46. Ronquist, F. Larget, B., Huelsenbeck, J. P., Kadane, J. B., Simon, D. and P. van der Mark. 2006. Comment on "Phylogenetic MCMC algorithms are misleading on mixtures of trees". Science 312: 367. pdf
45. Nieves-Aldrey, J. L., Vårdal, H. and F. Ronquist. 2005. Comparative morphology of terminal-instar larvae of Cynipoidea: phylogenetic implications. Zoologica Scripta. 34: 15-36. pdf
44. Huelsenbeck, J. P. and F. Ronquist. 2005. Bayesian analysis of molecular evolution using MrBayes. In: Nielsen, R. (ed.), Statistical Methods in Molecular Evolution. Springer,
43. Ronquist, F., Huelsenbeck, J. P. and T. Britton. 2004. Bayesian
supertrees. In: Bininda-Emonds, O. R.
P. (ed.), Phylogenetic Supertrees:
Combining Information to Reveal the Tree of Life. Kluwer,
42. Ronquist, F. Bayesian inference of character evolution. Trends in Ecology and Evolution 19: 475-481. pdf
41. Altekar, G., S. Dwarkadas, J. P. Huelsenbeck and F. Ronquist. 2004. Parallel
Metropolis-coupled Markov chain
40. Sanmartin, I. and F. Ronquist. 2004. Southern Hemisphere biogeography analyzed with event-based models: Plant versus animal patterns. Systematic Biology 53: 216-243. pdf
39. Nylander, J., F. Ronquist, J. P. Huelsenbeck and J. L. Nieves-Aldrey. 2004. Bayesian phylogenetic analysis of combined data. Systematic Biology 53: 47-67. pdf
38. Ronquist, F. and U. Gärdenfors. 2003. Taxonomy and biodiversity inventories: Time to deliver. Trends in Ecology and Evolution 18: 269-270. pdf
37. Ronquist, F. and J. P. Huelsenbeck. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574. pdf
36. Vårdal, H., Sahlén, G. and F. Ronquist. 2003. Morphology and evolution of the cynipoid egg (Hymenoptera). Zoological Journal of the Linnean Society 139: 247-260. pdf
35. Sanmartin,
34. Fontal-Cazalla, F. M., Buffington, M., Nordlander, G., Liljeblad, J., Ros-Farré, P., Nieves-Aldrey, J. L., Pujade-Villar, J. and F. Ronquist. 2002. Phylogeny of the Eucoilinae (Hymenoptera: Cynipoidea: Figitidae). Cladistics 18:154-199. pdf
33. Huelsenbeck, J. P. H., Larget, B., Miller, R. E. and F. Ronquist. 2002. Potential applications and pitfalls of Bayesian inference of phylogeny. Systematic Biology 51:673-688. pdf
32. Rokas, A., J. A. A. Nylander, F. Ronquist and G. N. Stone. 2002. A maximum-likelihood analysis of eight molecular markers in gallwasps (Hymenoptera: Cynipidae): Implications for insect phylogenetic studies. Molecular Phylogenetics and Evolution 22:206-219. pdf
31. Ronquist, F. 2002. Parsimony analysis of coevolving species associations.
Pp. 22-64 in R. D. M. Page, ed. Tangled
trees: Phylogeny, cospeciation and coevolution.
30. Huelsenbeck, J. P. & Ronquist, F. 2001. MRBAYES. Bayesian inference of phylogeny. Bioinformatics 17: 754-755. pdf
29. Huelsenbeck, J. P., F. Ronquist, R. Nielsen and J. P. Bollback. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294: 2310-2314. pdf
28. Nylin, S., K. Nyblom, F. Ronquist, N. Janz, J. Belicek, and M. Källersjö. 2001. Phylogeny of Polygonia, Nymphalis and related butterflies (Lepidoptera: Nymphalidae): a total-evidence analysis. Zoological Journal of the Linnean Society 132: 441-468. pdf
27. Ronquist, F., and J. Liljeblad. 2001. Evolution of the gall wasp-host plant association. Evolution 55: 2503-2522. pdf
26. Ronquist, F., and J. L. Nieves Aldrey. 2001. A new subfamily of Figitidae (Hymenoptera: Cynipoidea). Zoological Journal of the Linnean Society 14: 483-494. pdf
25. Sanmartín,
24. Zink, R. M., R. C. Blackwell-Rago, and F. Ronquist. 2000.
The shifting roles of dispersal and vicariance in biogeography. Proceedings of the Royal Society of
23. Ros-Farré, P., F. Ronquist, and J. Pujade-Villar. 2000. Redescription of Acanthaegilips Ashmead, 1897, with characterization of the Anacharitinae and Aspiceratinae (Hymenoptera: Cynipoidea: Figitidae). Zoological Journal of the Linnean Society 129: 467-488. pdf
22. Ronquist, F. 1999. Phylogeny of the Hymenoptera (Insecta): The state of the art. Zoologica Scripta 28:3-11. pdf
21. Ronquist, F. 1999. Phylogeny, classification and evolution of the Cynipoidea. Zoologica Scripta 28:139-164. pdf
20. Ronquist, F., A. P. Rasnitsyn, A. Roy, K. Eriksson, and M. Lindgren. 1999. Phylogeny of the Hymenoptera: A cladistic reanalysis of Rasnitsyn's (1988) data. Zoologica Scripta 28:13-50. pdf
19. Ronquist, F. 1998. Phylogenetic approaches in coevolution and biogeography. Zoologica Scripta 26:313-322.
18. Ronquist, F. 1998. Three-dimensional cost matrix optimization and maximum cospeciation. Cladistics 14:167-172. pdf
17. Ronquist, F. 1998. Fast Fitch-parsimony algorithms for large data sets. Cladistics 14:387-400. pdf
16. Liljeblad, J., and F. Ronquist. 1998. A phylogenetic analysis of higher-level gall wasp relationships (Hymenoptera: Cynipidae). Systematic Entomology 23:229-252. pdf
15. Ronquist, F. 1997. Dispersal-vicariance analysis: A new approach to the quantification of historical biogeography. Systematic Biology 46: 193-201.
14. Ronquist, F. 1996. Matrix representation of trees, redundancy, and weighting. Systematic Biology 45: 247-253.
13. Ronquist, F. 1996. Reconstructing the history of host-parasite associations using generalised parsimony. Cladistics 11: 73-89.
12. Nordlander, G., Z. Liu, and F. Ronquist. 1996. Phylogeny and historical biogeography of the cynipoid wasp family Ibaliidae (Hymenoptera). Systematic Entomology 21:151-166.