Publications

Book

Paradis E. 2012. Analysis of Phylogenetics and Evolution with R (Second Edition). Springer, New York.

Paradis E. 2006. Analysis of Phylogenetics and Evolution with R. Springer, New York.

Book chapters

Paradis E. 2014. An introduction to the phylogenetic comparative method. In: L. Z. Garamszegi (ed.), Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology. Pages 3–18. Springer-Verlag Berlin Heidelberg.

Paradis E. 2014. Simulation of phylogenetic data. In: L. Z. Garamszegi (ed.), Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology. Pages 335–350. Springer-Verlag Berlin Heidelberg.

Articles

59. Tougard C., García-Dávila C. R., Römer U., Duponchelle F., Cerqueira F., Guinand B., Paradis E., Chávez C. A., Salas V., Quérouil S., Sirvas S. & Renno J.-F. 2017. Tempo and rates of diversification in the South American cichlid genus Apistogramma (Teleostei: Perciformes: Cichlidae). PLoS ONE in press.
58. Maggia M. E., Vigouroux Y., Renno J. F., Duponchelle F., Desmarais E., Nunez J., García-Dávila C., Carvajal F., Paradis E., Martin J. F. & Mariac C. 2017. DNA metabarcoding of Amazonian ichthyoplankton swarms. PLoS ONE 12: e0170009. doi:10.1371/journal.pone.0170009
57. Bertranpetit É., Jombart T., Paradis E., Pena H., Dubey J., Su C., Mercier A., Devillard S. & Ajzenberg D. 2017. Phylogeography of Toxoplasma gondii points to a South American origin. Infection, Genetics and Evolution 48: 150–155. doi:10.1016/j.meegid.2016.12.020
56. Tedesco P. A., Paradis E., Lévêque C. & Hugueny B. 2017. Explaining global-scale diversification patterns in actinopterygian fishes. Journal of Biogeography 44: 773–783. doi:10.1111/jbi.12905
55. Paradis E., Gosselin T., Grünwald N. J., Jombart T., Manel S. & Lapp H. 2017. Towards an integrated ecosystem of R packages for the analysis of population genetic data. Molecular Ecology Resources 17: 1–4. doi:10.1111/1755-0998.12636
54. Paradis E., Gosselin T., Goudet J., Jombart T. & Schliep K. 2017. Linking genomics and population genetics with R. Molecular Ecology Resources 17: 54–66. doi:10.1111/1755-0998.12577
53. Jombart T., Schliep K., Kamvar Z., Archer F., Harris R., Paradis E., Goudet J. & Lapp H. 2017. apex: phylogenetics with multiple genes. Molecular Ecology Resources 17: 19–26. doi:10.1111/1755-0998.12567
52. Paradis E. 2016. The distribution of branch lengths in phylogenetic trees. Molecular Phylogenetics and Evolution 94: 136–145. doi:10.1016/j.ympev.2015.08.010
51. Paradis E. 2015. Random phylogenies and the distribution of branching times. Journal of Theoretical Biology 387: 39–45. doi:10.1016/j.jtbi.2015.09.005
50. Laenen B., Shaw B., Schneider H., Goffinet B., Paradis E., Désamoré A., Heinrichs J., Villarreal J. C., Gradstein S. R., McDaniel S. F., Long D. G., Forrest L. L., Hollingsworth M. L., Crandall-Stotler B., Davis E. C., Engel J., Von Konrat M., Cooper E. D., Patiño J., Cox C. J., Vanderpoorten, A. & Shaw A. J. 2014. Extant diversity of bryophytes emerged from successive post-Mesozoic diversification bursts. Nature Communications 5: 6134. doi:10.1038/ncomms6134
49. Paradis E., Tedesco P. A. & Hugueny B. 2013. Quantifying variation in speciation and extinction rates with clade data. Evolution 67: 3617–3627. doi:10.1111/evo.12256
48. Morvan C., Malard F., Paradis E., Lefébure T., Konecny-Dupré L. & Douady C. J. 2013. Timetree of Aselloidea reveals species diversification dynamics in groundwater. Systematic Biology 62: 512–522. doi:10.1093/sysbio/syt015
47. Paradis E. 2013. Molecular dating of phylogenies by likelihood methods: a comparison of models and a new information criterion. Molecular Phylogenetics and Evolution 67: 436–444. doi:10.1016/j.ympev.2013.02.008
46. Kadarusman, Hubert N., Hadiaty R. H., Sudarto, Paradis E. & Pouyaud L. 2012. Cryptic diversity in Indo-Australian rainbowfishes revealed by DNA barcoding: implications for conservation in a biodiversity hotspot candidate. PLoS ONE 7: e40627. doi:10.1371/journal.pone.0040627
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 28: 1536–1537. doi:10.1093/bioinformatics/bts184
44. Paradis E. 2012. Shift in diversification in sister-clade comparisons: a more powerful test. Evolution 66: 288–295. doi:10.1111/j.1558-5646.2011.01429.x
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. doi:10.1002/ece3.19
42. Paradis E. 2011. Time-dependent speciation and extinction from phylogenies: a least squares approach. Evolution 65: 661–672. doi:10.1111/j.1558-5646.2010.01179.x
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. [PDF]
