| 45. | Popescu A.-A. and Huber K. T. & Paradis E. 2012. ape 3.0: New tools for distance based phylogenetics and evolutionary analysis in R. Bioinformatics in press. |
| 44. | Paradis E. 2012. Shift in diversification in sister-clade comparisons: a more powerful test. Evolution 66: 288–295. |
| 43. | Hubert N., Paradis E., Bruggemann H. & Planes S. 2011. Community assembly and diversification in Indo-Pacific coral reef fishes. Ecology and Evolution 1: 229–277. |
| 42. | Paradis E. 2011. Time-dependent speciation and extinction from phylogenies: a least squares approach. Evolution 65: 661–672. |
| 41. | Kadarusman, Sudarto, Paradis E. & Pouyaud L. 2010. Description of Melanotaenia fasinensis, a new species of rainbowfish (Melanotaeniidae) from West Papua, Indonesia with comments on the rediscovery of M. ajamaruensis and the endangered status of M. parva. Cybium 34: 207–215. |
| 40. | Sudarto, Lalu X. C., Kosen J. D., Tjakrawidjaja A. H., Kusumah R. V., Sadhotomo B., Kadarusman, Pouyaud L., Slembrouck J. & Paradis E. 2010. Mitochondrial genomic divergence in coelacanths (Latimeria): slow rate of evolution or recent speciation? Marine Biology 156: 2253–2262. |
| 39. | Paradis E. 2010. pegas: an R package for population genetics with an integrated–modular approach. Bioinformatics 26: 419–420. [PDF] |
| 38. | Pouyaud L., Sudarto & Paradis E. 2009. The phylogenetic structure of habitat shift and morphological convergence in Asian Clarias (Siluriformes: Clariidae). Journal of Zoological Systematics and Evolutionary Research 47: 344–356. |
| 37. | Duponchelle F., Paradis E., Ribbink A. J. & Turner G. F. 2008. Parallel life history evolution in mouthbrooding cichlids from the African Great Lakes. Proceedings of the National Academy of Sciences USA 105: 15475–15480. [PDF] |
| 36. | Paradis E. 2008. Asymmetries in phylogenetic diversification and character change can be untangled. Evolution 62: 241–247. |
| 35. | Galewski T., Tilak M.-k., Sanchez S., Chevret P., Paradis E. & Douzery E. J. P. 2006. The evolutionary radiation of Arvicolinae rodents (voles and lemmings): relative contribution of nuclear and mitochondrial phylogenies. BMC Evolutionary Biology 6: 80. [PDF] |
| 34. | Deffontaine V., Libois R., Kotlík P., Sommer R., Nieberding C., Paradis E., Searle J. B. & Michaux J. R. 2005. Beyond the Mediterranean Peninsulas: Evidence of Central European glacial refugia for a temperate forest mammal species, the bank vole (Clethrionomys glareolus). Molecular Ecology 14: 1727–1739. |
| 33. | Sénégas F., Paradis E. & Michaux J. 2005. Homogeneity of fossil assemblages extracted from mine dumps: an approach with plio-pleistocene caves in South Africa. Lethaia 38: 315-322. |
| 32. | Paradis E. 2005. Statistical analysis of diversification with species traits. Evolution 59: 1–12. |
| 31. | Claude J., Tong H., Pritchard P., Paradis E. & Auffray J.-C. 2004. Ecological correlates and evolutionary divergence in the skull of turtles: a geometric morphometric assessment. Systematic Biology 53: 933–948. |
| 30. | Michaux J. R., Libois R., Paradis E. & Filippucci M.-G. 2004. Phylogeographic history of the yellow-necked fieldmouse (Apodemus flavicollis) in Europe and in the Near and Middle East. Molecular Phylogenetics and Evolution 32: 788–798. |
| 29. | Paradis E. 2004. Can extinction rates be estimated without fossils? Journal of Theoretical Biology 229: 19–30. |
| 28. | Paradis E., Claude J. & Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289–290. [PDF] |
| 27. | Paradis E. 2003. Analysis of diversification: combining phylogenetic and taxonomic data. Proceedings of the Royal Society of London. Series B. Biological Sciences 270: 2499–2505. |
| 26. | Michaux J. R., Magnanou E., Paradis E. & Libois R. 2003. Mitochondrial phylogeography of the Woodmouse (Apodemus sylvaticus) in the Western Palearctic region. Molecular Ecology 12: 685–697. |
| 25. | Claude J., Paradis E., Tong H. & Auffray J.-C. 2003. A geometric morphometric assessment of the effects of environment and cladogenesis on the evolution of the turtle shell. Biological Journal of the Linnean Society 79: 485–501. |
| 24. | Paradis E. & Claude J. 2002. Analysis of comparative data using generalized estimating equations. Journal of Theoretical Biology 218: 175–185. |
