Substitution models of evolution describe the process of genetic variation through fixed
mutations and constitute the basis of the evolutionary analysis at the molecular level. Almost …

Efficient algorithms and programs for the analysis of the ever-growing amount of biological
sequence data are strongly needed in the genomics era. The pace at which new data and …

Despite the rapid increase of size in phylogenomic data sets, a number of important nodes
on animal phylogeny are still unresolved. Among these, the rooting of the placental mammal …

Most eukaryotic genes undergo alternative splicing (AS), but the overall functional
significance of this process remains a controversial issue. It has been noticed that the …

Positive selection is widely estimated from protein coding sequence alignments by the
nonsynonymous-to-synonymous ratio ω. Increasingly elaborate codon models are used in a …

Gene duplications are an important factor in plant evolution, and lineage-specific expanded
(LSE) genes are of particular interest. Receptor-like kinases expanded massively in land …

Recombination is a fundamental process with significant impacts on genome evolution.
Predicted consequences of the loss of recombination include a reduced effectiveness of …

The spread of maternally inherited microorganisms, such as Wolbachia bacteria, can induce
indirect selective sweeps on host mitochondria, to which they are linked within the …

The nearly neutral theory of molecular evolution predicts that small populations should
accumulate deleterious mutations at a faster rate than large populations. The analysis of …

Phylogenetic analysis is an increasingly common and valuable component of plant science.
Knowledge of the phylogenetic relationships between plant groups is a prerequisite for …