June 25, 2017 (and updated since then)
These are some notes and annotated references relevant to my talk with Stacey Smith in the symposium "SSB Symposium Phylogenetic approaches to connecting genotypes to phenotypes" at Evolution 2017.
If you are interested in any of this work let me know. I am moving to Yale and looking for people to join the new research group.
Papers, resources, and analyses that I mentioned (or are relevant to) the talk today
Agalma, our tool for phylogenetic and gene expression analyses
Dunn, CW, F Zapata, C Munro, S Siebert, A Hejnol (2017) Pairwise comparisons are problematic when analyzing functional genomic data across species. bioRxiv preprint: doi:10.1101/107177. Git code repository: https://github.com/caseywdunn/comparative_expression_2017.
A re-examination of two recent comparative functional genomic studies that used pairwise comparisons.
- Dunn, CW, C Munro (2016) Comparative genomics and the diversity of life. Zoologica Scripta 45:5-13. doi:10.1111/zsc.12211.
This paper touches on the false dichotomy between "descriptive" and "hypothesis driven" research projects. It also describes a few other challenges in evolutionary genomics, including the diminishing usefulness of orthology and paralogy as well as biases that may be introduced in analyses focused on single copy genes.
- Hejnol, A, CW Dunn (2016) Animal Evolution: Are Phyla Real? Current Biology 26:R424–R426. doi:10.1016/j.cub.2016.03.058.
A critique of Levin et al.'s conclusion that the origin of animal phyla was associated with distinctive changes in develomental gene expression.
- Dunn, CW, X Luo, Z Wu (2013) Phylogenetic analysis of gene expression. Integrative and Comparative Biology 53:847-856. doi:10.1093/icb/ict068
Challenges and approaches for phylogenetic analysis of gene expression. It isn't statistically valid to map RNA-seq counts onto a phylogeny, but certain ratios of counts can be reconstructed on trees.