Laboratory of Artificial & Natural Evolution

(Michel C. Milinkovitch’s lab)



For our publications after 2005, please click this link.

Access to our publications

  1. BulletThis icon indicates that the corresponding publication is ‘Open Access’: just click on the reference link to freely access the PDF file;

  2. If you have a subscription to the journal, just click on the reference link to reach the corresponding journal web page;

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Book chapters

List at the bottom of this page.

Articles in Peer-Reviewed International Journals


  1. 55.Rosa S., Milinkovitch M.C., Van Waerebeek K., Berck J., Oporto J., Alfaro-Shigueto J., Van Bressem M.F., Goodall N. & I. Cassens
    Population structure of nuclear and mitochondrial DNA variation among South American Burmeister’s porpoises (Phocoena spinipinnis)
    Conservation Genetics 6: 431–443 (2005)

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  3. 56.Bossuyt F., Meegaskumbura M., Beenaerts N., Gower D.J., Pethiyagoda R., Roelants K., Mannaert A., Wilkinson M., Bahir M.M., Manamendra-Arachchi K., Ng P.K.L., Schneider C. J., Oommen O.V. & M. C. Milinkovitch
    Biodiversity in Sri Lanka and the Western Ghats
    Science, 308: 199 (2005)

  4. BulletDownload a FREE reprint (PDF) of the article

  5. 57.Mardulyn P. & M. C. Milinkovitch
    Inferring contemporary levels of gene flow and demographic history in a local population of leaf beetles (Gonioctena olivacea) from mitochondrial DNA sequence variation
    Molecular Ecology 14: 1641-1653 (2005)

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  7. 58.Szpirer C. Y. & M. C. Milinkovitch
    Separate-Component-Stabilization (SCS) System for protein and DNA production without the use of antibiotics
    Biotechniques 38: 775-781 (2005)

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  9. 59.Cassens I., Mardulyn P. & M. C. Milinkovitch
    Evaluating Intraspecific “Network” Construction Methods Using Simulated Sequence Data: Do Existing Algorithms Outperform the Global Maximum Parsimony Approach?
    Systematic Biology 54: 363-372 (2005)

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  11. BulletAppendix_1

  12. 60.Cassens I., Van Waerebeek K., Best P.B., Tzika A., Van Helden A.L., Crespo E.A. & M. C. Milinkovitch
    Evidence for male dispersal along the coasts but no migration in pelagic waters in dusky dolphins (Lagenorhynchus obscurus)
    Molecular Ecology, 14 : 107-121 (2005)

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  14. 61.Bossuyt F., Meegaskumbura M., Beenaerts N., Gower D.J., Pethiyagoda R., Roelants K., Mannaert A., Wilkinson M., Bahir M. M., Manamendra-Arachchi K., Ng P.K.L., Schneider C. J., Oommen O.V. & Michel C. Milinkovitch
    Local Endemism Within the Western Ghats-Sri Lanka Biodiversity Hotspot
    Science, 306: 479-481 (2004)

  15. BulletDownload a FREE reprint (PDF) of the article

  16. BulletOpen Access: supplementary data

  17. BulletCoverage: this week in  Science

  18. 62.Milinkovitch M. C., Caccone A. & G. Amato
    Molecular phylogenetic analyses indicate extensive morphological convergence between the ‘‘yeti’’ and primates
    (April’s fool day paper in the 1st of April Issue of MPE)

    Molecular Phylogenetics and Evolution 31: 1–3 (2004)

  19. BulletThe Yeti story ^_^

  20. BulletThe Yeti page on our website

  21. 63.Radjef N., Gordien E., Ivaniushina V., Gault E., Anaïs P., Drugan T., Trinchet J.C., Roulot D., Tamby M., Milinkovitch M.C. & P. Dény
    Molecular Phylogenetic Analyses Indicate a Wide and Ancient Radiation of African Hepatitis Delta Virus, Suggesting a Deltavirus Genus of at Least Seven Major Clades
    Journal of Virology, 78:2537-2544 (2004)

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  23. 64.Milinkovitch M.C., Monteyne D., Gibbs J.P., Fritts T.H., Tapia W., Snell H.L., Tiedemann R., Caccone A. & J. R. Powell
    Genetic analysis of a successful repatriation program: Giant Galápagos tortoises
    Proceedings of the Royal Society, London, B, 271: 341-345 (2004)

