Books | Peer-Reviewed Articles | On-line Publications | Invited Articles | Book Chapters | Book Reviews | Article Reviews | Reviewing

Publications

Books

Paradis E. 2022. R Programming and Development: From Basics to Advanced Topics. https://hal.ird.fr/ird-03850685/.
NEW Solutions to the exercises can be found HERE. (This is work in progress.)

Paradis E. 2020. Population Genomics with R. Chapman & Hall, Boca Raton.

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.

Peer-Reviewed Articles

2024
80. Bouret S., Paradis E., Prat S., Castro L., Gilissen E. & Garcia C. 2024. Linking the evolution of two prefrontal brain regions to social and foraging challenges in primates. eLife 12:RP87780
DOI: https://doi.org/10.7554/eLife.87780. HAL: hal-04753797.
2023
79. Azizan A., Anile S., Nielsen C., Paradis E. & Devillard S. 2023. Population density and genetic diversity are positively correlated in wild felids globally. Global Ecology and Biogeography 32: 1858–1869.
DOI: https://doi.org/10.1111/geb.13727. HAL: hal-04162821.
78. Paradis E. 2023. Information-energy equivalence and the emergence of self-replicating biological systems. BioSystems 226: 104885.
DOI: 10.1016/j.biosystems.2023.104885. HAL: ird-04892566.
77. Paradis E., Claramunt S., Brown J. & Schkiep K. 2023. Confidence intervals in molecular dating by maximum likelihood. Molecular Phylogenetics and Evolution 178: 107652.
DOI: 10.1016/j.ympev.2022.107652. Share link: https://authors.elsevier.com/a/1g5DL3m3nN6QhS. HAL: ird-04892561.
2022
76. Pothasin P., Paradis E., Brockelman W. Y., Nathalang A., Khemrugka T., Lomwong N., Tripob P., Saenprasert R. & Chanthorn W. 2022. Seed size variation of trees and lianas in a tropical forest of Southeast Asia: allometry, phylogeny and trait-trait relationships. Frontiers in Plant Science 13
DOI: 10.3389/fpls.2022.852167. HAL: ird-03699157.
75. Paradis E. 2022. Probabilistic unsupervised classification for large-scale analysis of spectral imaging data. International Journal of Applied Earth Observations and Geoinformation 107: 102675.
DOI: 10.1016/j.jag.2022.102675. HAL: ird-03699062.
74. Paradis E. 2022. Reduced multidimensional scaling. Computational Statistics 37: 91–105.
DOI: 10.1007/s00180-021-01116-0. HAL: ird-03699153.
2021
73. Bochaton C., Paradis E., Bailon S., Grouard S., Ineich I., Lenoble A., Lorvelec O., Tresset A. & Boivin N. 2021. Large-scale reptile extinctions following European colonization of the Guadeloupe Islands. Science Advances 7: eabg2111.
DOI: 10.1126/sciadv.abg2111. HAL: hal-03264827.
72. Piyapong C., Chamroensaksri N., Aroonsrimorakot S., Eyosawat L., Khankhum S., Rattana S., Sunthamala N., Warapetcharayu P. & Paradis E. 2021. A predictive model of the impact of urbanization on bacterial loads in watersheds. Journal of Cleaner Production 297: 126704.
DOI: 10.1016/j.jclepro.2021.126704. HAL: ird-03699134.
71. Azizan A. & Paradis E. 2021. Patterns and drivers of genetic diversity among Felidae species. Biodiversity and Conservation 30: 519–546.
DOI: 10.1007/s10531-020-02103-5. HAL: ird-03699141.
2020
70. Paradis E. 2020. Forest gains and losses in Southeast Asia over 27 years: the slow convergence towards reforestation. Forest Policy and Economics 122: 102332.
DOI: 10.1016/j.forpol.2020.102332. HAL: hal-03493968.
69. Paradis E. 2020. A review of computer tools for prediction of ecosystems and populations: we need more open-source software. Environmental Modelling & Software 134: 104872.
DOI: 10.1016/j.envsoft.2020.104872. HAL: hal-03491480.
68. Piyapong C., Tattoni C., Ciolli M., Dembski S. & Paradis E. 2020. Modelling the geographical distributions of one native and two introduced species of crayfish in the French Alps. Ecological Informatics 60: 101172.
DOI: 10.1016/j.ecoinf.2020.101172. HAL: hal-03492984.
67. Paradis E. 2020. Modelling transition in land cover highlights forest losses and gains in Southeast Asia. Biodiversity and Conservation 29: 2539–2551.
DOI: 10.1007/s10531-020-01987-7. SharedIt link: https://rdcu.be/b4kWf. HAL: ird-03699097.
66. Kadarusman, Sugeha H. Y., Pouyaud L., Hocdé R., Hismayasari I. B., Gunaisah E., Widiarto S. B., Arafat G., Widyasari F., Mouillot D. & Paradis E. 2020. A thirteen-million-year divergence between two lineages of Indonesian coelacanths. Scientific Reports 10: 192.
DOI: 10.1038/s41598-019-57042-1. HAL: ird-02438220.
2019
65. Atindehou M., Adéoti K., Yêyinou Loko L. E., Beulé T., Paradis E., Djedatin G., Tranchant-Dubreuil C., Sabot F., Lagnika L. & Jaligot E. 2019. MooSciTIC: training of trainers in West African research and higher education. PLoS Biology 17: e3000312.
DOI: 10.1371/journal.pbio.3000312. HAL: ird-02365690.
64. Paradis E. & Schliep K. 2019. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35: 526–528.
DOI: 10.1093/bioinformatics/bty633. Free access link: https://academic.oup.com/.... HAL: ird-01920132.
2018
63. Warren B. H., Hagen O., Gerber F., Thébaud C., Paradis E. & Conti E. 2018. Evaluating alternative explanations for an association of extinction risk and evolutionary uniqueness in multiple insular lineages. Evolution 72: 2005–2024.
DOI: 10.1111/evo.13582. HAL: ird-01920133.
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. HAL: ird-01920131.
61. Paradis E. 2018. Multidimensional scaling with very large data sets. Journal of Computational and Graphical Statistics 27: 935–939.
DOI: 10.1080/10618600.2018.1470001. HAL: ird-01920130.
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. HAL: ird-02063037.
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. HAL: ird-01887318.
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. HAL: ird-02063040.
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. HAL: ird-02063041.
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. HAL: ird-02063958.
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. HAL: ird-02062888.
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. HAL: ird-02062359.
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.
HAL: ird-02061421.

On-line Publications

R for beginners (2002, 2005).

Invited Articles

Book Chapters

Book Reviews

Article Reviews

Reviewing

I was a member of the editorial board of Methods in Ecology and Evolution from 2010 until 2019.

I reviewed at least once for the following journals:
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