Shaffer gene tree lecture
This lecture goes over the fundamental reasons why gene-tree species-tree conflicts arise, and some of the reasons why one might or might not worry about each for particular clades. It also provides a few (of very many possible) empirical examples of gene-tree species-tree conflicts, including some from our lab group (its turtles and salamanders, so you gotta love that). The pdf for the lecture is called ShafferLecture.pdf, and you should feel free to use anything from it.
References
Below are some of the references supporting this lecture. For other references on BEST, see Bob Thomson's references.
Carstens, B. C. and L. L. Knowles. 2007. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Syst. Biol. 56:400-411.
Edwards, S. V. Is a new and general theory of molecular systematics emerging? Evolution 63:1-19.
Fitzpatrick, B. M., J. R. Johnson, D. K. Kump, H. B. Shaffer, J. J. Smith and S. R. Voss. Rapid fixation of non-native alleles revealed by genome-wide SNP analysis of hybrid tiger salamanders. (Submitted to BMC Evolutionary Biology).
Hudson, R. R., and J. A. Coyne. 2002. Mathematical consequences of the genealogical species concept. Evolution 56:1557-1565.
Irestedt, M. and J. I. Ohlson. 2008. The division of the major songbird radiation into Passerida and 'core Corvoidea' (Aves: Passeriformes)— the species tree vs. gene trees. Zoologica Scripta 37:305-313.
Liu, L., D.K. Pearl, R.T. Brumfield, S.V. Edwards. 2008. Estimating species trees using multiple-allele DNA sequence data. Evolution 62: 2080-2091.
Maddison, W. P. 1997. Gene trees in species trees. Syst. Biol. 46:523-536.
Oliver, J. C. 2008. AUGIST: inferring species trees while accommodating gene tree uncertainty. Bioinformatics 24:2932-2933.
Page, R. D. M., and M. A. Charleston. 1997. From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem. Mol. Phylogen. Evol. 7:231-240.
Pollard, D. A., V. N. Iyer, A. M. Moses and M. B. Eisen. 2006. Widespread discordance of gene trees with species tree in Drosophila: Evidence for incomplete lineage sorting. 2:1634-1647.
Riley, S.P.D., H.B. Shaffer, S.R. Voss, and B.M. Fitzpatrick. 2003. Hybridization between a rare, native tiger salamander (Ambystoma californiense) and its introduced congener. Ecological Applications 13:1263-1275.
Spinks, P. Q. and H. B. Shaffer. Conflicting mitochondrial and nuclear phylogenies for the widely disjunct Emys (Testudines: Emydidae) Species Complex, and what they tell us about biogeography and hybridization. (Systematic Biology).
Thomson, R. C., A. M. Shedlock, S. V. Edwards, and H. B. Shaffer. 2008. Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles. Molecular Phylogenetics and Evolution 49:514-525.
