Phylogenomics articles from across Nature Portfolio

Phylogenetic trees from whole-genome sequencing datasets with the pipeline Sequoia are reconstructed to define the evolutionary history of clonally expanding cells and to clarify how somatic mutations shape normal cell behavior.

Highly pathogenic avian influenza virus subtype H5 is an important pathogen of wild birds and poultry that has also caused infection in humans and other mammals. Here the authors use wild bird movement tracking data and virus genome sequences to quantify how seasonal bird migration facilitates global dispersal of the virus.

Heeren et al study the evolutionary genomics of leishmaniasis in Peru and Bolivia to show that parasite hybridization increases the prevalence, diversity and spread of viruses that have been previously associated with disease severity and treatment failure.

A genomic epidemiology approach describes the population structure of Salmonella monophasic Typhimurium ST34 from Vietnam, and identifies Southeast Asia as a potential hub for the emergence and international spread of multidrug resistant Salm. ST34.

A recent study uncovered the geographical origins of the Black Death pandemic, offering a new perspective on the phylogenetic polytomy that served as a foundation for the expansion of Yersinia pestis across Eurasia and North Africa more than 600 years ago.

Two new studies report the assembled genomes of the Australian lungfish (Neoceratodus forsteri) and the African lungfish (Protopterus annectens), which provide insights into the water-to-land transition.

A study in Molecular Biology and Evolution reports de novo genome sequences for 17 bumblebee species spanning all 15 subgenera. This valuable resource should provide a deeper biological understanding of these commercially and ecologically important pollinators.

Improvements to the Genome Taxonomy Database provide a complete bacterial and archaeal taxonomy.