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  25. Check also the “News Feature” in Nature (2004, vol. 429: pages 498-500) “One of a kind” by H. Nicholls

  26. BulletCoverage in Nature

  27. 65.Burns C.E., Ciofi C., Beheregaray L.B., Fritts T.H., Gibbs J.P., Márquez C., M. C. Milinkovitch, Powell J.R. & A. Caccone
    The origin of captive Galápagos tortoises based on DNA analysis: Implications for the management of natural populations
    Animal Conservation, 6: 329 – 337 (2003)

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  29. 66.Löytynoja A. & M. C. Milinkovitch
    A hidden Markov model for progressive multiple alignment
    Bioinformatics, 19: 1505–1513 (2003)

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  31. Check also Gardner et al. (2005): Nucleic Acids Research, Vol. 33, 2433-2439. They performed a benchmark of multiple sequence alignment programs upon structural RNAs, and their analyses indicate that ProAlign generally outperforms other sequence-based algorithms, under the broadest range of applications

  32. BulletGardner_etal_NAR_2005.pdf

  33. 67.Cassens I., Van Waerebeek K., Best P. B., Crespo E.A., Reyes J. & M. C. Milinkovitch
    The phylogeography of dusky dolphins (Lagenorhynchus obscurus): a critical examination of network methods and rooting procedures
    Molecular Ecology, 12: 1781-1792 (2003)

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  35. 68.Mardulyn P., Termonia A. & M. C. Milinkovitch
    Structure and evolution of the mitochondrial control region in leaf beetles (Coleoptera: Chrysomelidae): a hierarchical analysis of genetic variation
    Journal of Molecular Evolution, 56: 38-45 (2003)

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  37. 69.Meegaskumbura M., Bossuyt F., Pethiyagoda R., Manamendra-Arachchi K., Bahir M.,Milinkovitch M. C. & C. J. Schneider
    Sri Lanka: An Amphibian Hotspot
    Science, 298: 379 (2002)

  38. BulletDownload a FREE reprint (PDF) of the article

  39. BulletSupporting Material

  40. 70.Ciofi C., Milinkovitch M. C., Gibbs J.P., Caccone A. & J. R. Powell
    Microsatellite analysis of genetic divergence among populations of giant Galápagos tortoises
    Molecular Ecology, 11: 2265-2283 (2002)

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  42. BulletAppendix

  43. 71.Fournier D., Aron S. & M. C. Milinkovitch
    Investigation of the Population Genetic Structure and Mating System in the Ant Pheidole pallidula
    Molecular Ecology, 11: 1805-1814 (2002)

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  45. 72.Lemmon A. R. & M. C. Milinkovitch
    The metapopulation genetic algorithm: an efficient solution for the problem of large phylogeny estimation
    PNAS, 99: 10516-10521 (2002)

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  47. BulletSupplementary Material

  48. BulletCoverage: Science Editor Choice

  49. BulletDownload the metaPIGA software

  1. 73.Termonia A., Pasteels J.M., Windsor D.M. & M. C. Milinkovitch
    Dual Chemical Sequestration, a Key Mechanism in Transitions Among Ecological Specializations
    Proceedings of the Royal Society, London, B, 269: 1-6 (2002)

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  3. 74.Milinkovitch M. C. & I. Cassens
    Deciphering River Dolphin Evolution
    Science (Letter, not a research paper), 294, 787 (2001)

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  5. 75.Löytynoja A. & M. C. Milinkovitch
    Molecular Phylogenetic Analyses of the Mitochondrial ADP-ATP Carriers (AAC): The Plantae/Fungi/Metazoa Trichotomy Revisited
    PNAS, 98: 10202-10207 (2001)

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  7. BulletSupplementary Materials

  8. 76.Löytynoja A. & M. C. Milinkovitch
    SOAP, a program for cleaning multiple alignments from unstable blocks
    Bioinformatics, 17: 573-574 (2001)

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  10. 77.Bossuyt F. & M. C. Milinkovitch
    Amphibians as Indicators of Early Tertiary 'Out-of-India' Dispersal of Vertebrates
    Science 292: 93-95 (2001)

