Laboratory of Artificial & Natural Evolution

(Michel C. Milinkovitch’s lab)



Access to our publications

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Book chapters

List at the bottom of this page.

Articles in Peer-Reviewed International Journals


  1. 1.Manukyan L., Montandon S.A., Fofonjka A., Smirnov S. & M.C. Milinkovitch
    A Living Mesoscopic Cellular Automaton Made of Skin Scales  
    Nature 544: 173-179 (2017) - doi:10.1038/nature22031

  2. If you don’t have access to a Nature subscription:

  3. SharedIt version (view-only)

  4. Send an email request to Michel C. Milinkovitch

  5. Supplementary videos:

  6. BulletVideo 1 - Video 2 - Video 3 - Video 4 - Video 5 - Video 6 - Video 7 - Video 8

  7. News&Views by Leah Edelstein-Keshet (University of British Columbia)

  8. Coverage by the New York Times

  9. 2.Daljit Singh J. Dhillon, Michel C. Milinkovitch & Matthias Zwicker
    Bifurcation Analysis of Reaction Diffusion Systems on Arbitrary Surfaces 
    Bulletin of Mathematical Biology (2017)- doi:10.1007/s11538-017-0255-8
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  1. 3.Guerreiro S., Gitto S., Novoa A., Codourey J., Nguyen Huynh T.H., Gonzalez F, Milinkovitch M.C.,
    Mallo M., & D. Duboule
    Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan 
    eLife 2016;5:e16087

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  1. 4.Di-Poï N. & M. C. Milinkovitch
    The Anatomical Placode in Reptile Scale Morphogenesis Indicates Shared Ancestry
    Among Skin Appendages in Amniotes 
    Science Advances 2, e1600708 (2016) -   doi: 10.1126/sciadv.1600708

  2. BulletOpen Access

  3. BulletSupporting movie

  4. Additional coverage

  5. Bulletcheck here


  1. 5.Many authors including Athanasia Tzika & Asier Ullate-Agote
    The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases 
    Nucleic Acids Research (2015)   -   doi: 10.1093/nar/gkv1310

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  1. 6.Saenko S.V., Lamichhaney S., Martinez Barrio A., Rafati N., Andersson L. & M. C. Milinkovitch
    Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 gene 
    Scientific Reports 5, 17118 (2015)

  2. BulletOpen Access

  3. BulletDownload the Supplementary Materials file

  1. 7.Tzika A.C., Ullate-Agote A., Grbic D. & M. C. Milinkovitch
    Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics
    Genome Biol. Evol.  7: 1827-1841 (2015)

  2. BulletOpen Access

  3. BulletDownload the Supplementary Materials file

  4. BulletDatabase website: Reptilian-Transcriptomes v2.0

  5. 8.Martins A., Bessant M., Manukyan L. & M.C. Milinkovitch.
    R2OBBIE-3D, a Fast Robotic High-Resolution System for Quantitative Phenotyping of Surface Geometry and Colour-Texture
    PLOS ONE 10(6): e0126740 (2015) - doi:10.1371/journal.pone.0126740
  6. BulletOpen Access

  7. BulletSupporting File 1 (Supp. Figs A-I, Legends of Supp. Movies S1-S5, Links to Supp. 3D-Model Files).

  8. BulletSupporting Movies on the PLOS ONE web site

  9. BulletSupporting movies S1-S5

  10. Coverage

  11. Bulletcheck here

  1. 9.Grbic D., Saenko S.V., Randriamoria T.M., Debry A., Raselimanana A.P. & M.C. Milinkovitch.
    Phylogeography and Support Vector Machine Classification of Colour Variation in Panther Chameleons
    Molecular Ecology (2015) 24, 3455–3466

  2. BulletOpen Access

  3. BulletAdditional File 1 (Additional Discussion, Tables S1-S4, Figs. S1-S6).

  4. Coverage

  5. Bulletcheck here

  1. 10.Teyssier J., Saenko S.V., van der Marel D. & M.C. Milinkovitch.
    Photonic Crystals Cause Active Colour Change in Chameleons
    Nature Communications 6: 6368 (2015)

