New species boundaries and the diversification history of marsh rat taxa clarify historical connections among ecologically and geographically distinct wetlands of South America

Health of Holochilus chacarius (Rodentia: Cricetidae) in rice agroecosystem in a neotropical wetland assessed by histopathology

Small mammals have a short lifetime and are strictly associated with their environment. This work aimed to use histopathology to assess the health of Holochilus chacarius in a rice agroecosystem in the Pantanal of Mato Grosso do Sul. During necropsy, fragments of the lung, kidney, skin, liver, and reproductive system of 33 animals were collected and submitted to histological processing. Tissue damages were evaluated as mild, moderate, and severe and arranged in a matrix for further statistical analysis. Furthermore, we used generalized linear models to verify the influence of tissue changes on the body condition, obtained by a regression between body mass and length. In the lungs, we found an intense inflammatory infiltrate associated with anthracosis that had a negative influence on the body's condition. Also, we observed degenerative and inflammatory changes in the liver, kidneys, skin, and reproductive system that ranged from mild to moderate. The histopathological lesions observed in this study may be associated with environmental alterations of anthropic origin such as the exposure to soot from wildfires and heavy metals, evidenced by lesions in the lung, kidney, and liver. The present study provided a histopathological matrix as a new approach that allows to classify and quantify the tissue alterations. Tissue changes when associated with body condition demonstrated to be an effective tool to assess the health of small free-living mammals, showing that these animals can be used as bioindicators of environmental condition.

Phylogenomics and species delimitation of an abundant and little-studied Amazonian forest spiny rat

Species delimitation studies based on integrating different datasets such as genomic, morphometric, and cytogenetics data are rare in studies focused on Neotropical rodents. As a consequence, the evolutionary history of most of these genera remains poorly understood. Proechimys is a highly diverse and widely distributed genus of Neotropical spiny rats with unique traits like multiple sympatry, micro-habitat segregation, and fuzzy species limits. Here, we applied RAD-Seq to infer the phylogenetic relationships, estimate the species boundaries, and estimate the divergence times for Proechimys, one of the most common and least studied small mammals in the Amazon. We tested whether inferred lineages in the phylogenetic trees could be considered distinct species based on the genomic dataset and morphometric data. Analyses revealed the genus is not monophyletic, with Proechimys hoplomyoides sister to a group of Hoplomys gymnurus + all other Proechimys species, contesting the generic status of Hoplomys. There are five main clades in Proechimys stricto sensu (excluding H. gymnurus and P. hoplomyoides). Species delimitation analyses supported 25 species within the genus Proechimys. The five main clades in Proechimys stricto sensu also showed similar ages for their origins, and two rapid diversification events were identified in the Early Pliocene and in the Early Pleistocene. Most cases of sympatry in Proechimys occur among species from the different main clades, and although Proechimys is an inhabitant of the Amazon, three species occupied the Cerrado biome during the Pleistocene. We could associate available nominal taxon, cytogenetics information, and DNA sequences in Genbank to most of the 25 species we hypothesized from our delimitation analyses. Based on our analyses, we estimate that eight forms represent putative new species that need a taxonomic revision.

First mitochondrial genome of the Amazonian marsh rat Holochilus sciureus Wagner 1842 (Rodentia, Cricetidae, Sigmodontinae)

The Amazonian marsh rat, Holochilus sciureus, is a member of the subfamily Sigmodontinae, the second-largest subfamily of muroid rodents, with 410 species and ca. 84 genera in 12 tribes. This semiaquatic rodent is distributed in South America and is of great economic and epidemiological importance. In this study, we obtained the first mitochondrial genome of the genus Holochilus obtained from a tissue sample associated with a museum voucher specimen. The generated mitogenome sequence of H. sciureus is 16,358 bp length. It comprises a control region and a conserved set of 37 genes encoding for 2 rRNA genes, 22 tRNA genes and 13 protein-coding genes. We conducted a phylogenetic analysis that included H. sciureus and the only five other published mitochondrial genomes of this poorly studied subfamily of rodents.

