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The tribe Oryzomyini is an impressive group of rodents, comprising 30 extant genera and an estimated 147 species. Recent remarkable advances in the understanding of the diversity, taxonomy and systematics of the tribe have mostly derived from analyses of single or few genetic markers. However, the evolutionary history and biogeography of Oryzomyini, its origin and diversification across the Neotropics, remain unrevealed. Here we use a multi-locus dataset (over 400 loci) obtained through anchored phylogenomics to provide a genome-wide phylogenetic hypothesis for Oryzomyini and to investigate the tempo and mode of its evolution. Species tree and supermatrix analyses produced topologies with strong support for most branches, with all genera confirmed as monophyletic, a result that previous studies failed to obtain. Our analyses also corroborated the monophyly and phylogenetic relationship of three main clades of Oryzomyini (B, C and D). The origin of the tribe is estimated to be in the Miocene (8.93–5.38 million years ago). The cladogenetic events leading to the four main clades occurred during the late Miocene and early Pliocene and most speciation events in the Pleistocene. Geographic range estimates suggested an east of Andes origin for the ancestor of oryzomyines, most likely in the Boreal Brazilian region, which includes the north bank of Rio Amazonas and the Guiana Shield. Oryzomyini rodents are an autochthonous South America radiation, that colonized areas and dominions of this continent mainly by dispersal events. The evolutionary history of the tribe is deeply associated with the Andean cordillera and the landscape history of Amazon basin.

Background Since 1996, when Vivo questioned how many species of mammals occur in Brazil, there has been a huge effort to assess this biodiversity. In this contribution, we present new records for rare species of the sigmodontine rodent genera Rhagomys and Neusticomys previously unknown to Brazilian Amazon. We provided detailed information on the morphologic variation to allow the proper identification of these species. We also furnished updated information on their collection, aiming to establish hypothesis of their geographic distribution, based on SDM’s, aiming to hypothesize potential occurrence areas for these species. Methods Rodent specimens were sampled in separate inventories in two sites of Rondônia State (Hydroelectric Dam Jirau and Parque Nacional de Pacaás Novos) and one site in Pará State (Pacajá), Brazil, and were compared to specimens from museum collections to apply appropriate names. The SDM were conducted using two algorithms for rare species, MaxEnt and randomForest (RF), and were based on seven localities for Rhagomys, and 10 for Neusticomys. Results All specimens were collected with pitfall traps. One specimen of genus Rhagomys was trapped in the Hydroelectric Dam Jirau. We identified this specimen as R. longilingua, and the SDM species indicates suitable areas for its occurrence at high elevations near on the Andes and lowlands of Amazon Basin to the South of the Rio Amazonas. Two specimens of Neusticomys were recorded, and we identified the specimen from Pacaás Novos as N. peruviensis, with SDM suggesting main areas of occurrence on Western Amazon. We applied the name N. ferreirai to the specimen from Pacajá, with SDM recovering suitable areas in Eastern Amazon. Discussion We reinforced the importance of pitfall traps on the study of Neotropical rodents. We described morphologic variation within and among all species that do not invalidate their specific status, but in the near future a re-evaluation will be mandatory. The new records extended the species distribution considerably. SDM was successful to predict their distributions, as the two algorithms presented important differences in range size recovered by the models that can be explained by differences in the thresholds used for the construction of the models. Most suitable areas coincide with the areas facing most of the deforestation in Amazon. We added two rare species of sigmodontine rodents to the list of Brazilian Mammals, which now comprises 722 species (or 775 valid nominal taxa). Although more information is available than in 1996, it is essential that mammal experts maintain inventory and revisionary programs to update and revise this information. This is even more important, as changes in Brazilian environmental legislation are being discussed, suggesting reduced need for environmental impact reports prior to beginning commercial enterprises, resulting in the loss of information about native biodiversity in the affected areas.

Sorting specimens at the Museum National d’Histoire Naturelle, Paris, we recovered a presumable specimen of

Aim To infer areas of endemism for the tribe Oryzomyini in South America by employing a database of species richness and geographical distribution, and to compare these results with areas of endemism and species richness proposed in the literature for other taxa. Location We analysed specimens of the tribe Oryzomyini distributed throughout South and Central America, which are housed in European, North and South American museums and collections. Methods We analysed 2768 occurrence records for 102 species of the tribe Oryzomyini using the ndm/vndm algorithm and three different grid sizes to assess the possible effects of grid cell area on the results. Results Using the overlap of consensus areas in South America, we identified three generalized areas of endemism for the Oryzomyini: north-western South America (NWSA), eastern South American (ESA), and northern South America

Sooretamys is a monotypic genus of the family Cricetidae, subfamily Sigmodontinae, that is distributed throughout eastern South America in the Atlantic Forest Biome, including Argentina, Brazil, and Paraguay. The taxonomic history of the forms associated with this genus is long and relatively complex, and few studies have evaluated the taxonomic problems of this genus. To this end, our goal was to describe the degree and geographical pattern of morphological and molecular variation in this genus to test the current hypothesis that the genus is monotypic, and, as a consequence, to determine the status of the nominal forms associated with Sooretamys. Accordingly, we employed morphometric, morphological, and molecular tools, according to an integrative taxonomy approach. The results show that some level of morphometric discontinuity is present between the individuals from Paraguay and those from adjacent localities in Brazil and Argentina; sharp discontinuities were not observed in qualitative traits. Molecular analyses of the mitochondrial cytochrome b gene showed that the Paraguayan populations have some degree of genetic differentiation, but the haplotypic variants do not form a monophyletic group. Thus, the evidence so far suggests a difference in the genes and morphology of the Paraguayan population, but there is no consistent resolution (e.g. lack of monophyly) to show that specimens from Paraguay represent a distinct population that would merit taxonomic recognition. Thus, we recognize a single species within the genus Sooretamys, named Sooretamys angouya. The pattern of morphological and genetic differentiation of Sooretamys could be the result of divergence with gene flow. However, our data also correspond in some aspects with the model advanced by Carnaval & Moritz, which claims the existence of stable Atlantic Forest areas where the forest biota persisted during the Quaternary climatic fluctuations. Whatever process has occurred, S. angouya represents one species with a complex evolutionary history, and the analysis of additional samples would be welcome to further elucidate the process of diversification of this taxon. © 2014 The Linnean Society of London