  2. BulletOpen Access

  3. BulletSupporting Information (Suppl Figs 1-4, Suppl Table 1, Suppl Text and Refs)

  4. BulletSupporting movies S1-S5

  5. Coverage

  6. Bulletcheck here

  1. 11.Ullate-Agote A., Milinkovitch M.C. & A.C. Tzika
    The genome sequence of the corn snake (Pantherophis guttatus), a valuable resource
    for EvoDevo studies in squamates
    Int. J. Dev. Biol. 58: 881-888 (2014)

  2. BulletOpen Access

  3. BulletDownload the Cover

  1. 12.Cornelis G., Vernochet C., Malicorne S., Souquerre S., Tzika A.C., Goodman S.M., Catzeflis F., Robinson T.J., Milinkovitch M.C., Pierron G., Heidmann O., Dupressoir A. & T. Heidmann
    Retroviral envelope syncytin capture in an ancestrally diverged mammalian clade for placentation in the primitive Afrotherian tenrecs
    PNAS 2014, 111: E4332-E4341
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  1. 13.Dhillon D.S., Teyssier J., Single M., Gaponenko I.,  Milinkovitch M.C. & M. Zwicker
    Interactive Diffraction from Biological Nanostructures
    Computer Graphics forum 33: 177-188 (2014)

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  1. 14.Montandon S.A.*, Tzika A.C.*, Martins A., Chopard B. & M. C. Milinkovitch (*=co-first authors)
    Two Waves of Anisotropic Growth Generate Enlarged Follicles in the Spiny Mouse
    EvoDevo 2014, 5: 33

  2. BulletOpen Access

  3. BulletSupplementary text, appendices, and supplementary figures

  4. BulletSupplementary movie 1

  5. BulletSupplementary movie 2

  1. 15.Saenko S., Teyssier J., van der Marel D. & M. C. Milinkovitch
    Precise colocalization of interacting structural and pigmentary elements generates extensive color pattern variation in Phelsuma lizards
    BMC Biology 2013, 11: 105

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  3. BulletMovies

  1. 16.Delpretti S., Montavon T., Leleu M., Joye E., Tzika A.C., Milinkovitch M.C. and D. Duboule
    Multiple enhancers and the Hotdog lncRNA gene regulate HoxD genes in a topological domain during caecum budding
    Cell Reports 5: 1–14 (2013)

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  3. BulletComment by Jeremy S. Dasen

  1. 17.Di-Poï N. & M.C. Milinkovitch
    Crocodylians Evolved Scattered Multi-Sensory Micro-Organs
    EvoDevo 2013, 4:19

  2. BulletOpen Access

  3. Coverage

  4. Check Q&A in Biome: online highlights from BioMed Central journals

  5. Check coverage (TV programs, Websites, and News Papers) HERE

  1. 18.Hautier L., Bennett N.C., Viljoen H., Howard L., Milinkovitch M.C., Tzika A.C., Goswami A. & R.J. Asher
    Patterns of ossification in southern vs. northern placental mammals
    Evolution 67: 1994-2010 (2013)

  2. BulletDownload

  1. 19.Brykczynska U., Tzika A.C., Rodriguez I. & M. C. Milinkovitch
    Contrasted evolution of the vomeronasal receptor repertoires in Mammals and Squamate reptiles
    Genome Biology & Evolution 5: 389-401 (2013)

  2. BulletOpen Access

  3. BulletDownload the Supplementary Materials file

  4. Access to the Reptilian Transcriptome web site

  1. 20.Milinkovitch M.C., Kanitz R., Tiedemann R., Tapia W., Llerena F., Caccone A., Gibbs J.P., Powell J.R.
    Recovery of a nearly extinct Galápagos tortoise despite minimal genetic variation
    Evolutionary Applications 6, 377–383 (2013)

