Hidden diversity of the genus Trinomys (Rodentia: Echimyidae): phylogenetic and populational structure analyses uncover putative new lineages

Trinomys, one of the most species-rich spiny rat genera in Brazil, is widely distributed in Caatinga, Cerrado and Atlantic Forest biomes, and currently includes ten recognized species, three of which are polytypic. Although some studies employing molecular data have been conducted to better characterize phylogenetic relationships among species, 19 nominal taxa have been suggested, implying considerable incongruence regarding species boundaries. We addressed this incongruence by intensively sampling all species across the geographic distribution of the genus. In addition to publicly available data, we generated 182 mt-Cytb gene sequences, and employed phylogenetic and computational species delimitation methods to obtain a clearer picture of the genus diversity. Moreover, we evaluated populational diversity within each accepted species, considering their geographical distribution and a timescale for the evolution of the genus. Beyond confirming the general patterns described for the evolution of the group, this new analysis suggests that Trinomys is comprised of at least 16 evolutionary lineages, 13 of them recognized as species or subspecies, and three never before characterized. This study highlights the importance of increased sample sizes and computational species delimitation methods in uncovering hidden diversity in Trinomys.

Phylogenetic, Allometric, and Ecological Factors Affecting Morphological Variation in the Scapula and Humerus of Spiny Rats (Rodentia: Echimyidae)

Locomotion, as a fundamental function in mammals directly associated with the use of ecological resources, is expected to have anatomical structures functionally committed that evolved under intense selective pressure, possibly carrying specializations for different locomotor habits. Among caviomorph rodents, the family Echimyidae stands out for having the greatest species richness, with relatively well-resolved phylogenetic relationships, wide variation in body mass, and remarkable diversity of locomotor habits, including arboreal, scansorial, semi-aquatic, semifossorial, and terrestrial forms. Thus, Echimyidae constitutes a promising model for understanding how phylogenetic, allometric, and ecological factors affect the evolution of postcranial structures directly linked to locomotor function. We investigated the influence of these three factors on scapular and humeral morphological variation in 38 echimyid species using two-dimensional geometric morphometry and phylogenetically informed comparative methods. Scapular and humeral shape variation had a low correlation with body mass and structure size, conveying a small or negligible allometric effect. Conversely, a significant moderate to strong phylogenetic signal was detected in both structures, suggesting that an important part of their morphometric variation results from shared evolutionary history. Notably, morphological variation of the scapula was extensively structured by phylogeny, without the marked influence of locomotor habits, suggesting that its shape may be a suitable taxonomic marker. Finally, locomotor habits were important in structuring the morphological variation of the humerus. Our results suggest that the morphologies of the scapula and humerus, despite being anatomically and functionally interconnected, were differentially shaped by ecological factors associated with locomotor habits.

Behavioral repertoire of the Brazilian spiny-rats, Trinomys setosus and Clyomys laticeps: different levels of sociality

Behavior is a useful trait for comparative studies that provide the comprehension of phylogenetic relationships among species. Here, we present a description of two spiny-rats species' behavioral repertoire, Clyomys laticeps and Trinomys setosus (Rodentia: Echimyidae). The affiliative and agonistic behavioral patterns were sampled during a three-year study of captive populations of wild animals. Observational data were collected in two phases under different arrangements of individuals in groups. We also compare the behavioral traits of T. setosus and C. laticeps with the known behavioral patterns of Trinomys yonenagae. We add categories to the previous descriptions of T. setosus and a standard ethogram for C. laticeps. Trinomys setosus showed a visual and vocal display we called foot-trembling, which was not described in this form and function for other species studied until now. We discuss the differences in their sociality levels and similarities and differences among behavior patterns and repertoires.

Effects of size, phylogeny and locomotor habits on the pelvic and femoral morphology of South American spiny rats (Rodentia: Echimyidae)

The rodent family Echimyidae (spiny rats, hutias and coypu) is notable for its high phylogenetic and ecological diversity, encompassing ~100 living species with body mass ranging from 70 to 4500 g, including arboreal, epigean (non-arboreal or scansorial), fossorial and semi-aquatic taxa. In view of this diversity, it was hypothesized that echimyid morphological variation in the pelvis and femur should reflect: (1) allometric association with body mass; (2) morphofunctional specializations for the different locomotor habits; and (3) phylogenetic history. To test these propositions, we examined 30 echimyid species, in addition to eight species of two other octodontoid families, Abrocomidae and Octodontidae. Pelvic and femoral variation was assessed with linear morphometry, using bivariate and multivariate statistical methods, part of which was phylogenetically informed. Approximately 80% of the total variation among echimyids was explained by body mass, and some univariate measurements were found potentially to be effective as body mass estimators after simple allometric procedures, notably in the pelvis. Even considering the significant phylogenetic signal, variation in shape was largely structured by locomotor habits, mainly in the pelvis, suggesting that the echimyid hindlimb diversification was driven, in part, by selective pressures related to locomotor habits. Finally, echimyid femoral disparity was considerably greater than in other octodontoids, contrasting with their relatively modest cranial variation. Thus, this study suggests that hindlimb diversity constitutes a key factor for the exceptional echimyid ecological and phyletic diversification.

Cytogenetic analyses in Trinomys (Echimyidae, Rodentia), with description of new karyotypes

Trinomys Thomas (1921) is a terrestrial genus of spiny rats endemic to the Brazilian areas of Atlantic Forest and the transitional areas of Cerrado and Caatinga. Although most species have been already karyotyped, the available cytogenetic information is mostly restricted to diploid and fundamental numbers. We analyzed the chromosomes of two Trinomys species: Trinomys moojeni (2n = 56, FN = 106) and Trinomys setosus setosus (2n = 56, FN = 106 and 2n = 56, FN = 108). Our analyses included GTG- and CBG-banding, silver-staining of the nucleolar organizer regions, and chromosome mapping of telomeres and 45S rDNA by fluorescent in situ hybridization (FISH). Comparative GTG- and CBG-banding suggested that the interspecific variation may be due to rearrangements such as pericentric inversions, centromere repositioning, and heterochromatin variation. We report two new karyotypes for T. s. setosus and describe for the first time the banding patterns of the two Trinomys species.