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.

Caviomorph rodents from the Pampean region (Argentina) in the historical Santiago Roth Collection in Switzerland.

Here I reviewed the Pleistocene caviomorphs collected by Santiago Roth (collection from Catalog No. 5) and housed at the paleontological collection of the Paläontologisches Institut und Museum, Universität Zürich, Zurich (Switzerland). The fossils were found in Pleistocene strata from Buenos Aires and Santa Fé provinces (Argentina) during the late nineteenth century. The material includes craniomandibular remains assigned to Lagostomus maximus (Chinchilloidea: Chinchillidae), craniomandibular and postcranial (thoracic and sacral vertebra, left scapula, left femur, and right tibia) bones identified as Dolichotis sp. (Cavioidea: Caviidae), and a fragmented hemimandible and isolated tooth of Myocastor sp. (Octodontoidea: Echimyidae). Other rodent specimens from this collection (Ctenomys sp. and Cavia sp.) are possibly sub-recent materials.

En este trabajo se estudian los caviomorfos del Pleistoceno colectados por Santiago Roth (colección del Catálogo Nro. 5) y conservados en la colección paleontológica del Paläontologisches Institut und Museum, Universität Zürich, Zurich (Switzerland). Los fósiles fueron recuperados de niveles del Pleistoceno de las provincias de Buenos Aires y Santa Fé (Argentina) hacia fines del siglo 19. Los materiales incluyen restos craniomandibulares asignados a Lagostomus maximus (Chinchilloidea: Chinchillidae), elementos craniomandibulares y postcraneanos (vértebras torácicas y sacras, escápula izquierda, femúr izquierdo y tibia derecha), identificados como Dolichotis sp. (Cavioidea: Caviidae), y un fragmento de una hemimandíbula y un diente aislado de Myocastor sp. (Octodontoidea: Echimyidae). Otros roedores de esta colección (Ctenomys sp. y Cavia sp.) posiblemente son materiales subrecientes.

Ancient DNA Suggests Single Colonization and Within-Archipelago Diversification of Caribbean Caviomorph Rodents.

Reconstructing the evolutionary history of island biotas is complicated by unusual morphological evolution in insular environments. However, past human-caused extinctions limit the use of molecular analyses to determine origins and affinities of enigmatic island taxa. The Caribbean formerly contained a morphologically diverse assemblage of caviomorph rodents (33 species in 19 genera), ranging from ∼0.1 to 200 kg and traditionally classified into three higher-order taxa (Capromyidae/Capromyinae, Heteropsomyinae, and Heptaxodontidae). Few species survive today, and the evolutionary affinities of living and extinct Caribbean caviomorphs to each other and to mainland taxa are unclear: Are they monophyletic, polyphyletic, or paraphyletic? We use ancient DNA techniques to present the first genetic data for extinct heteropsomyines and heptaxodontids, as well as for several extinct capromyids, and demonstrate through analysis of mitogenomic and nuclear data sets that all sampled Caribbean caviomorphs represent a well-supported monophyletic group. The remarkable morphological and ecological variation observed across living and extinct caviomorphs from Cuba, Hispaniola, Jamaica, Puerto Rico, and other islands was generated through within-archipelago evolutionary radiation following a single Early Miocene overwater colonization. This evolutionary pattern contrasts with the origination of diversity in many other Caribbean groups. All living and extinct Caribbean caviomorphs comprise a single biologically remarkable subfamily (Capromyinae) within the morphologically conservative living Neotropical family Echimyidae. Caribbean caviomorphs represent an important new example of insular mammalian adaptive radiation, where taxa retaining "ancestral-type" characteristics coexisted alongside taxa occupying novel island niches. Diversification was associated with the greatest insular body mass increase recorded in rodents and possibly the greatest for any mammal lineage.

Boehmiella wilsoni (Nematoda, Heligmosomoidea, Boehmiellidae fam. nov.), found in Amazonian rodents.

