Conservation Genetics,

Population Genetics &



Additional information on specific projects is available below


Check here our project on the phylogeography of colour variation in Panther Chameleons (F. pardalis) from Madagscar.


Check here our project on the captive breeding program & management of natural populations of this endemic Jamaican snake


Check here our work on the population genetics, phylogeography, & management of captive-breeding programs of these fascinating endemic reptiles


Check here our work on the population genetics & phylogeography of these large endemic lizard


Check here our work on the management of wild & captive populations of the largest extant lizard species


Check here our work on the conservation genetics of dusky dolphins & Burmeister’s porpoises

IN-SILICO (computer) simulations

Check here our simulations of large mammal populations using  individual-based stochastic models

IN-VIVO simulations

Check here our work on laboratory-controlled populations of nematods


It is indisputable that environmental changes, including major climatic events and human disturbances, have a striking impact on the biodiversity of ecosystems.  However, understanding the mechanisms that affect and influence the evolution of biodiversity is not a simple task.  We approach the problem at the level of model organisms’ genomes. We attempt to describe the genetic diversity variations (in time and space) caused by natural history (e.g., social systems), genetic (e.g., mitochondrial vs. nuclear DNA), but also historical (e.g., environmental changes and human exploitation) parameters. Given their predictive value, the results of these endeavours can significantly contribute, among others, to environment policy decisions. Several of our analyses have lead to practical recommendations for natural or captive population management (South-American dolphins, Galápagos giant tortoises, Galápagos land iguanas, Jamaican boas …). Check the left column of this web page for additional information.

Analyses of molecular data

By integrating phylogenetic, coalescence, and population genetic approaches, we investigate in several natural populations of (mostly vertebrate) species, the influence of historical factors on the present stratification and levels of genetic diversity. We use multiple molecular markers including microsatellites and SNPs. Furthermore, when gene flow remains low, intra-specific genealogical lineages can be investigated through phylogenetic methods and their diversity correlated to their geographic distribution (= phylogeographic approach). We will concentrate our efforts in the near future on populations of South-American dolphins as well as on large reptile species (such as the Galápagos giant tortoises, Galápagos land iguanas, Jamaican boas, and Komodo dragons).

In-silico and in-vitro simulations

Beside gathering and analyzing new molecular markers in natural populations, we also use population models in computer simulation studies. This approach allows investigating the influence of any combination of relevant parameters on the dynamic of population structure and diversity. The predictions made during simulation studies can then be validated with real data from natural populations. Furthermore, using Caenorhabditis remanei as an eukaryotic model, we have developed in vitro simulations of population events for testing the efficiency and accuracy of existing analytical methods for the inference of population size variation, levels of gene flow, and fragmentation events.

Selected publications

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

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  3. 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)

  4. BulletOpen Access

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

  6. BulletCoverage in Nature

  7. 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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  9. 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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  11. 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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  13. 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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  15. 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)

  16. Bullete-mail: Article

  17. Bullete-mail: Supplementary File

  18. 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)

  19. BulletOpen Access

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

  21. Coverage

  22. Bulletcheck here

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