Melbourne Systematics Forum

References and links from the March 2015 presentation by David Baum on genealogical discordance

The program (BUCKy) is described here:
C. Ané, B. Larget, D.A. Baum, S.D. Smith, A. Rokas (2007). Bayesian estimation of concordance among gene trees. Molecular Biology and Evolution 24(2), 412-426.
Larget, B. R., Kotha, S. K., Dewey, C. N., & Ané, C. (2010). BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics 26(22), 2910-2911.

This paper describes the approach from a more biological/systematic and conceptual perspective:
Baum, D. A. 2007. Concordance trees, concordance factors, and the exploration of reticulate genealogy. Taxon 56: 417-426.

These papers describe some applications of the method (from colleagues at UW):
Rodriguez, F., Wu, F., Ané, C., Tanksley, S., & Spooner, D. M. (2009). Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history?. BMC evolutionary biology 9(1), 191.
White, M. A., Ané, C., Dewey, C. N., Larget, B. R., & Payseur, B. A. (2009). Fine-scale phylogenetic discordance across the house mouse genome. PLoS Genetics 5(11), e1000729.
Ané C. in Knowles, L. L., & Kubatko, L. S. (Eds.). (2011). Estimating species trees: practical and theoretical aspects. John Wiley and Sons.

My conceptual approach to species and taxonomy is summarized in:
Baum, D. A. 2009. Species as ranked taxa. Systematic Biology 58:74–86.
Baum, D. A. and Smith, S.D. 2013. Tree-thinking: An Introduction to Phylogenetic Biology. Roberts & Company. (especially chapter 6)