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Notes to accompany my talk.

Evolution 2017

June 25, 2017 (and updated since then)

Casey Dunn, , @caseywdunn

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

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.

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.


This document can be accessed via the delightful github url shortener at .

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k8hertweck commented Jun 25, 2017

This is a great way to share information about your talk, thanks!

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johnsolk commented Mar 5, 2018

Here is the link to "SSB Symposium - Phylogenetic approaches to connecting genotypes to phenotypes" at Evolution 2017. (The one above appears broken.)

Thank you for sharing these notes and for your talk and visit at UC Davis last week!

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