The main objectives of this work are:a) To test the predictions of suppressed-recombination chromosomal speciation models on two different lineages of mammals: rodents and rimates. Suppressed-recombination chromosomal speciation is still quite elusive as a mode of speciation in mammals. Experimental results are scarce and the first objective of this work is to analyze whole-genome data looking for traces of events of chromosomal speciation. Rodent and primate lineages were chosen for this search, not just because of their particular biological and cytological characteristics, which make them good candidates to have speciated by this mechanism, but also because they were the first mammalian organisms to be fully sequenced. b) To study the effects of chromosomal rearrangements on genic evolutionary rates. As have been seen in the introduction, there are many of potential interactions among chromosomal rearrangements and evolutionary rates, so the second goal of this work was to try to understand the impact of chromosomal rearrangements over substitution rates by means of other mechanisms not related with speciation. c) To distinguish individual contributions of different genomic factors in the potential association among chromosomal rearrangements and evolutionary rates.The third main goal of this thesis was to discern among the different factors that could be explaining the many associations between chromosomal and genic evolution that were detected in different studies.