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  1. 21.Milinkovitch M.C., Manukyan L., Debry A., Di-Poï N., Martin S., Singh D., Lambert D., Zwicker M.
    Crocodile Head Scales Are Not Developmental Units But Emerge from Physical Cracking
    Science 339, 78-81 (2013)
    DOI: 10.1126/science.1226265

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

  3. BulletDownload the Supplementary Materials file

  4. BulletWatch the Supplementary Movie (also available HERE and in YouTube)

  5. BulletCheck the slideshow from Science

  6. BulletCheck Sarah C. P. Williams’ article in ScienceNOW

  7. Coverage

  8. BulletCheck the slideshow from BBC Nature

  9. BulletCheck the Movie illustrating the Computer Graphics Tools (version 2)

  1. 22.Werneburg I., Tzika A.C., Hautier L., Asher R.J., Milinkovitch M.C. & M.R. Sanchez-Villagra
    Development and embryonic staging in non-model organisms: the case of an afrotherian mammal
    Journal of Anatomy 222: 2-18 (2013)

  2. BulletOpen Access

  3. BulletDownload the Article with the Cover

  4. BulletDownload the Supplementary files 1-3

  1. 23.Tzika A.C., Helaers R., Schramm G. & M. C. Milinkovitch
    Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent 
    Sauropsida lineages and the phylogenetic position of turtles
    EvoDevo 2011, 2: 19
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  3. Access to the Reptilian Transcriptome web site

  4. 24.Li X., Liu Y., Tzika A.C., Van Doninck K., Zhu Q. & M.C. Milinkovitch
    Analysis of global and local population stratification of finless porpoises Neophocaena phocaenoides in Chinese waters
    Marine Biology, 158: 1791–1804 (2011)

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  6. 25.Tiedemann R., Paulus K.B., Havenstein K., Thorstensen S., Petersen A., Lyngs P. & M. C. Milinkovitch
    Alien eggs in duck nests: brood parasitism or a help from Grandma?
    Molecular Ecology 20, 3237–3250 (2011)

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  1. 26.Ciofi C., Tzika A.C., Natali C., Watts P.C., Sulandari S., Zein M.S.A. & M. C. Milinkovitch
    Development of a multiplex PCR assay for fine-scale population genetic analysis of the Komodo monitor Varanus komodoensis based on 18 polymorphic microsatellite loci
    Molecular Ecology Resources 11, 550–556 (2011)

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  3. 27.Milinkovitch M.C., Helaers R., Depiereux E., Tzika A.C., & T. Gabaldon
    Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses (a response to Vilella et al.’s correspondence)
    Genome Biology, 12: 401 (2011)

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  1. 28.Tzika A.C., D’Amico E., Alfaro-Shigueto J., Mangel J.C., Van Waerebeek K. & M.C. Milinkovitch
    Molecular identification of small cetacean samples from Peruvian fish markets
    Conservation Genetics 11: 2207-2218 (2010)

  2. Bullete-mail: Article

  3. Bullete-mail: Supplementary File

  4. 29.Helaers R. & M.C. Milinkovitch
    MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics
    BMC Bioinformatics 2010, 11: 379

  5. BulletOpen Access

  6. BulletDownload the metaPIGA2 software here

  7. 30.Li X., Tzika A.C., Liu Y., Van Doninck K., Zhu Q. & M.C. Milinkovitch
    Preliminary Genetic Status of the Spotted Seal Phoca largha in Liaodong Bay Based on Microsatellite and Mitochondrial DNA Analyses
    Trends in Evolutionary Biology 2010, 2: e6

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  9. 31.Milinkovitch M.C., Helaers R., Depiereux E., Tzika A.C., & T. Gabaldon
    2X genomes - depth does matter
    Genome Biology, 11 (2): R16 (2010)
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  11. 32.Di-Poï N., Montoya-Burgos J.I., Miller H., Pourquié O., Milinkovitch M.C. & D. Duboule
    Changes in Hox genes’ structure and function during the evolution of the squamate body plan
    Nature, 464: 99-103 (2010)

