Abstract
Mooi & Gill (2010) have made a number of criticisms of statistical approaches to the phylogenetic analysis of molecular data as it is currently practiced. There are many different uses for molecular phylogenies, and for most of them statistical methods are entirely appropriate, but for taxonomic purposes the way that these methods have been used is questionable. In these cases it is necessary to introduce an extra step into the analysis – exploration of character conflict. Existing methods for exploring character conflict in molecular data such as spectral analysis, phylogenetic networks, likelihood mapping and sliding window analyses are briefly reviewed, but there is also a need for development of new tools to facilitate the analysis of large data sets. Incorporation of previous phylogenies as priors in Bayesian analyses could help to provide taxonomic stability, while still leaving room for new data to alter these conclusions if they contain sufficiently strong phylogenetic signal. Molecular phylogeneticists should make a clearer distinction between the different uses to which their phylogenies are put; methods suitable in one context may not be appropriate in others.References
Alfaro, M.E., Smith, D.K., Xia, X. & Yuen, K. (2005) The posterior and the prior in Bayesian phylogenetics. Annual Review of Ecology, Evolution and Systematics, 37, 19–42.
Cai, J.J., Smith, D.K., Xia, X. & Yuen, K. (2005) MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution. BMC Bioinformatics, 6, 64.
Charleston, M.A. (1998) Spectrum: spectral analysis of phylogenetic data. Bioinformatics, 14, 98–99.
Crow, K.D., Stadler, P.F., Lynch, V.J., Amemiya, C. & Wagner, G.P. (2006) The “fish-specific” Hox cluster duplication is coincident with the origin of Teleosts. Molecular Biology and Evolution, 23, 121–136.
Delsuc, F., Brinkmann, H. & Philippe, H. (2005) Phylogenomics and the reconstruction of the tree of life. Nature Reviews Genetics, 6, 361–375.
Dunn, C.P. (2003) Keeping taxonomy based in morphology. Trends in Ecology and Evolution, 18, 270–271.
Edwards, S.V. (2009) Is a new general theory of molecular systematics emerging? Evolution, 63, 1–19.
Hendy, M.D. & Penny, D. (1993) Spectral analysis of phylogenetic data. Journal of Classification, 10, 5–24.
Huelsenbeck, J.P., Ronquist, F., Nielsen, R. & Bollback, J.P. (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science, 294, 2310–2314.
Huson, D.H. & Bryant, D. (2006) Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution, 23, 254–267.
Lockhart, P.J., Penny, D. & Meyer, A. (1995) Testing the phylogeny of swordtail fishes using split decomposition and spectral analysis. Journal of Molecular Evolution, 41, 666–674.
Marková, S., Šanda, R., Crivelli, A., Shumka, S., Wilson, I.F., Vukić, J., Berrebi, P. & Kotlík, P. (2010) Nuclear and mitochondrial DNA sequence data reveal the evolutionary history of Barbus (Cyprinidae) in the ancient lake systems of the Balkans. Molecular Phylogenetics and Evolution, 55, 488–500.
Mooi, R.D. & Gill, A.C. (2010) Phylogenies without synapomorphies – a crisis in fish systematics: time to show some character. Zootaxa, 2450, 26–40.
Paraskevis, D., Deforche, K., Lemey, P., Magiokinis, G., Hatzakis, A. & Vandamme, A.-M. (2005) SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference. Bioinformatics, 21, 1274–1275.
Philippe, H., Delsuc, F., Brenner, H. & Lartillot, N. (2005) Phylogenomics. Annual Review of Ecology, Evolution and Systematics, 36, 541–562.
Proutski, V. & Holmes, E. (1998) SWAN: sliding window analysis of nucleotide sequence variability. Bioinformatics, 14, 467–468.
Schmidt, H.A., Strimmer, K., Vingron, M. & von Haeseler, A. (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics, 18, 502–504.
Strimmer, K. & von Haeseler, A. (1997) Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proceedings of the National Academy of Sciences of the United States of America, 94, 6815–6819.
Sturmbauer, C., Salzburger, W., Duftner, N., Schelly, R. & Koblmüller, S. (2010) Evolutionary history of the Lake Tanganyika cichlid tribe Lamprologini (Teleostei: Perciformes) derived from mitochondrial and nuclear DNA data. Molecular Phylogenetics and Evolution, 57, 266–284.
Wang, D., Zhong, L., Wei, Q., Gan, X. & He, S. (2010) Evolution of MHC class I genes in two ancient fish, paddlefish (Polyodon spathula) and Chinese sturgeon (Acipenser sinensis). FEBS Letters, 584, 3331–3339.