OSF-Builder: A New Tool for Constructing and Representing Evolutionary Histories Involving Introgression.

Introgression is an evolutionary process which provides an important source of innovation for evolution. Although various methods have been used to detect introgression, very few methods are currently available for constructing evolutionary histories involving introgression. In this article, we propose a new method for constructing such evolutionary histories whose starting point is a species forest (consisting of a collection of lineage trees, usually arising as a collection of clades or monophyletic groups in a species tree), and a gene tree for a specific allele of interest, or allele tree for short.

PSIKO2: a fast and versatile tool to infer population stratification on various levels in GWAS.

Unlabelled: Genome-wide association studies are an invaluable tool for identifying genotypic loci linked with agriculturally important traits or certain diseases. The signal on which such studies rely upon can, however, be obscured by population stratification making it necessary to account for it in some way. Population stratification is dependent on when admixture happened and thus can occur at various levels.

A novel and fast approach for population structure inference using kernel-PCA and optimization.

Population structure is a confounding factor in genome-wide association studies, increasing the rate of false positive associations. To correct for it, several model-based algorithms such as ADMIXTURE and STRUCTURE have been proposed. These tend to suffer from the fact that they have a considerable computational burden, limiting their applicability when used with large datasets, such as those produced by next generation sequencing techniques.

Lassoing and corralling rooted phylogenetic trees.

The construction of a dendogram on a set of individuals is a key component of a genomewide association study. However, even with modern sequencing technologies the distances on the individuals required for the construction of such a structure may not always be reliable making it tempting to exclude them from an analysis. This, in turn, results in an input set for dendogram construction that consists of only partial distance information, which raises the following fundamental question.

ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R.

Unlabelled: Reflecting its continuously increasing versatility and functionality, the popularity of the ape (analysis of phylogenetics and evolution) software package has grown steadily over the years. Among its features, it has a strong distance-based component allowing the user to compute distances from aligned DNA sequences based on most methods from the literature and also build phylogenetic trees from them. However, even data generated with modern genomic approaches can fail to give rise to sufficiently reliable distance estimates.