Digging for the spiny rat and hutia phylogeny using a gene capture approach, with the description of a new mammal subfamily.

Next generation sequencing (NGS) and genomic database mining allow biologists to gather and select large molecular datasets well suited to address phylogenomics and molecular evolution questions. Here we applied this approach to a mammal family, the Echimyidae, for which generic relationships have been difficult to recover and often referred to as a star phylogeny. These South-American spiny rats represent a family of caviomorph rodents exhibiting a striking diversity of species and life history traits. Using a NGS exon capture protocol, we isolated and sequenced ca. 500 nuclear DNA exons for 35 species belonging to all major echimyid and capromyid clades. Exons were carefully selected to encompass as much diversity as possible in terms of rate of evolution, heterogeneity in the distribution of site-variation and nucleotide composition. Supermatrix inferences and coalescence-based approaches were subsequently applied to infer this family's phylogeny. The inferred topologies were the same for both approaches, and support was maximal for each node, entirely resolving the ambiguous relationships of previous analyses. Fast-evolving nuclear exons tended to yield more reliable phylogenies, as slower-evolving sequences were not informative enough to disentangle the short branches of the Echimyidae radiation. Based on this resolved phylogeny and on molecular and morphological evidence, we confirm the rank of the Caribbean hutias - formerly placed in the Capromyidae family - as Capromyinae, a clade nested within Echimyidae. We also name and define Carterodontinae, a new subfamily of Echimyidae, comprising the extant monotypic genus Carterodon from Brazil, which is the closest living relative of West Indies Capromyinae.

ATLANTIC MAMMAL TRAITS: a data set of morphological traits of mammals in the Atlantic Forest of South America.

Measures of traits are the basis of functional biological diversity. Numerous works consider mean species-level measures of traits while ignoring individual variance within species. However, there is a large amount of variation within species and it is increasingly apparent that it is important to consider trait variation not only between species, but also within species. Mammals are an interesting group for investigating trait-based approaches because they play diverse and important ecological functions (e.g., pollination, seed dispersal, predation, grazing) that are correlated with functional traits. Here we compile a data set comprising morphological and life history information of 279 mammal species from 39,850 individuals of 388 populations ranging from -5.83 to -29.75 decimal degrees of latitude and -34.82 to -56.73 decimal degrees of longitude in the Atlantic forest of South America. We present trait information from 16,840 individuals of 181 species of non-volant mammals (Rodentia, Didelphimorphia, Carnivora, Primates, Cingulata, Artiodactyla, Pilosa, Lagomorpha, Perissodactyla) and from 23,010 individuals of 98 species of volant mammals (Chiroptera). The traits reported include body mass, age, sex, reproductive stage, as well as the geographic coordinates of sampling for all taxa. Moreover, we gathered information on forearm length for bats and body length and tail length for rodents and marsupials. No copyright restrictions are associated with the use of this data set. Please cite this data paper when the data are used in publications. We also request that researchers and teachers inform us of how they are using the data.

Mitogenomic Phylogeny, Diversification, and Biogeography of South American Spiny Rats.

Echimyidae is one of the most speciose and ecologically diverse rodent families in the world, occupying a wide range of habitats in the Neotropics. However, a resolved phylogeny at the genus-level is still lacking for these 22 genera of South American spiny rats, including the coypu (Myocastorinae), and 5 genera of West Indian hutias (Capromyidae) relatives. Here, we used Illumina shotgun sequencing to assemble 38 new complete mitogenomes, establishing Echimyidae, and Capromyidae as the first major rodent families to be completely sequenced at the genus-level for their mitochondrial DNA. Combining mitogenomes and nuclear exons, we inferred a robust phylogenetic framework that reveals several newly supported nodes as well as the tempo of the higher level diversification of these rodents. Incorporating the full generic diversity of extant echimyids leads us to propose a new higher level classification of two subfamilies: Euryzygomatomyinae and Echimyinae. Of note, the enigmatic Carterodon displays fast-evolving mitochondrial and nuclear sequences, with a long branch that destabilizes the deepest divergences of the echimyid tree, thereby challenging the sister-group relationship between Capromyidae and Euryzygomatomyinae. Biogeographical analyses involving higher level taxa show that several vicariant and dispersal events impacted the evolutionary history of echimyids. The diversification history of Echimyidae seems to have been influenced by two major historical factors, namely (1) recurrent connections between Atlantic and Amazonian Forests and (2) the Northern uplift of the Andes.

