Divergence without difference: phylogenetics and taxonomy ofChlamydiaresolved

Reticulation, divergence, and the phylogeography-phylogenetics continuum.

Phylogeography, and its extensions into comparative phylogeography, have their roots in the layering of gene trees across geography, a paradigm that was greatly facilitated by the nonrecombining, fast evolution provided by animal mtDNA. As phylogeography moves into the era of next-generation sequencing, the specter of reticulation at several levels-within loci and genomes in the form of recombi...

Genetypes: a concept to help integrate molecular phylogenetics and taxonomy

In order to better integrate molecular phylogenetics and taxonomy, genetic sequences from type materials should be explicitly identified in publications using a consistent nomenclature. Despite relatively frequent sampling of sequences from types (particularly topotypes—samples from the type locality), the practice of explicitly noting that these materials were sampled is uncommon. Because of t...

Molecular Phylogenetics and Taxonomy of the Subgenus Pika (ochotona, Lagomorpha)

A phylogenetic analysis based on partial sequences of 2 mitochondrial genes (cytochrome b and cytochrome c oxidase subunit I) confirmed that Ochotona alpina (Pallas, 1773) and O. turuchanensis Naumov, 1934, are sister taxa to all other Palearctic species of the subgenus Pika. O. hyperborea (Pallas, 1811) contains sufficient genetic heterogeneity to define 2 or 3 races within this species. Exami...

Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation

The use of fossil evidence to calibrate divergence time estimation has a long history. More recently, Bayesian Markov chain Monte Carlo has become the dominant method of divergence time estimation, and fossil evidence has been reinterpreted as the specification of prior distributions on the divergence times of calibration nodes. These so-called "soft calibrations" have become widely used but th...

Evolution without divergence.