  12. Bullete-mail: Article

  13. Bullete-mail: Supplementary File

  14. 33.Milinkovitch M.C., Helaers R., & A.C. Tzika
    Historical Constraints on Vertebrate Genome Evolution
    Genome Biololgy & Evolution 2010: 13-18 (2010)

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  16. 34.Van Doninck K., Mandigo M.L., Hur J.H., Wang P., Guglielmini J., Milinkovitch M.C., Lane W.S. & M. Meselson
    Phylogenomics of Unusual Histone H2A Variants in Bdelloid Rotifers
    PloS Genetics 5 (3): e1000401 (2009)

  17. BulletOpen Access

  18. 35.Ciofi C., Tzika A.C., Natali C., Chelazzi G., Naziridis T., & M.C. Milinkovitch
    Characterization of microsatellite loci in the European pond turtle Emys orbicularis
    Molecular Ecology Resources 9, 189–191 (2009)

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  20. 36.Tzika A. C., Remy C., Gibson R. & M. C. Milinkovitch
    Molecular Genetic Analysis of a Captive-Breeding Program: The Vulnerable Endemic Jamaican Yellow Boa
    Conservation Genetics 10:69–77 (2009)

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  22. 37.Rosa S.F.P, Monteyne D. & M. C. Milinkovitch
    Development of 10 highly-polymorphic microsatellite markers in the vulnerable Galápagos Land Iguanas (genus Conolophus)
    Molecular Ecology Resources 9, 376–379 (2009)

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  1. 38.Tzika A. C., Rosa S. F. P., Snell H. L., Snell H. M., Marquez C., Tapia W., Rassmann K., Gentile G.,
    & M. C. Milinkovitch
    Population genetics of Galápagos land iguana (genus Conolophus) remnant populations
    Molecular Ecology 17, 4943–4952 (2008)

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  3. 39.Mardulyn P., Vaesen M.A., & M. C. Milinkovitch
    Controlling population evolution in the laboratory to evaluate methods of historical inference
    PLoS ONE, 2008, 3(8): e2960

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  5. 40.Guglielmini J., Szpirer C., & M. C. Milinkovitch
    Automated Discovery and Phylogenetic Analysis of New Toxin-Antitoxin Systems
    BMC Microbiology, 8: 104 (2008)
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  7. 41.Tzika A. C., Koenig S., Miller R., Garcia G., Remy C. & M. C. Milinkovitch
    Population structure of an endemic vulnerable species, the Jamaican boa (Epicrates subflavus)
    Molecular Ecology 17, 533-544 (2008)

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  9. 42.Tzika A. C., Helaers R, Van de Peer Y. & M. C. Milinkovitch
    MANTiS: a phylogenetic framework for multi-species genome comparisons
    Bioinformatics, 24 (2):151-157 (2008)

  10. BulletOpen Access: article

  11. BulletOpenAccess: supplementary material

  12. BulletDownload the MANTiS software

  13. 43.Zheng J.S., Liao X.L., Tong J.G., Du H.J., Milinkovitch M.C., and D. Wang
    Development and characterization of polymorphic microsatellite loci in the endangered Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis)
    Conservation Genetics 9:1007–1009 (2008)

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  15. 44.Levasseur A., Orlando L., Bailly X, Milinkovitch M.C., Danchin E. & P. Pontarotti
    Conceptual bases for quantifying the role of the environment on gene evolution: the participation of positive selection and neutral evolution
    Biological reviews 82 (4): 551-572 (2007)

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  17. 45.Bleidorn C., Eeckhaut I., Podsiadlowski L., Schult N., Mchugh D., Halanych K.M., Milinkovitch M. C. & R. Tiedemann
    Mitochondrial genome and nuclear sequence data support Myzostomida as part of the annelid radiation
    Molecular Biology & Evolution 24(8): 1690–1701 (2007)

  18. BulletOpen Access

  19. 46.Catanzaro D., Pesenti R & M. C. Milinkovitch
    An Ant Colony Optimization Algorithm for Phylogeny Estimation under the Minimum Evolution Principle
    BMC Evolutionary Biology 7:228 (2007)
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  1. 47.Milinkovitch M.C. & A. C. Tzika
    Escaping the Mouse Trap; the Selection of New Evo-Devo Model Species
    Journal of Experimental Zoology (Mol. Dev. Evol.) 308B: 337–346 (2007)

