Identifying factors and the extent of their roles in the differentiation of populations is of great importance for understanding the evolutionary process in which a species is involved. Ctenomys minutus is a highly karyotype-polymorphic subterranean rodent, with diploid numbers ranging from 42 to 50 and autosomal arm numbers (ANs) ranging from 68 to 80, comprising a total of 45 karyotypes described so far. This species inhabits the southern Brazilian coastal plain, which has a complex geological history, with several potential geographical barriers acting on different time scales. We assessed the geographical genetic structure of C. minutus, examining 340 individuals over the entire distributional range and using information from chromosomal rearrangements, mitochondrial DNA (mtDNA) sequences and 14 microsatellite loci. The mtDNA results revealed seven main haplogroups, with the most recent common ancestors dating from the Pleistocene, whereas clustering methods defined 12 populations. Some boundaries of mtDNA haplogroups and population clusters can be associated with potential geographical barriers to gene flow. The isolation-by-distance pattern also has an important role in fine-scale genetic differentiation, which is strengthened by the narrowness of the coastal plain and by common features of subterranean rodents (that is, small fragmented populations and low dispersal rates), which limit gene flow among populations. A step-by-step mechanism of chromosomal evolution can be suggested for this species, mainly associated with the metapopulation structure, genetic drift and the geographical features of the southern Brazilian coastal plain. However, chromosomal variations have no or very little role in the diversification of C. minutus populations.

The rodent genus Ctenomys (tuco-tucos) comprises more than 60 described species, and shows extraordinary inter- and intraspecific karyotypic variation. The most widely distributed species of Ctenomys in Brazil is C. torquatus. Although several cytogenetic studies have been done, the karyotypic variability of this species is still poorly known. In this paper we report two new diploid numbers for C. torquatus: 2n = 40 and 2n = 42, both showing AN = 72. The new distribution limits of C. torquatus here reported include localities in the southern, central and western parts of Rio Grande do Sul (RS) State in southern Brazil. The phylogenetic relationship between C. torquatus from Alegrete, RS, and Ctenomys sp. from Corrientes, Argentina, is described by means of mtDNA cytochrome b analysis. Although both entities share similar karyotypes and sperm morphology, these two species are not phylogenetically close.