Why phylogenetics?

Erick Matsen

What can we do with phylogenetics?

Examples today:

  1. Felsenstein independent contrasts
  2. Understanding flu transmission

Independent contrasts

Say we measure two traits

Do traits \(X\) and \(Y\) look correlated?

Do traits \(X\) and \(Y\) look correlated?

Stars from left branch, squares from the right


Need to correct for evolutionary history to test evolution hypothesis.

Felsenstein 1985

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!

Dunn et al. reanalyze two papers

  • Kryuchkova-Mostacci, N., & Robinson-Rechavi, M. (2016). Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs. PLoS Computational Biology, 12(12), e1005274. [DOI]
  • Levin, M., Anavy, L., Cole, A. G., Winter, E., Mostov, N., Khair, S., … Yanai, I. (2016). The mid-developmental transition and the evolution of animal body plans. Nature, 531, 637. [DOI]


Let’s take a look.

Kryuchkova-Mostacci re-analysis


… 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.

Levin analysis

Levin re-analysis

For a paper that does it right…

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]

https://www.youtube.com/watch?v=3lxqv_iJeLY

Flu transmission patterns

Where does the flu come from?

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]

Infer trunk location

Infer trunk location

Where is flu going?


I.e. which virus is going to take over the population?

Local branching index

Local branching index in nextflu.org

Try it out

http://nextflu.org/

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]

http://nextstrain.org/

Hadfield, Megill, Bell, Huddleston, Potter, Callender, …, Bedford, Neher, (2018). Nextstrain: real-time tracking of pathogen evolution. Bioinformatics. [DOI]