Molecular Phylogenetics

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’; http://www.pass.be).
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
    

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