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Collaborations
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Publications Enabled by the CIPRES Science Gateway and CIPRES Portal

  1. Zimkus, B.M. (2009) "Patterns of speciation and diversity among African frogs (genus Phrynobatrachus)." Ph.D. dissertation, Harvard University.
  2. Toon, A., Finley, M., Staples, J., and Crandall, K.A. (2009) "Decapod phylogenetics and molecular evolution" in Decapod Crustacean Phylogenetics (Crustacean Issues) (J. Martin, D. L. Felder, and K. A. Crandall, eds.). CRC Press, Bocan Raton. pp.15-30.
  3. Felder DL, Robles R. (2009) "Molecular Phylogeny of Callianassidae." in Decapod Crustacean Phylogenetics (Crustacean Issues) (J. Martin, D. L. Felder, and K. A. Crandall, eds.). CRC Press, Bocan Raton: pp. 327-342.
  4. Robles R, Tudge CC, Dworschak PC, Poore GCB, Felder DL. "Molecular phylogeny of the Thalassinidea based on nuclear and mitochondrial genes." in Decapod Crustacean Phylogenetics (Crustacean Issues) (J. Martin, D. L. Felder, and K. A. Crandall, eds.). CRC Press, Bocan Raton: pp. 309-326.
  5. Dolapsakis, N. and Economou-Amilli, A. (2009) "A new marine species of Amphidinium (Dinophyceae) from Thermaikos Gulf, Greece." Acta Protozoologica 48(2):91-190. [abstract]
  6. Klassen, J.L. (2009) "Carotenoid diversity in novel Hymenobacter strains isolated from Victoria Upper Glacier, Antarctica, and implications for the evolution of microbial carotenoid biosynthesis." PhD thesis, University of Alberta, Edmonton, Canada.
  7. Klassen, J.L. (2009) "Pathway evolution by horizontal transfer and positive selection is accommodated by relaxed negative selection upon upstream pathway genes in purple bacterial carotenoid biosynthesis."  Journal of Bacteriology, in the press. [citation] [abstract]
  8. Spinks, P.Q. and Shaffer, H.B. (2009). "Conflicting mitochondrial and nuclear phylogenies for the widely disjunct Emys (Testudines: Emydidae) species complex, and what they tell us about biogeography and hybridization." Syst. Biol. 58(1):1–20. [citation] [abstract]
  9. Spinks, P.Q., Thomson, R.C., Lovely, G.A. and Shaffer, H.B. (2009) "Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles." BMC Evolutionary Biology 9:56. doi:10.1186/1471-2148-9-56. [citation] [abstract] [pdf]
  10. Penna, A., Fraga, S, Batocchi, C., Casabianca, S., Giacobbe, M.G., Riobò, P. and Vernesi, C. (2009) "A phylogeographic study of the toxic benthic dinoflagellate genus Ostreopsis Schmidt." Journal of Biogeography in the press.
  11. Hibbett, D.S. and Matheny, P.B. (2009) "The relative ages of ectomycorrhizal mushrooms and their plant hosts estimated using Bayesian relaxed molecular clock analyses." BMC Biology 7:13 doi:10.1186/1741-7007-7-13. [citation] [abstract] [pdf]
  12. Elias M. and Archibald J. M. (2009) "The RJL family of small GTPases is an ancient eukaryotic invention probably functionally associated with the flagellar apparatus." Gene 442(1-2):63-72. Epub 2009 Apr 22. doi:10.1016/j.gene.2009.04.011 [abstract] [publication]
  13. Gile, G.H., Novis, P.M., Cragg D.S., Zuccarello G.C., Keeling P.J. (2009) "The distribution of EF-1alpha, EFL, and a non-canonical genetic code in the Ulvophyceae: Discrete genetic characters support a consistent phylogenetic framework." J. Eukaryot. Microbiol. 56(4):367-372. [citation] [abstract]
  14. Jabaily, R.S. and Sytsma, K.J. (2009) "Phylogenetics of Puya (Bromeliaceae): Placement, major lineages and evolution of Chilean species." accepted: American Journal of Botany in the press.
