally labeled trees in which taxa may be placed at internal vertices and the tree may contain polytomies. FJ constructs such trees on the basis of pairwise distances and a distance threshold. We tested two methods for threshold selection, FJ-BIC and FJ-CV, which minimize BIC and CV error, respectively. When compared with related methods on simulated data, FJ-BIC was among the best at reconstructing the correct tree across a wide range of simulation scenarios. FJ-BIC was applied to HIV sequences sampled from individuals involved in a known transmission chain. The FJ-BIC tree was found to be compatible with almost all transmission events. On average, internal branches in the FJ-BIC tree have higher bootstrap support than branches in the leaf-labeled bifurcating tree constructed using RAxML. 36% and 25% of the internal branches in the FJ-BIC tree and RAxML tree, respectively, have bootstrap support greater than 70%. To the best of our knowledge the method presented here is the first attempt at modeling the evolutionary relationships of densely sampled pathogens using generally labeled trees.