DNA barcoding of the rodent genus Oligoryzomys (Cricetidae: Sigmodontinae): mitogenomic-anchored database and identification of nuclear mitochondrial translocations (Numts).

DNA barcoding has become a standard method for species identification in taxonomically complex groups. An important step of the barcoding process is the construction of a library of voucher-based material that was properly identified by independent methods, free of inaccurate identification, and paralogs. We provide here a cytochrome oxidase I (mt-Co1) DNA barcode database for species of the genus Oligoryzomys, based on type material and karyotyped specimens, and anchored on the mitochondrial genome of one species of Oligoryzomys, O. stramineus. To evaluate the taxonomic determination of new COI sequences, we assessed species intra/interspecific genetic distances (barcode gap), performed the General Mixed Yule Coalescent method (GMYC) for lineages' delimitation, and identified diagnostic nucleotides for each species of Oligoryzomys. Phylogenetic analyses of Oligoryzomys were performed on 2 datasets including 14 of the 23 recognized species of this genus: a mt-Co1 only matrix, and a concatenated matrix including mt-Co1, cytochrome b (mt-Cytb), and intron 7 of the nuclear fibrinogen beta chain gene (i7Fgb). We recovered nuclear-mitochondrial translocated (Numts) pseudogenes on our samples and identified several published sequences that are cases of Numts. We analyzed the rate of non-synonymous and synonymous substitution, which were higher in Numts in comparison to mtDNA sequences. GMYC delimitations and DNA barcode gap results highlight the need for further work that integrate molecular, karyotypic, and morphological analyses, as well as additional sampling, to tackle persistent problems in the taxonomy of Oligoryzomys.

An integrative appraisal of the diversification in the Atlantic forest genus Delomys (Rodentia: Cricetidae: Sigmodontinae) with the description of a new species.

Recent taxonomic studies on Neotropical mammals have benefited from the use of genetic data to unravel and recognize species diversity in a number of genera, including the Atlantic forest endemic genus Delomys. However, the success of this approach depends on ability to link genetically identified lineages to species names based on voucher specimens that lack genetic data. Cytogenetic studies in the Atlantic forest endemic rodent genus Delomys have revealed two widespread karyotypes, 2n=72/FN=90 and 2n=82/FN=80, which have been respectively ascribed to Delomys sublineatus (Thomas, 1903) and D. dorsalis (Hensel, 1872). More recently, a third karyotype, 2n=82/FN=86, reported from specimens collected on two montaintops in southeastern Brazil, was interpreted as evidence for a third species, D. collinus Thomas, 1917. This nominal form had originally been described as a subspecies of D. dorsalis from Itatiaia, one of the mountain ranges where the third karyotype was later detected. The detection of two sympatric karyotypes at the type locality of D. collinus in the Itatiaia mountain range, Southeastern Brazil, prompted a reevaluation of the association of karyomorphs and species names. In this paper, we assessed the congruence of molecular (cytochrome b), cytogenetic and morphological characters, to diagnose the species in the genus, including data from recently collected series and type specimens. Our results indicate that the genetic and morphological patterns are largely congruent with the recognition of three species, each of which is karyotypically and morphologically diagnosable. Our morphological analyses of sympatric samples from Itatiaia refute the former association of the 2n=82/FN=86 karyotype with the holotype of D. dorsalis collinus (which is more similar to D. dorsalis with 2n=82/FN=80). Instead, we recognize and describe a new species for the 2n=82/FN=86 populations from the highest altitudinal zones of the Itatiaia and Caparaó mountains. The geographical variation in D. dorsalis is also explored and the status of D. d. collinus is discussed in the light of the molecular and morphological evidence. Finally, we discuss biogeographic hypotheses concerning the disjunct distributions of D. dorsalis and the new species.

Morphological variation in the appendicular skeleton of Atlantic Forest sigmodontine rodents.

Rodents of the subfamily Sigmodontinae comprise a highly diversified group in the Atlantic Forest, with semifossorial, terrestrial, semiaquatic, scansorial, and arboreal forms. In this study, we analyzed morphometric variation in humerus, scapula, ulna, radius, femur, tibia, and pelvis to investigate its possible relationship with the different types of locomotion recorded in the literature. Skeletal characters were measured in 321 specimens belonging to 29 species and 19 genera either restricted to or recorded in this ecoregion. Multivariate morphometric analyses (principal component and canonical variate analyses) arranged individuals of different genera in groups congruent with the different types of locomotion. This arrangement was more clearly defined when analyses included only forelimb measurements, indicating that most of the variation in appendicular traits associated with the different locomotor modes occurs in the forelimb skeleton. Semifossorial forms exhibited the most distinct appendicular morphology, as well as the greatest frequency of endemism among analyzed species. These results suggest that this mode of locomotion led to greater differentiation in semifossorial Atlantic forest sigmodontines than in terrestrial and arboreal forms, which were found to have more subtle differentiation and fewer endemics. Scansorial species could not be set apart from terrestrial ones in terms of appendicular morphology, suggesting that these two modes of locomotion are the most similar and generalized for the group, as they occur in most lineages in the subfamily. The results of this study corroborate previous observations on the relevance of appendicular characters in the differentiation of species and genera in the subfamily Sigmodontinae.