The genus Boehmiella was initially described as a member of the family Trichostrongylidae. Subsequently, it was assigned to the subfamily Haemonchinae in the family Haemonchidae. We analyzed parasites of spiny tree-rats, Mesomys hispidus, collected in the Amazon rainforest, which were identified as B. wilsoni based on integrative taxonomy. Using morphology, morphometry, and scanning electron microscopy (SEM), we added new data to the original description of the species. We also inferred phylogenetic hypotheses for its relationships within the Trichostrongylina, based on partial nuclear 18S and 28S rRNA genes, through Maximum Likelihood and Bayesian analyses. In conclusion, B. wilsoni does not belong to the family Haemonchidae, nor is it closely related to any other trichostrongylin family, and therefore, we propose the establishment of a new family, Boehmiellidae fam. nov., to which the genus Boehmiella is allocated.

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.

Contenção farmacológica do rato-do-bambu (Dactylomys dactylinus Desmarest, 1817) e relato de ocorrência da espécie na região Sul do Brasil / Chemical restraint of the Amazon Bamboo Rat (Dactylomys dactylinus Desmarest, 1817) and of the occurrence of the species in southern Brazil

Um exemplar de rato-do-bambu (Dactylomys dactylinus) subadulto saudável do sexo feminino, de vida livre, com massa corporal de 0,32 kg, recebeu por via intramuscular, em uma única injeção, doses de tiletamina, zolazepam, xilazina e atropina calculadas por meio de extrapolação alométrica interespecífica, a partir das recomendações usuais para o cão doméstico de 10,0 kg (tiletamina/zolazepam - 5,0mg/kg, xilazina - 1,0mg/kg) e atropina - 0,05mg/kg). O rato perdeu a reação postural de endireitamento em 2,3 minutos pós-injeção (MPI) e recuperou a capacidade de deambular normalmente em 135 MPI. A frequência cardíaca variou de 360 a 188 bpm (226±62), a frequência respiratória de 128 a 112mpm (120±5), e a temperatura retal de 36,2 a 33,5°C (34,4±1,0). A analgesia e o miorrelaxamento foram considerados bons para a realização de procedimentos indolores ou pouco dolorosos de curta duração, como exame físico, colheita de material biológico, biometria, exames de imagem e marcação. A associação de fármacos permitiu a manipulação segura do animal por 63 MPI. A recuperação foi considerada satisfatória, porém prolongada. Destaca-se que este é primeiro registro de ocorrência da espécie na Região Sul do Brasil, e o primeiro relato de contenção farmacológica desse roedor neotropical.(AU)

One subadult healthy free-living female Amazon Bamboo Rat (Dactylomys dactylinus), weighting 0.32 kg, received tiletamine HCl, zolazepam HCl, xilazine HCl and atropine sulfate, combined in a single intramuscular injection. All doses were calculated by interspecific allometric scaling, using as model a 10.0 kg domestic dog (tiletamine/zolazepam -5.0mg/kg), xylazine -1.0mg/kg), and atropine - 0.05mg/kg). Immobilization occurred in 2.3 minutes after injection (MAI) and returno to normal ambulation was observed in 135 MAI. Heart rate remained between 360 and 188 beats/minute (226±62), respiratory rate between 128 and 112 breaths/minute (120±5), and body temperature ranged from 36.2 to 33.5°C (34.4±1.0). Analgesia and myorelaxation were considered good for painless or mild painful fast procedures as physical examination, biological sampling, biometrics, imaging tests and tagging. The proposed anesthetic protocol was safe and effective, allowing safe manipulation of the animal during 63 MAI. The recovery was satisfactory, but prolonged. This is the first record of the species in Southern Brazil and the first report on its chemical restraint.(AU)

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.

Epilepsia espontânea em Trinomys yonenagae (Rodentia, Echimyidae: ocorrência e comportamento / Spontaneous epilepsy in trinomys yonenagae (rodentia, echimyidae): occurrence and behavior

