Alignment quality may have as much impact on phylogenetic reconstruction as the
phylogenetic methods used. Not only the alignment algorithm, but also the method used to …

I have addressed the biological rather than bioinformatics aspects of molecular sequence
alignment by covering a series of topics that have been under-valued, particularly within the …

As whole-genome sequence assemblies accumulate, a challenge is to determine how these
can be used to address fundamental evolutionary questions, such as inferring the process of …

Amazonia is famous for high biodiversity, and the highlands of the transition zone between
the Andes and the lowlands of the Amazon basin show particularly high species diversity …

We use a multigene data set (the mitochondrial locus and nine nuclear gene regions) to test
phylogenetic relationships in the South American “lava lizards”(genus Microlophus) and …

Aim The strawberry poison frog, Oophaga pumilio, has undergone a remarkable radiation of
colour morphs in the Bocas del Toro archipelago in Panama. This species shows extreme …

Insertions and deletions (indels) cause numerous genetic diseases and lead to pronounced
evolutionary differences among genomes. The macaque sequences provide an opportunity …

North American trapdoor spiders of the subfamily Euctenizinae (Cyrtaucheniidae) are
among the most diverse mygalomorph spiders (trapdoor spiders, tarantulas, and their …

Aligning multiple nucleotide sequences is a prerequisite for many if not most comparative
sequence analyses in evolutionary biology. These alignments are often recognized as …

The mygalomorph spider genera Antrodiaetus and Atypoides (Antrodiaetidae) belong to an
ancient lineage that has persisted since at least the Cretaceous. These spiders display a …