Leonora Pires Costa

Neotropical forest expansion during the last glacial period challenges refuge hypothesis

Significance The tropical forests of South America are among the most diverse and unique habitats in the world in terms of plant and animal species. One of the most popular explanations for this diversity and endemism is the idea that forests retracted and fragmented during glacial periods, forming ecological refuges, surrounded by dry lands or savannas. These historically stable forest refuges would have been responsible for maintaining the pattern of diversity and endemism observed today. Here, we show that the Atlantic Forest of eastern South America probably expanded, rather than contracted, during the last glacial period. In addition, the emerged Brazilian continental shelf played a major, yet neglected, role on the evolution of this biodiversity hotspot during the last glacial period. The forest refuge hypothesis (FRH) has long been a paradigm for explaining the extreme biological diversity of tropical forests. According to this hypothesis, forest retraction and fragmentation during glacial periods would have promoted reproductive isolation and consequently speciation in forest patches (ecological refuges) surrounded by open habitats. The recent use of paleoclimatic models of species and habitat distributions revitalized the FRH, not by considering refuges as the main drivers of allopatric speciation, but instead by suggesting that high contemporary diversity is associated with historically stable forest areas. However, the role of the emerged continental shelf on the Atlantic Forest biodiversity hotspot of eastern South America during glacial periods has been ignored in the literature. Here, we combined results of species distribution models with coalescent simulations based on DNA sequences to explore the congruence between scenarios of forest dynamics through time and the genetic structure of mammal species cooccurring in the central region of the Atlantic Forest. Contrary to the FRH predictions, we found more fragmentation of suitable habitats during the last interglacial (LIG) and the present than in the last glacial maximum (LGM), probably due to topography. We also detected expansion of suitable climatic conditions onto the emerged continental shelf during the LGM, which would have allowed forests and forest-adapted species to expand. The interplay of sea level and land distribution must have been crucial in the biogeographic history of the Atlantic Forest, and forest refuges played only a minor role, if any, in this biodiversity hotspot during glacial periods.

Small mammals in the diet of barn owls, Tyto alba (Aves: Strigiformes) along the mid-Araguaia river in central Brazil

We collected and analyzed 286 Barn owl, Tyto alba (Scopoli, 1769), pellets from two nests in different environments along the mid-Araguaia River in central Brazil. Our analyses revealed that these owls feed mainly on small mammals, especially rodents. Owls from the riverbanks at Fazenda Santa Fe had a more diverse diet, preying mainly on rodents that typically inhabit riparian grasslands - Holochilus sciureus Wagner, 1842 - and forests - Hylaeamys megacephalus (Fischer, 1814) and Oecomys spp., which probably also occur in forest borders or clearings. On the other hand, owls from an agroecosystem at Fazenda Lago Verde preyed mostly on rodent species common in these agrarian fields, Calomys tocantinsi Bonvicino, Lima & Almeida, 2003. Additionally, we compared small mammal richness estimates based on the analysis of owl pellets with estimates from live-trapping in the same areas. Owl pellets revealed two rodent species undetected by live traps - Euryoryzomys sp. and Rattus rattus (Linnaeus, 1758) - and four rodent species were trapped, but not found in owl pellets - Oecomys roberti Thomas, 1904, Pseudoryzomys simplex (Winge, 1887), Rhipidomys ipukensis Rocha, B.M.A. Costa & L.P. Costa, 2011, and Makalata didelphoides (Desmarest, 1817). Traps yielded higher species richness, but these two methods complement each other for surveying small rodents.

Phylogeographic Structure and Karyotypic Diversity of the Brazilian Shrew Mouse (Blarinomys breviceps, Sigmodontinae) in the Atlantic Forest

Blarinomys breviceps possesses cryptic and burrowing habits with poorly documented genetics and life history traits. Due to its rarity, only a few specimens and DNA sequences have been deposited in collections worldwide. Here, we present the most comprehensive cytogenetic and molecular characterization of this rare genus. Phylogenetic analyses based on partial cytochrome b sequences were performed, attempting to establish the relationships among individuals with distinct karyotypes along the geographic distribution of the genus in the Atlantic Forest. Classical and molecular cytogenetics, using banding patterns and FISH of telomeric and whole chromosome X-specific painting probes (obtained from the Akodontini Akodon cursor) were used to characterize and compare the chromosomal complements. Molecular phylogenetic analyses recovered 2 main geographically structured clades, northeastern and southeastern with pairwise sequence divergences among specimens varying between 4.9 and 8.4%. Eight distinct karyomorphs are described: (A) 2n = 52 (50A, XX), (B) 2n = 52 (48A, XY+2Bs), (C) 2n = 45 (42A, XY+1B), (D) 2n = 43 (37A, XX+4Bs), (E) 2n = 37 (34A, XY+1B), (F) 2n = 34 (32A, XX), (G) 2n = 31 (27A, XX+2Bs), (H) 2n = 28 (26A, XY), all with the same number of autosomal arms (FNA = 50). Variation of 0–4 supernumerary chromosomes (Bs) presenting heterogeneity in morphology and distribution of interstitial telomeric sequences (ITSs) is reported. ITSs are also found in some metacentric autosomes. The phylogeographic separation between 2 major lineages with high levels of genetic divergence, and the wide karyotypic diversity indicate that B. breviceps is a diverse group that warrants taxonomic re-evaluation.

