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The spiny rats, genus Proechimys, have the highest species richness within the Echimyidae family, as well as species with high genetic variability. The genus distribution includes tropical South America and Central America south to Honduras. In this study, we evaluate the phylogeographic histories of Proechimys guyannensis and P. cuvieri using cytochrome b, in a densely sampled area in northeastern Amazon where both species are found in sympatry in different environments. For each species, Bayesian and Maximum Likelihood phylogenetic analysis were congruent and recovered similar clades in the studied area. Bayesian phylogenetic analysis using a relaxed molecular clock showed that these clusters of haplotypes diversified during Pleistocene for both species. Apparently, the large rivers of the region did not act as barriers, as some clades include specimens collected from opposite banks of Oiapoque, Araguari and Jari rivers. Bayesian skyline plot analysis showed recent demographic expansion in both species. The Pleistocene climatic changes in concert with the geologic changes in the Amazon fan probably acted as drivers in the diversification that we detected in these two spiny rats. Proechimys cuvieri and P. guyannensis show genetic structure in the eastern part of the Guiana region. Greater genetic distances observed in P. guyannensis, associated with highly structured groups, suggest that more detailed studies of systematics and ecology should be directed to this species.

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.

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.

Morphological, molecular and chromosomal studies in the genera Lonchothrix and Mesomys have contributed to a better understanding of taxonomic design, phylogenetic relationships and karyotypic patterns. Recent molecular investigations have shown a yet undescribed diversity, suggesting that these taxa are even more diverse than previously assumed. Furthermore, some authors have questioned the limits of geographic distribution in the Amazon region for the species M . hispidus and M . stimulax . In this sense, the current study sought to understand the karyotypic evolution and geographic limits of the genus Mesomys , based on classical (G- and C-banding) and molecular cytogenetic analysis (FISH using rDNA 18S and telomeric probes) and through the sequencing of mitochondrial genes Cytochrome b (Cytb) and Cytochrome Oxidase—Subunit I (CO using phylogeny, species delimitation and time of divergence, from samples of different locations in the Brazilian Amazon. The species M . stimulax and Mesomys sp. presented 2n = 60/FN = 110, while M . hispidus presented 2n = 60/FN = 112, hitherto unpublished. Molecular dating showed that Mesomys diversification occurred during the Plio-Pleistocene period, with M . occultus diverging at around 5.1 Ma, followed by Mesomys sp. (4.1 Ma) and, more recently, the separation between M . hispidus and M . stimulax (3.5 Ma). The ABGD and ASAP species delimiters support the formation of 7 and 8 potential species of the genus Mesomys , respectively. Furthermore, in both analyzes Mesomys sp. was recovered as a valid species. Our multidisciplinary approach involving karyotypic, molecular and biogeographic analysis is the first performed in Mesomys , with the description of a new karyotype for M . hispidus , a new independent lineage for the genus and new distribution data for M . hispidus and M . stimulax .

Abstract Behavior is a useful trait for comparative studies that provide the comprehension of phylogenetic relationships among species. Here, we present a description of two spiny-rats species’ behavioral repertoire, Clyomys laticeps and Trinomys setosus (Rodentia: Echimyidae). The affiliative and agonistic behavioral patterns were sampled during a three-year study of captive populations of wild animals. Observational data were collected in two phases under different arrangements of individuals in groups. We also compare the behavioral traits of T. setosus and C. laticeps with the known behavioral patterns of Trinomys yonenagae. We add categories to the previous descriptions of T. setosus and a standard ethogram for C. laticeps. Trinomys setosus showed a visual and vocal display we called foot-trembling, which was not described in this form and function for other species studied until now. We discuss the differences in their sociality levels and similarities and differences among behavior patterns and repertoires. Resumo O comportamento é uma característica útil para estudos comparativos que fornecem a compreensão das relações filogenéticas entre as espécies. Apresentamos aqui uma descrição do repertório comportamental de duas espécies de ratos-de-espinho Clyomys laticeps and Trinomys setosus (Rodentia: Echimyidae). Os padrões comportamentais afiliativos e agonísticos foram amostrados durante um estudo de três anos em populações de animais silvestres em cativeiro. Os dados foram coletados em duas fases sob diferentes arranjos de indivíduos em grupos sociais. Comparamos as características comportamentais de T. setosus e C. laticeps com as da espécie mais conhecida, T. yonenagae. Adicionamos categorias às descrições anteriores de T. setosus, e um etograma padrão para C. laticeps. Trinomys setosus mostrou uma exibição visual e vocal que chamamos de saltitar, que não foi descrito nesta forma e função para outras espécies do gênero estudado até agora. Discutimos diferenças nos níveis de socialidade e similaridades e diferenças entre os padrões comportamentais e repertórios.

