The Systematics Discussion Group at UC Berkeley


meets on Mondays in room 5053 VLSB from 1-2:00 PM. This semester Anna Thompson is handling the organizational responsibilities; for more information contact her at atbuster@socrates.berkeley.edu. Copies of the paper(s) for each week's discussion are posted in the Integrative Biology department office, the Museum of Vertebrate Zoology, in Insect Biology and outside Marty Wojciechowski's office (1114 VLSB).

This coming week, February 22nd, . . . Birds!!!! This week it'll be Diogo and birds and other cool stuff, so read on!! The paper for discussion is Hoelzer (1997), "Inferring Phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees revisited", Evolution 51(2): 622-626. This revisits a paper by Moore (1995, Evolution 49: 718-726) which Anna has also made available for anyone who wants to look at it. The general theme is the discordance between species and genes trees, and the papers ask if and when mtDNA is a preferable marker when what we care about is the species tree.


Partial list of interesting/potentially interesting systematics and phylogeny-oriented papers from the 1997 and 1998 issues of Systematic Biology, Evolution, and Molecular Biology and Evolution

(suggestions welcome)


Brochu, C.A. 1997. Morphology, fossils, divergence timing, and the phylogenetic relationships of Gavialis. Systematic Biology 46: 479-522.

Cantino, P.D., R.G. Olmstead, and S.J. Wagtaff. 1997. A comparison of phylogenetic nomenclature with the current system: a botanical case study. Systematic Biology 46: 313-331.

Cunningham, C.W. 1997. Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an interative procedure for choosing among phylogenetic methods. Systematic Biology 46: 464-478.

Engel, S.R., K.M. Hogan, J.F. Taylor, and S.K. Davis. 1998. Molecular systematics and paleobiogeography of the South American sigmodontine rodents. 15: 35-59. Molecular Biology and Evolution 15: 35-49.

Fang, Q.Q., S. Cho, J. Regier, C. Mitter, M. Matthews, R.W. Poole, T.P. Friedlander, and S. Zhao. 1997. A new nuclear gene for insect phylogenetics: Dopa Decarboxylase is informative of relationships within Heliothinae (Lepidoptera: Noctuidae). Systematic Biology 46: 269-283.

Hare, M.P., and J.C. Avise. 1998. Population structure in the American oyster as inferred by nuclear gene genealogies. Molecular Biology and Evolution 15: 119-128.

Hoelzer, G.A. 1997. Inferring phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees revisited. Evolution 51: 622-626.

Janz, N., and S. Nylin. 1998. Butterflies and plants: a phylogenetic study. Evolution 52: 486-502.

Kopf, A., N.E. Rank, H. Roininen, R. Julkunen-Titto, J.M. Pasteels, and J. Tahvanainen. 1998. The evolution of host-plant use and sequestration in the leaf beetle genus Phratora (Coleoptera: Chrysomelidae). Evolution 52: 517-528.

Kuzhoff, R.K., J.A. Sweere, D.E. Soltis, P.S. Soltis, and E.A. Zimmer. 1998. The phylogenetic potential of entire 26S rDNA sequences in plants. Molecular Biology and Evolution 15: 251-263.

Mardulyn, P., M.C. Milinkovitch, and J.M. Pasteels. 1997. Phylogenetic analyses of DNA and allozyme data suggest that Gonioctena leaf beetles (Coleoptera; Chrysomelidae) experienced convergent evolution in their history of host-plant family shifts. Systematic Biology 46: 722-747.

Markus, F., and D. Tautz. 1997. Evolution and phylogeny of the Diptera: a molecular phylogenetic analysis using 28S rDNA sequences. Systematic Biology 46: 722-747.

Moore, W.S. 1997. Mitochondrial-gene trees versus nuclear-gene trees, a reply to Hoelzer. Evolution 51: 627-629.

Mukai, T., K. Naruse, T. Sato, A. Shima, and M. Morisawa. 1997. Multiregional introgressions inferred from the mitochondrial DNA phylogeny of a hybridizing species complex of gobiid fishes, genus Tridentiger. Molecular Biology and Evolution 14: 1258-1265.

Nyman, T., H. Roininen, and J.A. Vuorinen. 1998. Evolution of different gall types in willow-feeding sawflies (Hymenoptera: Tenthredinidae). Evolution 52: 465-474.

O' Grady, P.M., J. B. Clark, and M. G. Kidwell. 1998. Phylogeny of the Drososophila saltans species group based on combined analysis of nuclear and mitochondrial DNA sequences. Molecular Biology and Evolution 15: 656-664.

Orti, G., and A. Meyer. 1997. The radiation of characiform fishes and the limits of resolution of mitochondrial ribosomal DNA sequences. Systematic Biology 46: 75-100.

Regier, J.C., and J.W. Shulz. 1998. Molecular phylogey of the major arthropod groups indicated polyphyly of crustaceans and a new hypothesis for the origin of hexapods. Molecular Biology and Evolution 14: 902-913.

Rice, K.A., M.J. Donoghue, and R.G. Olmstead. 1997. Analyzing large data sets: rbcL 500 revisited. Systematic Biology 46: 554-562.

Soltis, D.E., P.S. Soltis, M.E. Mort, M.W. Chase, V. Savolainen, S.B. Hoot, and C.M. Morton. 1998. Inferring complex phylogenies using parsimony: an empirical approac using three large DNA data sets for Angiosperms. Systematic Biology 47: 32-42.

Su, Z.-H., O. Tominaga, M. Okamoto, and S. Osawa. 1998. Origin ad diversification of hindwingless Damaster ground beetles within the Japanese islands as deduced from mitochondrial ND5 gene sequences (Coleoptera, Carabidae). Molecular Biology and Evolution 15: 1026-1039.

Wiens, J.J., and M.R. Servedio. 1998. Phylogenetic analysis and intraspecific variation: performance of parsimony, likelihood, and distance methods. Systematic Biology 47: 228-253.

Wooding, S., and R. Ward. 1997. Phylogeography and Pleistocene evolution in the North American black bear. Molecular Biology and Evolution 14: 1096-1013.

Yang, Z. 1998. On the best evolutionary rate for phylogenetic analysis. Systematic Biology 47: 125-233.

Zamudio, K.R., K.B. Jones, and R.H. Ward. 1997. Molecular systematics of short-horned lizards: biogeography and taxonomy of a widespread species complex. Systematic Biology 46: 284-305.

Zardoya, R., Y. Cao, M. Hasegawa, and A. Meyer. 1998. Searching for the closest living relative(s) of tetrapods through evolutionary analyses of mitochondrial and nuclear data. Molecular Biology and Evolution 15:506-517.