Molecular Diagnosis of Atlantic Forest Mammals Using Mitochondrial DNA Sequences: Didelphid Marsupials

Most living species of New World marsupials are classified in the family Didelphidae, with 98 species and 18 genera currently recognized. We sequenced fragments of two mitochondrial genes of didelphid marsupials from the At- lantic Forest of eastern South America, a biodiversity hotspot. We evaluated sequence divergences within and among spe- cies and contrasted the efficiency of cytochrome c oxidase subunit I (COI) with cytochrome b (CytB) in species-level di- agnosis. The average intraspecific genetic divergence of COI and CytB was 2.0% and 1.9%, respectively; which was about five times lower than the comparison among species of the same genus (11.2 and 10.8%). In both genes, divergence levels among closely related species are usually higher than within species. The barcoding gap is similar in COI and CytB, indicating that either gene can be used in molecular diagnoses of didelphid species. DNA barcodes are a welcome addition to traditional taxonomic methods when viewed as additional diagnostic characters in the context of integrative taxonomy.

Phylogeography of Rhipidomys (Rodentia: Cricetidae: Sigmodontinae) and description of two new species from southeastern Brazil

Abstract The genus Rhipidomys (sigmodontine rodents in the tribe Thomasomyini) is a poorly known radiation of Neotropical mice with few studies addressing their systematics and geographic distribution. We describe 2 new species of Rhipidomys (climbing mice) from southeastern Brazil. One of these species is known only from the type locality and 2 additional sites in the southeastern part of Minas Gerais, north of the Serra da Mantiqueira mountain complex. The other species occurs to the south of this mountain range in eastern Rio de Janeiro and São Paulo states, including coastal islands. These species can be distinguished from each other and from their congeners by morphological and molecular traits, and the new species from south of the Serra da Mantiqueira has a unique chromosomal complement of 2n  =  44 and FN  =  48, 49, or 50. Phylogenetic analysis of cytochrome-b sequences also revealed an additional unnamed clade of Rhipidomys from central and eastern Brazil, which is closely related to R. cariri from northeastern Brazil. A formal description of this clade requires additional morphological analyses, including specimens from the Guianas and other central Brazilian localities. In addition, the Amazonian species R. macconnelli and R. wetzeli appear as highly divergent from all other species included in the analysis. Finally, intraspecific morphological variation in species from mesic enclaves (brejos) in northeastern Brazil indicates the need for further taxonomic revision of R. mastacalis, R. macrurus, R. cariri, and Rhipidomys sp.

Measurement Properties of the Brazilian Portuguese Version of the MedRisk Instrument for Measuring Patient Satisfaction With Physical Therapy Care

STUDY DESIGN Clinical measurement study. OBJECTIVES To translate and cross-culturally adapt the MedRisk Instrument for Measuring Patient Satisfaction With Physical Therapy Care (MRPS) into Brazilian Portuguese and to test its measurement properties. BACKGROUND To date, there is no standardized instrument for measuring patient satisfaction with physical therapy care in Brazil. METHODS The MRPS was translated and cross-culturally adapted into Brazilian Portuguese. Patients completed the MRPS and a global change measure after 5 or more treatment visits. A subset of patients also completed the instrument a second time, 24 to 48 hours after the first assessment. We evaluated factorial validity, internal consistency, reproducibility, construct validity, and ceiling and floor effects. RESULTS Three hundred three patients with different musculoskeletal conditions receiving physical therapy care in Brazil participated in this study. A 3-factor solution labeled as interpersonal, convenience and efficiency, and patient education provided the best factor loadings. Cronbach alpha coefficients ranged from .63 to .77, intraclass correlation coefficients ranged from 0.64 to 0.79, and standard errors of measurement ranged from 0.86 to 1.75 points. Thirteen items of the MRPS were moderately correlated with the global measure of change. A large ceiling effect was detected. CONCLUSION Although we did not fully achieve the measurement properties suggested by the guidelines, we believe that the MRPS can be used among Brazilian Portuguese-speaking patients. Some differences with regard to factor structure of the Brazilian Portuguese MPRS compared with the English version were observed. The reason for this is likely a combination of cultural aspects, differences in clinical settings, and patient expectation.