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. doi:10.1007/s00227-010-1492-7
39. Paradis E. 2010. pegas: an R package for population genetics with an integrated–modular approach. Bioinformatics 26: 419–420. doi:10.1093/bioinformatics/btp696
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. doi:10.1111/j.1439-0469.2008.00507.x
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. doi:10.1073/pnas.0802343105
36. Paradis E. 2008. Asymmetries in phylogenetic diversification and character change can be untangled. Evolution 62: 241–247. doi:10.1111/j.1558-5646.2007.00252.x
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. doi:10.1186/1471-2148-6-80
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. doi:10.1111/j.1365-294X.2005.02506.x
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. doi:10.1080/00241160500355103
32. Paradis E. 2005. Statistical analysis of diversification with species traits. Evolution 59: 1–12. doi:10.1111/j.0014-3820.2005.tb00889.x
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. doi:10.1080/10635150490889498
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. doi:10.1016/j.ympev.2004.02.018
29. Paradis E. 2004. Can extinction rates be estimated without fossils? Journal of Theoretical Biology 229: 19–30. doi:10.1016/j.jtbi.2004.02.018
28. Paradis E., Claude J. & Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289–290. doi:10.1093/bioinformatics/btg412
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. doi:10.1098/rspb.2003.2513
26. Michaux J. R., Magnanou E., Paradis E., Nieberding C. & Libois R. 2003. Mitochondrial phylogeography of the Woodmouse (Apodemus sylvaticus) in the Western Palearctic region. Molecular Ecology 12: 685–697. doi:10.1046/j.1365-294X.2003.01752.x
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. doi:10.1046/j.1095-8312.2003.00198.x
24. Paradis E. & Claude J. 2002. Analysis of comparative data using generalized estimating equations. Journal of Theoretical Biology 218: 175–185. doi:10.1006/jtbi.2002.3066
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. doi:10.1034/j.1600-0706.2002.970215.x
22. Paradis E., Baillie S. R. & Sutherland W. J. 2002. Modelling large-scale dispersal distances. Ecological Modelling 151: 279–292. doi:10.1016/S0304-3800(01)00487-2
21. Emerson B., Paradis E. & Thébaud C. 2001. Revealing the demographic histories of species using DNA sequences. Trends in Ecology & Evolution 16: 707–716. doi:10.1016/S0169-5347(01)02305-9
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. doi:10.1890/0012-9658(2000)081[2112:SSIPOB]2.0.CO;2
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. doi:10.1046/j.1365-2664.2000.00555.x
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. doi:10.1046/j.1365-2664.2000.00547.x
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. doi:10.1098/rspb.2000.1017
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. doi:10.1080/106351599260463
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. doi:10.1046/j.1461-0248.1999.22060.x
14. Paradis E. 1998. Detecting shifts in diversification rates without fossils. American Naturalist 152: 176–187. doi:10.1086/286160
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. doi:10.1111/j.1469-7998.1998.tb00105.x
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. [PDF]
11. Paradis E. 1998. Interactions between spatial and temporal scales in the evolution of dispersal rate. Evolutionary Ecology 12: 235–244. doi:10.1023/A:1006539930788
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. doi:10.1046/j.1365-2656.1998.00215.x
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. doi:10.1098/rspb.1997.0158
8. Paradis E. 1997. Metapopulations and chaos: on the stabilizing influence of dispersal. Journal of Theoretical Biology 186: 261–266. doi:10.1006/jtbi.1996.0364
7. Paradis E. 1995. Chaos and scale. Trends in Ecology & Evolution 10: 335. doi:10.1016/S0169-5347(00)89121-1
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. doi:10.1139/z95-179
5. Paradis E. 1995. Survival, immigration and habitat quality in the Mediterranean pine vole. Journal of Animal Ecology 64: 579–591. doi:10.2307/5801
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. doi:10.2307/3809012
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.

Book Reviews

Reviewing

I am a member of the editorial board of Methods in Ecology and Evolution.

I reviewed at least once for the following journals:
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