Thesis abstract

          In this work two types of sequences are used. They come all two of the mitochondrial genome of different groups of Lemuriforms (endemic Primates of Madagascar). The first is a fragment of 357 bp belonging to the cytochrome b and whose translation provides a sequence of 119 amino acids, and on the other is a fragment of 393 bp belonging to the 12S rRNA.

        These sequences are used in order to get a phylogenetic reconstruction, the most believable possible, capable to be, subsequently, used to replace the sequences coming from Lemuriforms sub fossils.

        The Lemuriforms used in the survey understand representatives of most kinds of Lemuridae (Eulemur, Hapalemur, and Varecia), of Indriidae (Indri, Propithecus, Avahi), of Lepilemuridae, of Cheirogaleidae (Cheirogaleus, Microcebus, Mirza),and of Daubentoniidae. The sequences determined from a Lepilemuridae sub fossil (Megaladapis edwardsi) are included also in the analysis. We also used the Tupaia whose taxonomic position is controversial, some works including them in the Strepsirhini, whereas others place them completely outside of these. A part of the sequences has been determined at the Laboratory, the other are extracted from the EMBL database. For the cytochrome b the sequences of 357 bp as well as those regrouping only positions 1 and 3 of each codon, as well as the proteic sequences, are analyzed. For the 12S rRNA the sequences of 393 bp and those corresponding to the zones 'loop' deducted of the secondary structure, are treated.

        In a first time the general features (nucleotidic frequencies, types of sites, transitions and transversions, ….) for the sequences of the different groups are determined. For the cytochrome b this survey permits to show that the phylogenetic information contained in the second positions of the codon is very weak, and that it is thus possible not to take account of it in the treatments.

        After having tested the monophyletic origin of the group of the Lemuriformes with the two types of sequences (in presence of mitochondrial sequences coming from different Primates, Carnivores, Gnawing, Cetaceans and Birds), a survey is achieved in order to determine the optimal outgroup sequence to use for the reconstructions. For that to make a test, using the p-distances between the different groups of Lemuriformes and the unique sequences coming from groups taxonomically more or less distant of the Malagasy Prosimians, is practiced. The treatment is done with the p-distances because these represent the simplest model of calculation of distances, they are based on the proportions of variable sites for a given pair of sequences, and they don't imply any hypothesis as for the mode of evolution of the sequences.

        The phylogenetic reconstructions are done while using different methods: Neighbor Joining, Maximum Likelihood, Maximum Parsimony, Parsimony Ratchet and Quarter Puzzeling. For the methods all substitutions events, or solely transversions are used. In the same way the existence of substitution model following a gamma type distribution is tested. The different gotten topologies are compared then by means of LTR tests (Likelihood Ratio Test), what permits to define those driving to the ‘right tree '. Thus two topologies are selected, they can be represented of the following manner:

-          ((Cheirogaleidae, ((Indriidae, (Lepilemuridae, Megaladapis)), ((Eulemur,

Hapalemur), Varecia)), (Daubentoniidae, Tupaia))

-          (((((Eulemur, Hapalemur), Varecia), (Cheirogaleidae, (Megaladapis,

Lepilemuridae))), Indriidae), Daubentoniidae), Tupaia)

        In order to determine which of these two topologies must be kept, 'four clusters' tests are done. These tests permit to estimate the internal branch of a topology in which four groups of sequences are represented. While associations in the two topologies it is possible to show that the first is the most believable. In this topology one can note that the sub fossil Megaladapis is well associated to the cluster of the Lepilemuridae. On the other hand the Lemuriformes appear batched in two main clusters: one compound of the Lemuridae and the other of the Indriidae, Megaladapis and Lepilemuridae. To the basis of the cluster of the Lemuriformes the Cheirogaleidae are found. This topology is, in its big lines, in conformity with those that can be gotten while using different other criteria such as morphological or caryological features. However the distribution of the sequences in some kinds, as Hapalemur and Lepilemur, don't cut up entirely the already published phylogenies based on caryological data. But one has few data coming from the use of other techniques to help towards the validation of the reconstructions done. On the other hand the association, in a same cluster, of the Daubentoniidae and Tupaia is an important data, even though the place of the Tupaia was the subject of multiple controversies: for some authors this group is very detached of the Strepsirhini, to see even completely outside of the group of the Primates. As the Tupaia are not represented in Madagascar one can suppose then that two distinct colonizations of the island existed, one having given birth to the lineage of the Daubentoniidae and the other to the one of the set of the other Malagasy Strepsirhini.

        The topology defined like being the likeliest is used to test the existence of a global molecular clock, or of local molecular clocks. The survey of the nucleotidic substitutions by site shows indeed, on the set of the studied sequences, the existence of a heterogeneity of the substitution rate by site. For the different groups of Lemuriforms these rates are on the other hand also very variable. The appraised values of the shape parameter (alpha) of the gamma distribution vary  from 0.091595 for the Lepilemuridae to 0.504956 for the Indriidae. In other words the group of the Lepilemuridae presents a more important evolution rate than the one of the Indriidae. For the Cheirogaleidae and in the Eulemurs the rates are appreciably identical. These data permit to question the existence of local molecular clocks, rather than of a global molecular clock. The studies of these clocks, from the selected topology, permit to confirm the results gotten by the survey of the substitution rates, except with regard to the Cheirogaleidae. In summary the rates of evolution for the branches of the topology leading to the Hapalemur and Varecia are appreciably identical and this rate is a little more elevated for the branch leading to the Eulemurs. In the case of the Cheirogaleidae, if the value of the alpha parameter is raised relatively when it is calculated from the sequences of the representatives of the group, the rate of evolution for the branch leading to this group is the lowest of all those found. It can presume the existence of a slow evolution until the separation of the different Cheirogaleidae species. In the other groups one notes a general constancy, or a light reduction, of the evolution rate before and after the separation of the species.

        In order to can, subsequently, to replace in the definite Phylogenetic tree the sequences of sub fossil a last part of work consists in the assessment of the dates of divergence of the different groups, as well as in the determination of the ancestral sequences to the main nodes of the topology. The use of the method of the ‘linearized trees’ permit, while considering that the separation between Lorisidae and Strepsirhini intervened 62 millions of years ago (that is to say long after that Madagascar separated of  the African continent, there are about 150 millions years) the evaluation of the main dates of divergence. So the oldest separation (neighbor of 60 millions of years) is found for the Daubentoniidae and Tupaia divergence, whereas most recent (neighbor of 11 millions of years) is the one implying the Megaladapis and the Lepilemuridae. For the other groups the times of divergence distribute themselves between 48 and 29 millions years.

        In conclusion this work permitted, according to the sequences of the mitochondrial genes studied, to propose a topology defining the relations between the different groups of Lemuriforms and to estimate the dates to which these groups separated the some of the other. Data gotten during this survey will be used, thereafter, for the survey of the Lemuriformes sub fossils. The topology defined here, as well as the evaluation of ancestral sequences, will be used as guides to specify the relations capable to exist between these sub fossil and the present Lemuriforms.