Molecular Phylogenetics


Additional information on specific projects is available below


Check here our models, algorithms, and softwares for DNA & protein sequence alignment, for phylogeny inference, and other goals


Check here our work on the phylogenetic origin of cetaceans, phylogenetic relationships among the major groups of cetaceans, including river dolphins


Check here our work on the evolution and biogeography of amphibians (mostly ranid frogs)


Check here our phylogenetic analyses of  HIV & Hepatitis Delta Viruses


Check here our phylogenetic analyses of eukaryote major lineages, myzostomes, beetles, rotifers, poison-antidote genes, and others


Check here our work on the use of Short Interspersed Elements as phylogenetic markers


Analytical developments, Bioinformatics

Optimality-criterion based multiple-sequence alignment as well as phylogeny inference are notoriously difficult endeavours because the number of solutions increases explosively (factorially) with the number of taxa. Given the tremendous number of new questions in evolutionary biology that could be investigated through the use of larger taxon samplings, most researchers are ready to give up the quest for the absolute optimal tree, opting instead for the ability to analyze large data sets in practical computing times, provided that these methods yield optimal or near-optimal solutions with high probability. In response to this trend, much of the current research in phyloinformatics (i.e., computational phylogenetics) concentrates on the development of more efficient heuristic approaches.

We recently developed:

  1. A highly efficient genetic algorithm (metaGA, implemented in the software metaPIGA) for phylogeny inference;

  2. Hidden Markov model (HMM) progressive alignment algorithms

  3. Nucleotide substitution models

SOFTWARES and background information are available HERE.

Molecular Phylogenies

One of our contributions to the field of macro-evolutionary molecular genetics has been to infer historical information from DNA and protein sequences to uncover evolutionary modes and patterns of morphological, physiological, biogeographical, ecological, molecular, and epidemiological characters in taxonomic groups as diverse as HIV  & HDV viruses (molecular epidemiology), early eukaryotes, myzostomids, leaf beetles, amphibians, and cetaceans. Much additional information is available through these links:

  1. Phylogeny of cetaceans;

  2. Phylogeny of ranid frogs;

  3. Phylogenies and peidemiology of HIV & Hepatitis Delta virus;

  4. Other phylogenies (major eukaryotes, myzostomes, beetles, rotifers, and others).

Here are two old videos (filmed around 1998?) made for a science museum in Belgium (‘Le PASS: le Parc d’Aventures Scientifiques’, ‘The PASS, the Park of Scientific Adventures’;
Michel Milinkovitch explains how to generate and analyze molecular data for phylogeny inference (and he uses the example of the origin of cetaceans within mammals as well as the management of captive breeding in Galapagos tortoises).


Molecular Markers

Although we continue to produce new DNA sequence data that we analyze mostly with statistical (maximum likelihood) approaches, we also characterize promising molecular markers: SINEs (“Short Interspersed Nuclear Elements”).  It has been suggested that the insertion of a SINE at a given locus provides a perfect historical information because it would be void of “homoplasy” (i.e., noise).

Selected publications

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

  2. 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)

  3. 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)

  4. 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)

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

  6. 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)

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

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

  9. 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)

  10. 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)

  11. 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)

  12. 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

  13. 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)

  14. 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 PloS Genetics 5 (3): e1000401

Back to top