Checklist of the mammals (Mammalia) of Colombia

La actualización de la lista de especies presentes en un país es una tarea continua que llena vacíos de información y apoya la toma de decisiones. En los últimos cinco años, ha habido un aumento del número de especies de mamíferos descritas como nuevas en Colombia, así como primeros registros y cambios taxonómicos. Con el fin de actualizar la información de las especies de mamíferos de Colombia, realizamos una revisión exhaustiva de los cambios taxonómicos de las 528 especies registradas en listas previas. Agregamos nuevas especies descritas, así como nuevos registros de especies ya descritas. Discutimos especies cuya presencia ha sido sugerida recientemente en Colombia, pero que no es respaldada por especímenes de museo. La lista actual de mamíferos en Colombia tiene 543 especies, con cuatro descritas en el último año. Esperamos que la lista sea una herramienta apoyar las necesidades de investigación, en especial las extensiones de distribución, los problemas taxonómicos y la conservación de los mamíferos del país. Finalmente, recomendamos que las actualizaciones de la lista sigan estándares nacionales e internacionales como Darwin Core, utilizado por el Repositorio de Información Global sobre Biodiversidad - GBIF, y el Sistema de Información sobre Biodiversidad de Colombia – SiB.

Habitat Heterogeneity and Geographic Location as Major Drivers of Cerrado Small Mammal Diversity Across Multiple Spatial Scales

The Cerrado biome is one of the global hotspots of biodiversity, and non-volant small mammals represent a significant portion of Cerrado species richness (45%) and endemism (86%). Nevertheless, we still lack a comprehensive picture of small mammal diversity patterns and drivers throughout the Cerrado. Here we surveyed small mammals across 45 sites to address species richness, abundance, and composition patterns and their drivers within and across sites, habitats, and localities at the world’s most diverse tropical savanna. As hypothesized, we found: (1) rich assemblages (12–21 species) characterized by few abundant and several intermediate-level and rare species; dominated by oryzomyine and akodontine cricetid rodents, and thylamyine and marmosine within marsupials, each tribe showing distinct habitat requirements; (2) strong habitat selectivity, with assemblages composed of forest dwellers, savanna specialists, and grassland inhabitants; and (3) similar species richness (α-diversity) but high species turnover (β-diversity) across sites, habitats, and localities, suggesting that horizontal stratification (within localities) and geographic location (across the Cerrado) are key drivers of small mammal diversity in tropical savannas. Thus, habitat heterogeneity and geographic location can be inferred as the main factors shaping species richness, abundance, and composition across the analyzed multiple spatial scales. Moreover, we found that geographical distance as well as the distance to neighbor biomes better explained species turnover, indicating landscape history and phylogenetic constraints as the major determinants of Cerrado small mammal diversity, as also evidenced for plants and other animal groups. These data highlight the need to preserve the mosaic of habitats across the different regions of the biome to conserve most of the Cerrado biodiversity.

A new species of South America marsh rat (Holochilus, Cricetidae) from northeastern Brazil

Marsh rats of the genus Holochilus are broadly distributed and inhabit several distinct environments throughout South America. As an enigmatic group with a somewhat uncertain taxonomy, the composition and names of taxa have shifted throughout history, including the boundaries of Holochilus sciureus, a species formerly distributed in the lowlands of the Guianas, Peru, Bolivia, and northern, central, and northeastern of Brazil. Based on a combination of morphological and morphometric traits, and genomic sequences, we redefined species boundaries and split this wide concept of H. sciureus into three separated species, including a redefined H. sciureus, the newly erected from synonymy H. nanus, and an unnamed taxon. We describe this unnamed species, and provide emended diagnoses for the two redefined species. The newly named taxon inhabits the northeastern part of Brazil and differs from the other congeners by a unique combination of phenotypic and genomic characters.

Phenotypic and genomic differences between biomes of the South America marsh rat, Holochilus brasiliensis

Abiotic factors can influence genetic and phenotypic divergence in several ways, and identifying the mechanisms responsible for generating this variation is challenging. However, when evaluated in combination, ecological characteristics and genetic and phenotypic information can help us to understand how habitat preferences can influence morphological and genetic patterns exhibited by taxa distributed between distinct biomes, such as the Atlantic Forest and Pampas biomes in South America. By combining distributional, environmental, phenotypic and genomic information from a habitat-specialist semi-aquatic rodent (Holochilus brasiliensis), we quantified the relationship between ecological niche differences and the phenotypic and genetic variation. The results demonstrate notable segregation among the ecological niches of H. brasiliensis within each biome, although we could not refute the hypothesis of niche similarity or equivalency. Such differences are consistent with a solid morphometric variation associated with the size of these rodents. However, the ecological and morphometric differentiation is not accompanied by the same pattern of genetic variation. Despite differences in the connectivity patterns in both biomes, the genetic differences corroborate a consistent level of migration history between biomes. Additionally, the association tests show that the environment explains a small and non- significant part of the genetic variation but a significant portion of the morphometric variation.