Neotropical forest expansion during the last glacial period challenges refuge hypothesis.

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.

Taxonomic implications of morphological variation in three species of Trinomys (Rodentia: Echimyidae) from eastern Brazil.

Trinomys is a genus of terrestrial spiny rats from the Atlantic Forest, and three species occur in the state of Espírito Santo, eastern Brazil: T. gratiosus, T. paratus, and T. setosus. The levels of morphological variation within and among these species are virtually unknown, and their geographic ranges have not been properly assessed. These three species are externally very similar, hampering their identification in surveys and ecological studies that are not based on voucher specimens. We evaluated 162 specimens of Trinomys spp. from eastern Brazil, especially from the state of Espírito Santo, and used data from skulls, skins, and bacula to examine morphological variation and its taxonomic implications. We found extensive morphological variation in the skins and skulls even when diagnostic characters were examined, such as the number of dental lophs and bones contributing to the postorbital process. We also found variation in bacular shape among and within species, including polymorphism among individuals from the same population. The geographic range of each species in Espírito Santo was well defined: T. setosus occurred on the left (north) bank of the Doce River, and the other two species, T. gratiosus and T. paratus, occurred on the right (south) bank of this river; however, T. gratiosus was found at altitudes above 500 m, whereas T. paratus occurred below 580 m. Despite difficulties in species identification, the results of morphological and morphometric analyses are compatible with the current classification of these three species. In addition, the level of morphological variation found in specimens identified as T. g. panema--including types--falls within the range of T. g. gratiosus, confirming the taxonomic status of the former as a junior synonym of the latter.

New karyotypes of Atlantic tree rats, genus Phyllomys (Rodentia: Echimyidae).

Phyllomys (Echimyidae, Rodentia) is a genus of Neotropical rodents with available cytogenetic data restricted to six out of 13 species, mainly based on simple staining methods, without detailed analyses. In this work, we present new karyotypes for Phyllomys lamarum (diploid number 2n = 56, fundamental number or number of autosomal arms FN = 102) and Phyllomys sp. (2n = 74, FN = 140) from the state of Minas Gerais, southeastern Brazil. We provide the first GTG- and CBG-banding patterns, silver-staining of the nucleolar organizer regions (Ag-NORs), and fluorescence in situ hybridization (FISH) with telomeric and 45S rDNA probes of Phyllomys. In addition to examining their chromosomes and phenotypic characters, we sequenced mitochondrial DNA from the specimens analyzed to confirm their taxonomic identification. The comparison of the distinctive chromosome complements of our specimens with those of other species of Phyllomys already published allowed us to conclude that chromosome data may be very useful for the taxonomy of the genus, as no two species analyzed presented the same diploid and fundamental numbers (2n and FN).

A new species of porcupine, genus Coendou (Rodentia: Erethizontidae) from the Atlantic forest of northeastern Brazil.

We report the discovery of a new species of Coendou (Rodentia, Erethizontidae), here designated Coendou speratus sp. nov. This small porcupine, locally known as coandumirim, is found in the Pernambuco Endemism Centre in the Atlantic coast of northeastern Brazil north of the São Francisco river, one of the most important known biodiversity hotspots. The geographic range of C. speratus overlaps with that of the larger, widespread C. prehensilis, but not with that of C. insidiosus from the southeastern Atlantic forest, nor with that of C. nycthemera, an eastern Amazonian species. Coendou speratus is a small-bodied, long-tailed species that appears to be completely spiny because it lacks long dorsal fur. The dorsal quills have conspicuously brownish red tips that contrast with the blackish dorsal background color. The new species is overall similar to C. nycthemera, but the dorsal body quills are typically tricolored in the former and bicolored in the latter. The new species is externally very distinct from C. insidiosus, especially because the latter has bicolored dorsal quills that are almost completely hidden beneath longer and homogeneous pale or dark hairs.

