variancePartition: Interpreting drivers of variation in complex gene expression studies

variancePartition: Interpreting drivers of variation in complex gene expression studies

Gabriel E Hoffman, Eric E Schadt

Macroevolutionary trade-offs in plant-feeding insects

Macroevolutionary trade-offs in plant-feeding insects

Daniel Peterson, Nate B. Hardy, Benjamin B. Normark

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform

Po-E Li, Chien-Chi Lo, Joseph J. Anderson, Karen W. Davenport, Kimberly A. Bishop-Lilly, Yan Xu, Sanaa Ahmed, Shihai Feng, Vishwesh P. Mokashi, Patrick S. G. Chain

DNA Methylation profiles of diverse Brachypodium distachyon aligns with underlying genetic diversity

DNA Methylation profiles of diverse Brachypodium distachyon aligns with underlying genetic diversity

Steven R Eichten, Tim Stuart, Akanksha Srivastava, Ryan Lister, Justin O Borevitz

Assessing the relationship between height growth and molecular genetic variation in Douglas-fir (Pseudotsuga menziesii) provenances

Charalambos Neophytou, Anna-Maria Weisser, Daniel Landwehr, Muhidin Ĺ eho, Ulrich Kohnle, Ingo Ensminger, Henning Wildhagen

MetaPalette: A K-mer painting approach for metagenomic taxonomic profiling and quantification of novel strain variation

MetaPalette: A K-mer painting approach for metagenomic taxonomic profiling and quantification of novel strain variation

David Koslicki, Daniel Falush

A simple, general result for the variance of substitution number in molecular evolution

A simple, general result for the variance of substitution number in molecular evolution
Bahram Houchmandzadeh, Marcel Vallade
(Submitted on 16 Feb 2016)

The number of substitutions (of nucleotides, amino acids, …) that take place during the evolution of a sequence is a stochastic variable of fundamental importance in the field of molecular evolution. Although the mean number of substitutions during molecular evolution of a sequence can be estimated for a given substitution model, no simple solution exists for the variance of this random variable. We show in this article that the computation of the variance is as simple as that of the mean number of substitutions for both short and long times. Apart from its fundamental importance, this result can be used to investigate the dispersion index R , i.e. the ratio of the variance to the mean substitution number, which is of prime importance in the neutral theory of molecular evolution. By investigating large classes of substitution models, we demonstrate that although R\ge1 , to obtain R significantly larger than unity necessitates in general additional hypotheses on the structure of the substitution model.