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We present the most comprehensive study to date of species groups in Ctenomys (tuco-tucos), a species-rich genus of Neotropical rodents. To explore phylogenetic relationships among 38 species and 12 undescribed forms we sequenced the complete mitochondrial cytochrome-b genes of 34 specimens and incorporated 50 previously published sequences. Parsimony, likelihood, and Bayesian phylogenetic analyses were performed using additional hystricognath rodents as outgroup taxa. The basal dichotomy of Ctenomys splits C. sociabilis from the remaining tuco-tucos, within which 8 main species groups were identified: boliviensis, frater, mendocinus, opimus, magellanicus, talarum, torquatus, and tucumanus. Whereas most of these groups refer to previous clades proposed on the basis of chromosomes or morphology, the torquatus and magellanicus species groups are novel taxonomic hypotheses. However, relationships among species groups are poorly resolved. Furthmore, the positions of C. leucodon, C. maulinus, and C. tuconax are conflicting or unresolved, and they might represent additional independent lineages. On the basis of molecular dating, we estimate that most species groups originated approximately 3 million years ago.

BackgroundMuch debate has focused on how transitions in life history have influenced the proliferation of some clades. Rodents of the subfamily Sigmodontinae (family Cricetidae) comprise one of the most diverse clades of Neotropical mammals (~400 living species in 86 genera). These rodents occupy a wide range of habitats and lifestyles so that ecological context seems relevant to understand the evolution of this group. Several changes in the landscape of South America through the Neogene might have provided vast resources and opportunity to diversify. The aim of this study was to examine whether transitions between i) lowland and montane habitats, ii) open vegetation and forest, and iii) distinct molar architectures are correlated with shifts in diversification rates and to characterize the general pattern of diversification.ResultsBased on a dense taxon sampling of 269 species, we recovered a new phylogeny of Sigmodontinae that is topologically consistent with those of previous studies. It indicates that the subfamily and its major lineages appeared during the Late Miocene. Analyses suggest that vegetation type and elevational range are correlated with diversification rates, but not molar architecture. Tropical lowlands accumulated more lineage diversity than other areas and also supported high speciation rates. Across the radiation the subfamily Sigmodontinae appear to have experienced a decline in diversification rate through time. We detected mixed evidence for lineage-specific diversification rate shifts (e.g., leading to the clades of Akodon, Bibimys, Calomys and Thomasomys).ConclusionWe report that the evolution of habitat preference (considering vegetation type and elevational range) was associated with diversification rates among sigmodontine rodents. We propose that the observed diversification slowdown might be the result of ecological or geographical constraints. Our results also highlight the influence of the tropical lowlands -which might have acted as both “a cradle and a museum of species.” The tropical lowlands accumulated greater diversity than the remainder of the group's range.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0440-z) contains supplementary material, which is available to authorized users.