Phylogenetic relationships among species of Lutzomyia, subgenus Lutzomyia (Diptera: Psychodidae).

Lutzomyia França is the largest and most diverse sand fly genus in the New World and contains all the species involved in the transmission of American visceral leishmaniasis (AVL). Morphological characters were used to test the monophyly and to infer phylogenetic relationships among members of the Lutzomyia subgenus. Fifty-two morphological characters from male and female adult specimens belonging to 18 species of Lu. (Lutzomyia) were scored and analyzed. The resulting phylogeny confirms the monophyly of this subgenus and reveals four main internal clades. These four clades, however, do not support the classification of the subgenus in two series, longipalpis and cavernicola, because neither is necessarily monophyletic. Knowledge on phylogenetic relationships among these relevant vectors of AVL should be used as a tool for monitoring target taxa and a first step for establishing an early warning system for disease control.

Siphonaptera associated with wild mammals from the Central Atlantic Forest Biodiversity Corridor in southeastern Brazil.

We collected 379 samples of eight flea species from 235 specimens of wild mammals captured in three areas of the Central Atlantic Forest Corridor in the state of Espírito Santo, southeastern Brazil, between August 2006 and February 2008. Among the 22 mammal species, we found eight species of marsupials (order Didelphimorphia), 13 species of rodents (order Rodentia), and one species of wild cat (order Carnivora). The total prevalence of infestation was 28.1%, with similar percentages in rodents (26.4%) and marsupials (29.5%). The infestation in the southern area was 3 times higher than that observed in the northern area. The infestation by single flea species was > 6 times higher than the total number of double and triple infestations. The mean abundance of fleas was 1.61. The flea female/male ratio was 1.38, ranging from 0.95 in Adoratopsylla (Tritopsylla) intermedia intermedia (Wagner) to 1.81 in Hechtiella nitidus (Johnson) in the most flea species infested. We report three new records of flea species in the state of Espírito Santo, and eight new host records.

Ecomorphological diversification among South American spiny rats (Rodentia; Echimyidae): a phylogenetic and chronological approach.

The phylogeny of South American spiny rats (Rodentia; Echimyidae) was studied using the exon 28 of the von Willebrand Factor nuclear gene (vWF). Sequences were analysed separately and in combination with a mitochondrial dataset (cyt b, 12S and 16S rRNAs) used in previous publications. The basal polytomy of echimyids was partially resolved and unexpected intergeneric clades were recovered. Thus, the intimate nested position of Myocastor within echimyids is evidenced. A well-supported clade is identified, including all the arboreal genera, and a group formed by Myocastor, Thrichomys, and Proechimys+Hoplomys. The clustering of Euryzygomatomys+Clyomys with Trinomys is also suggested. On the opposite, the phylogenetic position of Capromys as well as the relationships among arboreal genera remain unclear. Molecular divergence times were estimated using a Bayesian relaxed molecular clock and suggest a Middle Miocene origin for most of modern genera. The ecomorphological diversification of echimyids is discussed in the light of these new results and past environmental modifications in South America.

Evolution of South American spiny rats (Rodentia, Echimyidae): the star-phylogeny hypothesis revisited.

We analyzed the phylogenetic relationships of echimyid genera based on sequences of the cytochrome b, 12S, and 16S mitochondrial genes. Our results corroborate the monophyly of Octodontoidea and the rapid diversification of echimyid rodents as previously proposed. The analyses indicate that the family Echimyidae, including Myocastor to the exclusion of Capromys, is paraphyletic, since Capromys and Myocastor are well-supported sister-taxa. We therefore suggest the inclusion of both Capromys and Myocastor in the family Echimyidae. Five other suprageneric clades are well supported: Dactylomys+Kannabateomys, Euryzygomatomys+Clyomys, Proechimys+Hoplomys, Mesomys+Lonchothrix, and Makalata+(Echimys+Phyllomys). Trinomys and Thrichomys have no clear close relatives, and Isothrix emerged as sister to Mesomys+Lonchothrix, but with no support. We suggest that most of the cladogenesis leading to the extant echimyid genera probably occurred during the Late Miocene, about eight million years ago.