  15. Weirauch, C. and Munro, J. (2009) "Molecular phylogeny of the assassin bugs (Hemiptera: Reduviidae), based on mitochondrial and nuclear ribosomal genes." Molecular Phylogenetics & Evolution 53: 287-299. doi:10.1016/j.ympev.2009.05.039 [abstract]
  16. Wilson, N. G., Rouse, G. W., and Giribet, G. (2009) "Assessing the molluscan hypothesis Serialia (Monoplacophora + Polyplacophora) using novel molecular data." Mol Phylogenet Evol. Jul 30. [Epub ahead of print]. doi:10.1016/j.ympev.2009.07.028 [abstract]
  17. Segade, F. (2009) "Functional evolution of the microfibril-associated glycoproteins." Gene 439:43–54. [abstract]
  18. Welsh, A.K., Dawson, J.O., Gottfried, G.J., and Hahn, D. "Diversity of Frankia in root nodules of geographically isolated Arizona alder in central Arizona (USA)." Applied and Environmental Microbiology (in press). [citation] [abstract]
  19. Mirza, B.S., Welsh, A.K., and Hahn, D. (2009) "Growth of Frankia strains in leaf litter-amended soil and the rhizosphere of a nonactinorhizal plant." FEMS Microbiology Ecology 70:132-141 Epub 2009 Jul 21. [citation] [abstract]
  20. Welsh, A.K, B.S. Mirza, J.P. Rieder, M.W. Paschke, D. Hahn. (2009) "Diversity of frankiae in nodules of Morella pensylvanica grown in soils from five continents." Systematic and Applied Microbiology 32: 201-210. doi:10.1016/j.syapm.2009.01.002  [abstract]
  21. Mirza, B.S., A.K. Welsh, G. Rasul, J.P. Rieder, M.W. Paschke, D. Hahn. (2009) "Variation in Frankia populations of the Elaeagnus host infection group in nodules of six host plant species after inoculation with soil." Microbial Ecology 58:384-393. doi:10.1007/s00248-009-9513-0 [abstract]
  22. Li, J-t., Che, J., Murphy, R.W., Zhao, H., Zhao, E.-m., Rao, D.-q., and Zhang, Y.-p. (2009) "New insights to the molecular phylogenetics and generic assessment in the Rhacophoridae (Amphibia: Anura) based on five nuclear and three mitochondrial genes, with comments on the evolution of reproduction." Molecular Phylogenetics and Evolution 53: 509–522. doi:10.1016/j.ympev.2009.06.023 [abstract]
  23. Murienne, J., Karaman, I., and Giribet, G. (2009) "Explosive evolution of an ancient group of Cyphophthalmi (Arachnida: Opiliones) in the Balkan Peninsula." J. Biogeography Published online, Oct 14, 2009 [citation] [abstract]
  24. Schulte II, J.A., and Cartwright, E.M. (2009) Phylogenetic relationships among iguanian lizards using alternative partitioning methods and TSHZ1: A new phylogenetic marker for reptiles. Molecular Phylogenetics and Evolution 50:391-396. doi:10.1016/j.ympev.2008.10.018 [abstract]
  25. Armbruster, W.S., Leed,J., and Baldwind, B.G. (2009) "Macroevolutionary patterns of defense and pollination in Dalechampia vines: Adaptation, exaptation, and evolutionary novelty" Proc. Natl. Acad. Sci USA. Oct 19 e-pub ahead of publication. [abstract]
  26. Zimkus, B.M., Rödel, M.-C., and Hillers, A. (2009) Complex patterns of continental speciation: molecular phylogenetics and biogeography of sub-Saharan puddle frogs (Phrynobatrachus) manuscript submitted.
  27. Chen, W.-J., Lheknim, V. and Mayden, R. L. (2009). "Molecular phylogeny of the Cobitoidea (Teleostei: Cypriniformes) revisited: position of enigmatic loach Ellopostoma Vaillant resolved with six nuclear genes." Journal of Fish Biology 75, In press.
  28. Chen, W.-J. and Mayden, R. L. (2009). Molecular systematics of the Cyprinoidea (Teleostei: Cypriniformes), the world’s largest clade of freshwater fishes: Further evidence from six nuclear genes. Molecular Phylogenetics and Evolution 52, 544-549. doi:10.1016/j.ympev.2009.01.006   
  29. Mayden, R. L., Chen, W.-J., Bart, H. L., Doosey, M. H., Simons, A. M., Tang, K. L., Wood, R. M., Agnew, M. K., Yang, L., Hirt, M. V., Clements, M. D., Saitoh, K., Sado, T., Miya, M. and Nishida, M. (2009). "Reconstructing the phylogenetic relationships of the Earth’s most diverse clade of freshwater fishes — Order Cypriniformes (Actinopterygii: Ostariophysi): a case study using multiple nuclear loci and the mitochondrial genome." Molecular Phylogenetics and Evolution 51, 500-514. doi:10.1016/j.ympev.2008.12.015