This is the opening paper in the special issue of Fungal Diversity, which collates the data on
defining species. Defining and recognizing species has long been a controversial issue …

Genome-scale data and the development of novel statistical phylogenetic approaches have
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …

Phylogenomic studies have resolved countless branches of the tree of life, but remain
strongly contradictory on certain, contentious relationships. Here, we use a maximum …

There can be no doubt that early land plant evolution transformed the planet but, until
recently, how and when this was achieved was unclear. Coincidence in the first appearance …

Background Phylogenetic and population genetic studies often deal with multiple sequence
alignments that require manipulation or processing steps such as sequence concatenation …

Background The quality of multiple sequence alignments plays an important role in the
accuracy of phylogenetic inference. It has been shown that removing ambiguously aligned …

Background Next-generation sequencing has provided a wealth of plastid genome
sequence data from an increasingly diverse set of green plants (Viridiplantae). Although …

To tackle incongruence, the topological conflict between different gene trees, phylogenomic
studies couple concatenation with practices such as rogue taxon removal or the use of …

In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are
two extremes of a continuum. Despite their dominance in phylogenetic inference, it is …

Although population genomic studies using next generation sequencing (NGS) data are
becoming increasingly common, studies focusing on phylogenetic inference using these …