  11. BulletDownload a FREE reprint (PDF) of the article

  12. 78.Termonia A., Hsiao T. H., Pasteels J.M. & M. C. Milinkovitch
    Feeding specialization and host-derived chemical defense in Chrysomeline leaf beetles did not lead to an evolutionary dead end
    PNAS, 98: 3909-3914 (2001)

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  14. 79.Shedlock A.M., Milinkovitch M. C. & N. Okada
    SINE evolution, missing data, and the origin of whales
    Systematic Biology, 49: 808-817 (2000)

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  16. 80.Cassens I., Vicario S., Waddell V. G., Balchowsky H., Van Belle D., Wang Ding, Chen Fan, Lal Mohan R.S., Simões-Lopes P. C., Bastida R., Meyer A., Stanhope M. J. & M. C. Milinkovitch
    Independent Adaptation to Riverine Habitats Allowed Survival of Ancient Cetacean Lineages
    PNAS, 97: 11343-11347 (2000)

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  1. 81.Eeckhaut I., McHugh D., Mardulyn P., Tiedemann R., Monteyne D., Jangoux M.,
    & M C. Milinkovitch
    Myzostomida: a Link between Trochozoans and Flatworms
    Proceedings of the Royal Society, London, B, 267: 1383-1392 (2000)

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  3. Cited as «A puzzling Metazoan Body Plan», Editor’s Choice Section; Science 289: 217.

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  1. 82.Bossuyt F. & M. C. Milinkovitch
    Convergent Adaptive Radiations in Madagascan and Asian Ranid Frogs Reveal Co-variation between Larval
    and Adult Traits

    PNAS 97: 6585-6590 (2000)

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  3. 83.Waddell V. G., Milinkovitch M. C., Bérubé M. & M. J. Stanhope
    Molecular phylogenetic examination of the Delphinoidea trichotomy: Congruent evidence from three nuclear loci indicates that porpoises (Phocoenidae) share a more recent common ancestry with white whales (Monodontidae) than they do with true dolphins (Delphinidae)
    Molecular Phylogenetics and Evolution, 15(2): 314–318 (2000)

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  5. 84.Tiedemann R., Hardy O., Vekemans X. & M. C. Milinkovitch
    Higher Impact of Female than Male Migration on Population Structure in Large Mammals
    Molecular Ecology, 9: 1159-1163 (2000)

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  7. 85.Goujon C. P., Schneider V. M., Grofti J., Montigny J., Jeantils V., Astagneau P., Rozenbaum W., Lot F., Frocrain-Herchkovitch C., Delphin N., Le Gal F., Nicolas J.C., Milinkovitch M. C. & P. Dény
    Phylogenetic Analyses Indicate an Atypical Nurse-to-Patient Transmission of HIV-1
    Journal of Virology, 74: 2525-2532 (2000)

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Before 2000

  1. 86.Tiedemann R. & M. C. Milinkovitch
    Culture and Genetic Evolution in Whales
    Science, 284: 2055a (1999)

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  3. 87.Gatesy J., Milinkovitch M. C., Waddelld V. & M. Stanhope
    Stability of Cladistic Relationships between Cetacea  and Higher Level Artiodactyl Taxa
    Systematic Biology, 48: 6-20 (1999)

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  5. 88.Milinkovitch M. C. & J.G.M. Thewissen
    Even-toed Fingerprints on Whale Ancestry
    Nature, 388: 622-624 (1997)

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  7. 89.Caccone A., Milinkovitch M. C., Sbordoni V. & J. R. Powell
    Mitochondrial DNA Rates and Biogeography in European Newts (Genus Euproctus)
    Systematic Biology, 46: 126-144 (1997)

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  9. 90.Mardulyn P., Milinkovitch M. C., & J. M. Pasteels
    Phylogenetic Analyses of DNA and Allozyme Data Suggest that Gonioctena Leaf Beetles (Coleoptera; Chrysomelidae) Experienced Convergent Evolution in Their History of Host-Plant Family Shifts
    Systematic Biology 46: 722-747 (1997)

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  11. 91.Hasegawa M., Adachi J., & M. C. Milinkovitch
    Novel Phylogeny of Whales Supported by Total Molecular Evidence
    Journal of Molecular Evolution, 44(Suppl 1): S117-S120 (1997)

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  13. 92.Milinkovitch M. C., Leduc R. G., Adachi J., Farnir F., Georges M., & M. Hasegawa
    Effects of character weighting and species sampling on phylogeny reconstruction: a case study based on DNA sequence data in cetaceans
    Genetics, 144: 1817-1833 (1996)

