Until recently, molecular phylogenies based on a single or few orthologous genes often
yielded contradictory results. Using multiple genes in a large concatenation was proposed to …

The recent discovery of RNA viruses in diverse unicellular eukaryotes and developments in
evolutionary genomics have provided the means for addressing the origin of eukaryotic RNA …

In phylogenomics the analysis of concatenated gene alignments, the so-called supermatrix,
is commonly accompanied by the assumption of partition models. Under such models each …

The use of probabilistic models of amino acid replacement is essential for the study of
protein evolution, and programs like ProtTest implement different strategies to identify the …

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML
versions used a fast algorithm performing nearest neighbor interchanges to improve a …

Despite recent advances achieved by application of high-performance computing methods
and novel algorithmic techniques to maximum likelihood (ML)-based inference programs …

Proportional and separate models able to apply different combination of substitution rate
matrix (SRM) and among‐site rate variation model (ASRVM) to each locus are frequently …

Plants produce a wide range of allelochemicals to defend against herbivore attack, and
generalist herbivores have evolved mechanisms to avoid, sequester, or detoxify a broad …

Tunicates or urochordates (appendicularians, salps and sea squirts), cephalochordates
(lancelets) and vertebrates (including lamprey and hagfish) constitute the three extant …

When modern humans left Africa ca. 60,000 years ago (60 kya), they were already infected
with Helicobacter pylori, and these bacteria have subsequently diversified in parallel with …