Apresentamos dados e argumentos que indicam que: a) as crises epilépticas apresentadas por Trinomys yonenagae em campo e em cativeiro são espontâneas e idiopáticas; e b) elas podem ser decorrentes de processos evolutivos. A epilepsia nesta espécie foi caracterizada em cativeiro a partir de um cadastro iniciado há 16 anos, formado por progenitores e descendentes de seis colônias de T. yonenagae, coletados na Caatinga de Ibiraba (BA), e adultos (129,90 ± 5,92g) e filhotes nascidos em cativeiro num total de 295 indivíduos. A prevalência e a incidência em indivíduos epilépticos (EE) foram estimadas e as crises epilépticas foram analisadas por meio das manifestações comportamentais, baseando-se na escala de Racine. Aspectos da procriação (n=11), a locomoção, a ansiedade (testes de arena, n= 35) e índices fisiológicos (balanço hídrico-alimentar, n=6), importantes ao fitness, foram mensurados. Somente duas colônias apresentaram EE representando 9% e 28% dos nascimentos. Do total de indivíduos (165 e 130) 9,8% são EE (n=29; 14 e 15), sendo que as representam 52% e os 48%. A prevalência é de 20 a 30% e a incidência variou de 2 a 10 casos/ano, nos últimos cinco anos. As crises são observadas somente em adultos (n=24) a menor latência é de 13m e a frequência é variável (1 a 24 em seis anos). A maioria iniciou-se por congelamento e 50% atingiram o estágio 5 da escala de Racine. Em todos os casais, de 5 a 50% dos filhotes são EE e ocorreu estro pós-parto, como esperado para a espécie. Os filhotes são saudáveis e tanto a média de filhotes por ninhada (1,9±0,3), como a média do número de ninhadas por casal (6,5±5,0) é igual à de casais não epilépticos (NE). O teste de arena indica que descendentes de EE (DE) e as EE são menos ansiosas que as NE. Não há diferença entre os grupos dos índices fisiológicos estimados. A diferença no número de EE nas colônias, a alta prevalência e % de filhotes EE, e a diferença de comportamento das fêmeas DE indicam a base genética desta epilepsia(AU)

We present data and discuss the possibility that: a) the seizures presented by Trinomys yonenagae in the wild and in captivity are spontaneous and idiopathic, and b) they may be due to evolutionary processes. Epilepsy was characterized in this species in captivity from a survey started 16 years ago, made up of parents and descendants from six colonies of T. yonenagae collected in the Caatinga of Ibiraba (BA), and adults (129.90 ± 5.92 g) and pups born in captivity in a total of 295 individuals. The prevalence and incidence in individuals with epilepsy (EE) were estimated and seizures were analyzed by behavioral manifestations, based on Racine´s scale. Locomotion and anxiety indexes (open-field test, n = 35), as well as aspects of breeding (n = 11) and physiological indicators (balance food and water, n = 6), important to fitness were measured. Only two colonies showed EE, representing 9% and 28% of births. Approximately 10% of total individuals (165 and 130 ) are EE (n = 29, 14 and 15 ), and the represent 52 and 48%. In the last five years prevalence is 20-30%, and incidence ranged from 2 to 10 cases/ year. Seizures are only observed in adults (n = 24), the lowest latency is 13 months and the frequency is variable (1 to 24 in six years). The first stage is freezing and 50% reached stage 5 of Racine´s scale. In all couples, 5-50% of puppies are EE and occurred postpartum estrus, as expected for the species. The puppies are healthy and both the average offspring per litter (1.9 ± 0.3), as well as the average number of litters per couple (6.5 ± 5.0) is equal to values presented by non-epileptic couples (NE). The open-field test indicates that descendants of EE (DE) and EE are less anxious than NE. There is no difference between EE and NE regarding food and water intake. The difference in the number of EE in the colonies, the high percentage of EE pups, and the difference in the behavior of DE indicate the genetic basis of this epilepsy(AU)

A new karyotype for the spiny rat Clyomys laticeps (Thomas, 1909) (Rodentia, Echimyidae) from Central Brazil.

Clyomys Thomas, 1916 is a semifossorial rodent genus of spiny rats represented by only one species, Clyomys laticeps, which inhabits the tropical savannas and grasslands of central Brazil and eastern Paraguay. Here we describe a new karyotype of Clyomys laticeps found in populations of Emas National Park, Goiás state, Brazil. The four analyzed specimens had a diploid number (2n) of 32 and a fundamental autosome number (FN) of 54. Cytogenetic data include conventional staining, CBG and GTG-banding. The karyotype presents 12 meta/submetacentric pairs (1 to 12) and 3 pairs of acrocentrics (13 to 15) with gradual decrease in size. The X chromosome is a medium submetacentric and the Y is a medium acrocentric. The semifossorial habits together with habitat specificity could have contributed to the karyological variations found on this genus.