DNA from owl pellet bones uncovers hidden biodiversity

Owl pellets are a useful tool for inventorying small mammals and a robust complement to traditional trapping methods. Here we assessed if bone samples recovered from Barn owl pellets in the Neotropics represent a viable source of modern DNA. We used the upper incisor of rodents and jaws of marsupials of pellet material for DNA extraction and amplification. Extraction and amplification success depended on the type of bone element used, being much higher from rodent incisors. The amplification success of small (429 bp) and large (801 bp) mitochondrial cytochrome b fragments was relatively similar, suggesting that DNA was not severely degraded, probably because our pellet samples were less than 8 years old. Eleven species of small mammals were identified, from which two are new to the study area: Gracilinanus emiliae and Marmosops pinheiroi. These records represent the southeastern boundary of both species, and extended their geographic distribution 370 km (G. emiliae) and 700 km (M. pinheiroi) to the south. Moreover, two of three detected species of Oecomys occurring in sympatry may represent undescribed species. The use of molecular analysis as a complement to morphological analysis of pellet bones is very effective in species identification, especially considering poorly known and elusive species, such as those reported here. The search for owl pellets during fieldwork should be a common practice among mammalogists in the Neotropics because this material provides a valuable non-invasive source of DNA, often revealing previously undetected species and sometimes uncovering new species.

Seasonal flooding regime and ecological traits influence genetic structure of two small rodents

Although codistributed species are affected by the same abiotic factors, such as rivers and seasonal flooding regimes, ecological traits, such as locomotion habits and habitat preferences, may also influence differences in levels of genetic diversity and differentiation. We examined population genetic structure and diversity of Hylaeamys megacephalus and Oecomys aff. roberti, two cricetid rodent species from the mid-Araguaia River in central Brazil, using mitochondrial DNA sequence data. Specifically, we aim to test whether the Araguaia River acts as a barrier to the gene flow of these two species and to assess how ecological traits, such as locomotion habits and habitat preferences, may influence differences in levels of genetic diversity and differentiation. As both species occur in flooded forests, neither showed genetic differences related to river banks. Oecomys aff. roberti showed stronger population structure that appears to be associated with isolation by distance. This arboreal species maintained stable populations in the Araguaia River, while the terrestrial H. megacephalus was more affected by seasonal floods, resulting in a genetic signature of population expansion. Our initial predictions were largely supported by our results given that locomotion habits and habitat preferences of each species appears to have played a role on the genetic structure of these two sympatric rodent species.

The Araguaia River as an Important Biogeographical Divide for Didelphid Marsupials in Central Brazil

The riverine barrier model suggests that rivers play a significant role in separating widespread organisms into isolated populations. In this study, we used a comparative approach to investigate the phylogeography of 6 didelphid marsupial species in central Brazil. Specifically, we evaluate the role of the mid-Araguaia River in differentiating populations and estimate divergence time among lineages to assess the timing of differentiation of these species, using mitochondrial DNA sequence data. The 6 didelphid marsupials revealed different intraspecific genetic patterns and structure. The 3 larger and more generalist species, Didelphis albiventris, Didelphis marsupialis, and Philander opossum, showed connectivity across the Araguaia River. In contrast the genetic structure of the 3 smaller and specialist species, Gracilinanus agilis, Marmosa (Marmosa) murina, and Marmosa (Micoureus) demerarae was shaped by the mid-Araguaia. Moreover, the split of eastern and western bank populations of the 2 latter species is consistent with the age of Araguaia River sediments formation. We hypothesize that the role of the Araguaia as a riverine barrier is linked to the level of ecological specialization among the 6 didelphid species and differences in their ability to cross rivers or disperse through the associated habitat types.

Independent reversals to terrestriality in squirrels (Rodentia: Sciuridae) support ecologically mediated modes of adaptation.

The family Sciuridae is one of the most widespread and ecologically diverse lineages of rodents and represents an ideal model for investigating the evolution of locomotion modes and the historical biogeography of terrestrial mammals. We used a comprehensive database on locomotion modes, an updated phylogeny and novel biogeographic comparative methods to reassess the evolution of locomotion of squirrels and to investigate whether these locomotion modes evolved convergently in different continents. We found that locomotion changes occurred in different independent lineages of the family, including four reversals to terrestriality and one evolution of gliding. We also found evidence for Eurasia as the centre of origin of Sciuridae, challenging the classification of the oldest squirrel fossil records from the early Oligocene in North America. Additionally, Eurasia is also the possible centre of origin for most of squirrel subfamilies and tribes, and where locomotion changes have occurred. Parallel locomotion shifts could be explained by the adaptation towards different ecological niches followed by colonization of new continents.