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 …

Knowing phylogenetic relationships among species is fundamental for many studies in
biology. An accurate phylogenetic tree underpins our understanding of the major transitions …

Background To leverage the potential of multi-omics studies, exploratory data analysis
methods that provide systematic integration and comparison of multiple layers of omics …

Determining the phylogenetic origin of mitochondria is key to understanding the ancestral
mitochondrial symbiosis and its role in eukaryogenesis. However, the precise evolutionary …

We present Procrustean Approach to Cophylogeny (PACo), a novel statistical tool to test for
congruence between phylogenetic trees, or between phylogenetic distance matrices of …

Phylogenomic subsampling is a procedure by which small sets of loci are selected from
large genome-scale data sets and used for phylogenetic inference. This step is often …

Stramenopiles or heterokonts constitute one of the most speciose and diverse clades of
protists. It includes ecologically important algae (such as diatoms or large multicellular …

The large phylogenetic distance separating eukaryotic genes and their archaeal orthologs
has prevented identification of the position of the eukaryotic root in phylogenomic studies …

Phylogenomic analyses of long sequences, consisting of many genes and genomic
segments, reconstruct organismal relationships with high statistical confidence. But, inferred …

ABSTRACT Building the Tree of Life (ToL) is a major challenge of modern biology, requiring
advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that …