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  1. 93.Milinkovitch M.C.
    Molecular Phylogeny of Cetaceans Prompts Revision of Morphological transformations
    Trends in Ecology and Evolution, 10: 328-334 (1995)

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  3. 94.Milinkovitch M. C., Ortí G. & A. Meyer
    Novel Phylogeny of Whales Revisited but not Revised
    Molecular Biology & Evolution, 12: 518-520 (1995)

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  5. 95.Milinkovitch M. C., Meyer A. & J. R. Powell
    Phylogeny of All Major Groups of Cetaceans Based on DNA Sequences from Three Mitochondrial Genes
    Molecular Biology & Evolution, 11: 939-948 (1994)

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  7. 96.Vrana P.B., Milinkovitch M.C., Powell J.R., & W.C. Wheeler
    Higher level relationships of the arctoid Carnivora based on sequence data and “total evidence”
    Molecular Phylogenetics and Evolution, 3: 47-58 (1994)

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  9. 97.Milinkovitch M. C., Dunn J. L. & J. R. Powell
    Exfoliated Cells as the Most Accessible DNA Source for Captive Whales and Dolphins
    Marine Mammal Science, 10: 125-128 (1994)

  10. 98.Caccone A., Milinkovitch M. C., Sbordoni V. & J. R. Powell
    Molecular Biogeography: Using the Corsica-Sardinia Microplate Disjunction to Calibrate Mitochondrial rDNA Evolutionary Rates in Mountain Newts (Euproctus)
    Journal of Evolutionary Biology, 7: 227-245 (1994)

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  12. 99.Milinkovitch M. C.
    The Coelacanth Controversy
    American Scientist, 81: 210 (1993)

  13. 100.Milinkovitch M. C., Ortí G. & A. Meyer
    Revised Phylogeny of Whales Suggested by Mitochondrial Ribosomal DNA Sequences
    Nature, 361: 346-348 (1993)

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  15. 101.Milinkovitch M. C.
    DNA-DNA Hybridizations Support Ungulate Ancestry of Cetacea
    Journal of Evolutionary Biology, 5: 149-160 (1992)

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Book chapters

  1. 5.Milinkovitch M. C., LeDuc R., Tiedemann R., & A. Dizon
    Applications of Molecular Data in Cetacean Taxonomy and Population Genetics with Special Emphasis
    on Defining Species Boundaries
    Pages 325-359 in: ‘Marine Mammals: Biology and Conservation’ (Evans, P. G. H., and J. A. Raga eds.),
    Kluwer Academic Press 2002

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  1. 6.Milinkovitch M. C., Bérubé M. & P. J. Palsbøll
    Cetaceans Are Highly Derived Artiodactyls
    Pages 113-131 in: ‘The Emergence of Whales: Evolutionary Patterns in the Origin of Cetacea’, (Thewissen Ed.),
    Plenum, New York 1998

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  1. 7.Milinkovitch M. C.
    The Phylogeny of Whales: a Molecular Approach
    Pages 317-338 in: ‘Molecular Genetics of Marine Mammals’, (A. Dizon et al. Eds.), Special Publication Number 3,
    The Society for Marine Mammology 1998

Papers we should probably not have published

  1. In two studies (listed below), we have used RASA (relative apparent synapomorphy analysis), a method developed by Lyons-Weiler et al. (Mol. Biol. Evol 13:749-757 (1996)) for detecting phylogenetic signal and selecting the best outgroups. However, Simmons et al. (Molecular Biology and Evolution 19:14-23 (2002)) convincingly demonstrated that the RASA method is vastly limited (if not flawed) in its ability to detect phylogenetic signal. We therefore suggest the reader to consider the analyses in the two papers below as dubious, at best.

  2. Lyons-Weiler J. & M.C. Milinkovitch
    A Phylogenetic Approach to the Problem of Differential Lineage Sorting
    Molecular Biology & Evolution, 14: 968-975 (1997)

  3. Milinkovitch M.C. & J. Lyons-Weiler
    Finding Optimal Ingroup Topologies and Convexities when the Choice of Outgroup Is not Obvious
    Molecular Phylogenetics & Evolution, 9: 348-357 (1998)


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