| 23. | Paradis E., Baillie S. R., Sutherland W. J. & Gregory R. D. 2002. Exploring density-dependent relationships in demographic parameters in natural populations of birds at a large spatial scale. Oikos 97: 293–307. |
| 22. | Paradis E., Baillie S. R. & Sutherland W. J. 2002. Modelling large-scale dispersal distances. Ecological Modelling 151: 279–292. |
| 21. | Emerson B., Paradis E. & Thébaud C. 2001. Revealing the demographic histories of species using DNA sequences. Trends in Ecology & Evolution 16: 707–716. |
| 20. | Paradis E., Baillie S. R., Sutherland W. J. & Gregory R. D. 2000. Spatial synchrony in populations of birds: effects of habitat, population trend, and spatial scale. Ecology 81: 2112–2125. |
| 19. | Baillie S. R., Sutherland W. J., Freeman S. N., Gregory R. D. & Paradis E. 2000. Consequences of large-scale processes for the conservation of bird populations. Journal of Applied Ecology 37: 88–102. |
| 18. | Paradis E., Baillie S. R., Sutherland W. J., Dudley C., Crick H. Q. P. & Gregory R. D. 2000. Large-scale spatial variation in the breeding performance of song thrushes Turdus philomelos and blackbirds T. merula in Britain. Journal of Applied Ecology 37: 73-87. |
| 17. | Debat V., Alibert P., David P., Paradis E. & Auffray J.-C. 2000. Independence of developmental stability and canalisation in the house mouse. Proceedings of the Royal Society of London. Series B. Biological Sciences 267: 423–430. |
| 16. | van Dijk M. A. M., Paradis E., Catzeflis F. & de Jong W. W. 1999. The virtues of gaps: Xenarthran (Edentate) monophyly supported by a unique deletion in αA-crystallin. Systematic Biology 48: 94–106. |
| 15. | Paradis E., Baillie S. R., Sutherland W. J. & Gregory R. D. 1999. Dispersal and spatial scale affect synchrony in spatial population dynamics. Ecology Letters 2: 114–120. |
| 14. | Paradis E. 1998. Detecting shifts in diversification rates without fossils. American Naturalist 152: 176–187. |
| 13. | Paradis E., Wang X., Guédon G. & Croset H. 1998. Body mass dynamics in the Mediterranean pine vole, Microtus duodecimcostatus. Journal of Zoology, London 245: 299–305. |
| 12. | Paradis E. 1998. Testing for constant diversification rates using molecular phylogenies: a general approach based on statistical tests for goodness of fit. Molecular Biology and Evolution 15: 476–479. |
| 11. | Paradis E. 1998. Interactions between spatial and temporal scales in the evolution of dispersal rate. Evolutionary Ecology 12: 235–244. |
| 10. | Paradis E., Baillie S. R., Sutherland W. J. & Gregory R. D. 1998. Patterns of natal and breeding dispersal in birds. Journal of Animal Ecology 67: 518–536. |
| 9. | Paradis E. 1997. Assessing temporal variations in diversification rates from phylogenies: estimation and hypothesis testing. Proceedings of the Royal Society of London. Series B. Biological Sciences 264: 1141–1147. |
| 8. | Paradis E. 1997. Metapopulations and chaos: on the stabilizing influence of dispersal. Journal of theoretical Biology 186: 261–266. |
| 7. | Paradis E. 1995. Chaos and scale. Trends in Ecology & Evolution 10: 335. |
| 6. | Paradis E. & Croset H. 1995. Assessment of habitat quality in the Mediterranean pine vole (Microtus duodecimcostatus) by study of survival rates. Canadian Journal of Zoology 73: 1511–1518. |
| 5. | Paradis E. 1995. Survival, immigration and habitat quality in the Mediterranean pine vole. Journal of Animal Ecology 64: 579–591. |
| 4. | Paradis E. & Guédon G. 1993. Demography of a mediterranenan microtine: the Mediterranean pine vole, Microtus duodecimcostatus. Oecologia 95: 47–53. |
| 3. | Paradis E. & Guédon G. 1993. Long lifespan in a population of Microtus (Pitymys) duodecimcostatus. Mammalia 57: 142–144. |
| 2. | Paradis E., Guédon G. & Pradel R. 1993. Estimation of sex- and age-related survival rates in a microtine population. Journal of Wildlife Management 57: 158–163. |
| 1. | Guédon G., Paradis E. & Croset H. 1992. Capture-recapture study of a population of the Mediterranean pine vole (Microtus duodecimcostatus) in Southern France. Zeitschrift für Säugetierkunde 57: 364–372. |
I am a member of the editorial board of Methods in Ecology and Evolution.
I reviewed at least once for the following journals: