Erick Matsen
Examples today:
Felsenstein, J. (1985). Phylogenies and the Comparative Method. The American Naturalist, 125(1), 1–15. [PDF]
Trait measurement is old-school. I am young and hip!
Trait measurement is old-school. I am young and hip!
… simulate under null… As in the original study, there is higher (P < 2e-16) correlation coefficient across orthologs (0.73) than paralogs (0.28) when not considering node age.
Schraiber, J. G., Mostovoy, Y., Hsu, T. Y., & Brem, R. B. (2013). Inferring evolutionary histories of pathway regulation from transcriptional profiling data. PLoS Computational Biology, 9(10), e1003255. [DOI]
Bedford, T., Cobey, S., Beerli, P., & Pascual, M. (2010). Global Migration Dynamics Underlie Evolution and Persistence of Human Influenza A (H3N2). PLoS Pathogens, 6(5), e1000918. [DOI]
I.e. which virus is going to take over the population?
Neher, R. A., & Bedford, T. (2015). nextflu: Real-time tracking of seasonal influenza virus evolution in humans. Bioinformatics . [DOI]
Neher, R. A., Russell, C. A., & Shraiman, B. I. (2014). Predicting evolution from the shape of genealogical trees. eLife, 3. [DOI]
Hadfield, Megill, Bell, Huddleston, Potter, Callender, …, Bedford, Neher, (2018). Nextstrain: real-time tracking of pathogen evolution. Bioinformatics. [DOI]