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 Šeho, 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.

The hidden complexity of Mendelian traits across yeast natural populations

The hidden complexity of Mendelian traits across yeast natural populations

Jing Hou, Anastasie Sigwalt, David Pflieger, Jackson Peter, Jacky de Montigny, Maitreya Dunham, Joseph Schacherer

annotatr: Associating genomic regions with genomic annotations

annotatr: Associating genomic regions with genomic annotations

Raymond G Cavalcante, Maureen A Sartor

The infinitesimal model

The infinitesimal model

Nick H Barton, Alison M Etheridge, Amandine Véber

Genome-wide histone modification patterns in Kluyveromyces Lactis reveal evolutionary adaptation of a heterochromatin-associated mark

Genome-wide histone modification patterns in Kluyveromyces Lactis reveal evolutionary adaptation of a heterochromatin-associated mark

Angela Bean, Assaf Weiner, Amanda Hughes, Eyal Itskovits, Nir Friedman, Oliver Rando

A tradeoff between the ecological and evolutionary stabilities of public goods genes in microbial populations

A tradeoff between the ecological and evolutionary stabilities of public goods genes in microbial populations

Joseph Rauch, Jané Kondev, Alvaro Sanchez

Maximum likelihood estimates of pairwise rearrangement distances

Maximum likelihood estimates of pairwise rearrangement distances
Stuart Serdoz, Attila Egri-Nagy, Jeremy Sumner, Barbara R. Holland, Peter Jarvis, Mark M. Tanaka, Andrew R. Francis

Accurate estimation of evolutionary distances between taxa is important for many phylogenetic reconstruction methods. Specifically, in the case of bacteria, distances can be estimated using a range of different evolutionary models, from single nucleotide polymorphisms to large-scale genome rearrangements. Most such methods use the minimal distance as a proxy for true distance, and only occasionally are improvements such as a Jukes-Cantor correction (for SNP models) available to improve this underestimate. In particular, for genome rearrangement models such as inversion, there is currently no way to correct for such underestimates. Here we introduce a maximum likelihood estimator for the inversion distance between a pair of genomes, using the group-theoretic approach to modelling inversions introduced recently. This MLE functions as a corrected distance in its ability to correct for multiple changes. In particular, we show that because of the way sequences of inversions interact with each other, it is quite possible for minimal distance and MLE distance to differently order the distances of two genomes from a third. This has an obvious implication for the use of minimal distance in phylogeny reconstruction.