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  3. BulletNews Coverage

  4. 48.Milinkovitch M.C., Monteyne D., Russello M., Gibbs J.P., Snell H.L., Tapia W., Marquez C., Caccone A.
    & J. R. Powell
    Giant Galápagos Tortoises: Molecular Genetic Analysis Reveals Contamination in a Repatriation Program of an Endangered Taxon
    BMC Ecology, 7:2 (2007)

  5. BulletOpen Access

  6. 49.Lemey P., Hillis D.M., Gonzalez Candelas F., Milinkovitch M.C., and T. Leitner
    Molecular HIV evidence backs accused medics - Expert opinion
    Nature (opinion, not a research paper) 444: 659-659 (2006)

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  8. 50.Gatto L., Catanzaro D. & M. C. Milinkovitch
    Assessing the Applicability of the GTR Nucleotide Substitution Model Through Simulations
    Evolutionary Bioinformatics Online 2: 153-163 (2006)

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  10. 51.Catanzaro D., Pesenti R. & M. C. Milinkovitch
    A nonlinear optimization procedure to estimate distances and instantaneous substitution rate matrices under the GTR model
    Bioinformatics, 22: 708-715 (2006)

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  12. 52.Schretter C. & M. C. Milinkovitch
    OligoFaktory: a visual tool for interactive oligonucleotide design
    Bioinformatics, 22: 115-116 (2006)

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  14. 53.Bossuyt F., Brown R.M., Hillis D.M., Cannatella D.C. & M. C. Milinkovitch
    Phylogeny and Biogeography of a Cosmopolitan Frog Radiation: Late Cretaceous Diversification Resulted in Continent-scale Endemism in the Family Ranidae
    Systematic Biology 55(4): 579)-594 (2006)

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  16. 54.Lanterbecq D., Rouse G.W., Milinkovitch M.C. & I. Eeckhaut
    Molecular Phylogenetic Analyses Indicate Multiple Independent Emergences of Parasitism in Myzostomida (Protostomia)
    Systematic Biology 55: 208–227 (2006)

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  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)

  46. BulletOpen Access

  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)

  6. BulletOpen Access

  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. 1.Tzika A.C., Helaers R.,  & M. C. Milinkovitch
    Mapping gene gains and losses among metazoan full genomes using an integrated phylogenetic framework
    Pages 173-184 (Chapter 9) in ‘Gene and Genome Duplication’ (K. Dittmar & D. Liberles eds.),
    Wiley-Blackwell 2010

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  3. BulletSupplementary material: colour versions of Fig.1 and Fig.2.

  1. 2.Ciofi C., Caccone A., Beheregaray L.B., Milinkovitch, M.C., Russello M., & J.R. Powell
    Genetics and conservation on islands: the Galápagos giant tortoise as a case study
    Pages 269-293 (Chapter 12) in ‘Population Genetics for Animal Conservation’ (Bertorelle G, Bruford M.W.,
    Hauffe H.C., Rizzoli A., & Vernesi C., eds.)
    Cambridge University Press 2009

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  1. 3.Mardulyn P., Cassens I. & M. C. Milinkovitch
    A comparison of methods for constructing evolutionary networks from intraspecific DNA sequence
    Pages 104-120 (Chapter 5) in ‘Population Genetics for Animal Conservation’ (Bertorelle G, Bruford M.W.,
    Hauffe H.C., Rizzoli A., & Vernesi C., eds.),
    Cambridge University Press 2009

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  1. 4.Tzika A. C. & M. C. Milinkovitch.
    A Pragmatic Approach for Selecting Evo-Devo Model Species in Amniotes
    Pages 119-140 (Chapter 7) in ‘Evolving Pathways; Key Themes in Evolutionary Developmental Biology’
    (A. Minelli & G. Fusco, eds.),
    Cambridge University Press 2008

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  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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