Abstract
Since its emergence in the 1980s, genomics has revolutionised many areas of the study of life. In particular, by providing vast data sets, it has enabled researchers to choose the molecular markers best suited to answer their biological question. During my thesis work, I studied the properties of two large groups of genes for comparative genomic analyses: orthologous genes (originating from a speciation event) and paralogous genes (sequences duplicated following a chromosomal event in a species). By constructing and analysing data sets at the rodent order scale, I have contributed to improving our knowledge of the relationships of rodents species related to mice, squirrels and chinchillas. In addition, I have applied myself to showing the impact of different molecular evolutionary characteristics of markers (e.g. evolutionary rates and nucleotide content) on phylogenetic reconstruction analyses. Finally, the study of the large family of olfactory receptor genes (about 1000 genes per species) has made it possible to demonstrate adaptations to the different lifestyles and diets found in these animals. In particular, burrowing species such as the different clades of mole rats (Bathyergidae and Spalacidae families) present a specific signature, found in a convergent manner in taxa that are phylogenetically distant.