In order to predict how populations will evolve in the future, we need to know how they are evolving right now. The rapid advance of genetic sequencing technology is creating the potential to do this on an unprecedented scale, but we need to figure out what sequences we need and how to interpret them. Doing so will require new analytical tools that ask questions that are only now becoming answerable.

Papers:

• Raghuram et al (2024), Average Nucleotide Identity based Staphylococcus aureus strain grouping allows identification of strain-specific genes in the pangenome
• Mehta et al (2023), Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes—please try it out on other species and let us know what you think!
• Ghafari et al (2022), Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern
• Ghafari et al (2020), Inferring transmission bottleneck size from viral sequence data using a novel haplotype reconstruction method
• Sobel Leonard et al (2017), Transmission Bottleneck Size Estimation from Pathogen Deep-Sequencing Data, with an Application to Human Influenza A Virus, and see correction. Try it out!
• Weissman and Hallatschek (2017), Minimal-assumption inference from population-genomic data—please try it out and let us know what you think!