Phylogeny articles from across Nature Portfolio

Genomic epidemiology studies have indicated southern Africa as likely sources of emergence of six Omicron lineages since November 2021. Here, the authors trace the geographic origins and dispersion patterns of these six lineages and highlight Gauteng province in South Africa as likely to have played a key role.

Microbial maximum growth rates vary widely across species, and their measurement is challenging, especially for uncultivated organisms. Here, Xu, Zakem & Weissman present Phydon, a framework for genome-based maximum growth rate prediction that combines codon statistics and phylogenetic information to enhance the precision of the estimates.

Non-invasive lineage tracing in humans relies on rare somatic mutations, which have limited throughput and temporal resolution. We developed a computational method, ‘MethylTree’, which uses epimutations on DNA methylation to accurately infer lineages across cell types, developmental stages and species, providing a superior alternative for non-invasive lineage tracing in humans and other organisms.

Metastatic dynamics are revealed by integrating single-cell lineage tracing and RNA sequencing.