Publications

Books

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

2018
64. Warren B. H., Hagen O., Gerber F., Thébaud C., Paradis E. & Conti E. Evaluating alternative explanations for an association of extinction risk and evolutionary uniqueness in multiple insular lineages. Evolution (accepted)
63. Paradis E. & Schliep K. 2018. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics (in press)
DOI: 10.1093/bioinformatics/bty633. Free access link: https://academic.oup.com/....
62. Paradis E. 2018. Nonlinear relationship between biodiversity and human population density: evidence from Southeast Asia. Biodiversity and Conservation 27: 2699–2712.
DOI: 10.1007/s10531-018-1563-5. SharedIt link: https://rdcu.be/Ql76.
61. Paradis E. 2018. Multidimensional scaling with very large data sets. Journal of Computational and Graphical Statistics (in press)
DOI: 10.1080/10618600.2018.1470001.
60. Paradis E. 2018. Analysis of haplotype networks: the randomized minimum spanning tree method. Methods in Ecology and Evolution 9: 1308–1317.
DOI: 10.1111/2041-210X.12969. HAL: ird-01822368.
2017
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 12: e0182618.
DOI: 10.1371/journal.pone.0182618. HAL: hal-01593655.
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. HAL: hal-01470522.
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. HAL: hal-01502248.
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. HAL: ird-01832665.
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. HAL: hal-01605538.
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. HAL: hal-01821977.
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. HAL: hal-01821911.
2016
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. HAL: hal-01821952.
2015
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. HAL: hal-01821944.
2014
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. HAL: hal-01821908.
2013
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. HAL: hal-01821922.
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. HAL: halsde-00837844.
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. HAL: ird-01813101.
2012
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. HAL: hal-01822119.
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. HAL: hal-01822124.
2011
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. HAL: hal-00722758.
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. HAL: hal-01822128.
2010
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.
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. HAL: hal-01822130.
2009
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.
2008
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. HAL: hal-01822133.
2006
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. HAL: halsde-00324005.
2005
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. HAL: hal-01822136.
2004
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.
2003
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.
2002
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.
2001
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.
2000
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.
1999
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.
1998
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.
DOI: 10.1093/oxfordjournals.molbev.a025946.
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.
1997
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.
1995
7. Paradis E. 1995. Chaos and scale. Trends in Ecology & Evolution 10: 335.
DOI: 10.1016/S0169-5347(00)89121-1. HAL: ird-01841222.
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.
1993
4. Paradis E. & Guédon G. 1993. Demography of a mediterranenan microtine: the Mediterranean pine vole, Microtus duodecimcostatus. Oecologia 95: 47–53.
DOI: 10.1007/BF00649505.
3. Paradis E. & Guédon G. 1993. Long lifespan in a population of Microtus (Pitymys) duodecimcostatus. Mammalia 57: 142–144.
HAL: hal-01827272.
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.
1992
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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