Pelvic morphology in mammals is shaped by several factors, including the functional commitment with parturition. Due to this, some mammalian clades, like primates, show a detectable evolutionary relationship between the magnitude of pelvic sexual dimorphism and cranial morphology of neonates. However, this correlation is less understood within the most diversified mammalian order, Rodentia. The present study aims to describe the general patterns of sexual dimorphism in pelvic shape among Neotropical spiny rats (Echimyidae), assessing its hypothesized coevolution with cranial morphology. We investigated the main sources of sexual variation in pelvic shape among 12 echimyid taxa using linear morphometry and subsequently tested the phylogenetically controlled correlation between male and female pelvic morphologies and craniometric variation. Results reveal that pelvic sexual dimorphism is concentrated in the pubis, with females showing a shorter and thicker pubic symphysis and a thinner cranial pubic ramus than males, a pattern already reported in other mammals and evidently related to obstetric demands. An evolutionary association was found between the intensity of pelvic femininization, the increase in pelvic sexual dimorphism, and the acquisition of relatively large crania and relatively inflated braincases; all of these traits are notably developed in the semi-fossorial broad-headed spiny rat, Clyomys laticeps . We argue that selection on the pelvis of female spiny rats, associated with their cranial morphologies and constraints linked to locomotory specializations, probably resulted in a correlated selective response in the pelvis of males. Our findings suggest that the magnitude of pelvic sexual dimorphism in echimyids is likely associated with obstetric demands imposed by cranial morphology.

We report the first occurrence of an arboreal spiny rat of the tribe Echimyini in the Early Holocene of southern South America. The specimen, a lower deciduous premolar, was recovered from fluvial deposits exposed along the right bank of Doll Creek, in northeastern Argentina. Morphological comparisons indicate strong affinities with the extant Amazonian genus Lonchothrix, although the fossil exhibits distinct traits such as thicker enamel and a transverse, short posterior mesofossettid. The available evidence of strong climatic niche conservatism in Echimyini supports its interpretation as an indicator of the transient presence of humid, Amazonian-like forests in the region around 10,000 years ago. Sedimentological and stratigraphic evidence correlates this warming phase with an Early Holocene transgression in the Paraná Delta. The absence of aff. Lonchothrix in the recent fauna may be the result of a post-optimum extinction event triggered by a drier phase during the Middle Holocene. This discovery provides novel evidence for a short-lived biogeographic connection between Amazonia and the southern cone during a climatic window of expansion for tropical biotas. It also highlights the role of the fossil record of Echimyidae as a sensitive proxy for reconstructing paleoenvironmental changes in temperate South America.

The Neotropics harbors a high diversity of species and several hypotheses have been proposed to account for this pattern. However, while species of forested domains are frequently studied, less is known of species from open vegetation formations occupying, altogether, a larger area than the Amazon Forest. Here we evaluate the role of historical barriers and the riverine hypothesis in the speciation patterns of small mammals by analyzing an ancient rodent lineage (Thrichomys, Hystricomorpha). Phylogenetic and biogeographic analyses were carried out with mitochondrial and nuclear DNA markers to analyze the evolutionary relationships between Thrichomys lineages occurring in dry domains along both banks of the Rio São Francisco. This river is one of the longest of South America whose course and water flow have been modified by inland tectonic activities and climate changes. Molecular data showed a higher number of lineages than previously described. The T. inermis species complex with 2n = 26, FN = 48 was observed in both banks of the river showing a paraphyletic arrangement, suggesting that river crossing had occurred, from east to west. A similar pattern was also observed for the T. apereoides complex. Thrichomys speciation occurred in Late Miocene when the river followed a different course. The current geographic distribution of Thrichomys species and their phylogenetic relationships suggested the existence of frequent past connections between both banks in the middle section of the Rio São Francisco. The extensive palaeodune region found in this area has been identified as a centre of endemism of several vertebrate species and is likely to be a center of Thrichomys diversification.

Abstract A new species of nematode parasite of the subfamily Pudicinae (Heligmosomoidea: Heligmonellidae) is described from the small intestine of Proechimys simonsi (Rodentia: Echimyidae) from the locality of Nova Cintra in the municpality of Rodrigues Alves, Acre state, Brazil. The genus Pudica includes 15 species parasites of Neotropical rodents of the families Caviidae, Ctenomyidae, Dasyproctidae, Echimyidae, Erethizontidae, and Myocastoridae. Four species of this nematode were found parasitizing three different species rodents of the genus Proechimys in the Amazon biome. Pudica wandiquei n. sp. can be differentiated from all other Pudica species by the distance between the ends of rays 6 and 8 and the 1-3-1 pattern of the caudal bursa in both lobes. Resumo Uma nova espécie de nematódeo da subfamília Pudicinae (Heligmosomoidea: Heligmonellidae) é descrito parasitando o intestino delgado de Proechimys simonsi (Rodentia: Echimyidae) em Nova Cintra, município de Rodrigues Alves, Estado do Acre, Brasil. O gênero Pudica inclui 15 espécies parasitas de roedores Neotropicais das famílias: Caviidae, Ctenomyidae, Dasyproctidae, Echimyidae, Erethizontidae e Myocastoridae. Destas, quatro espécies de nematódeos foram encontradas parasitando três diferentes espécies do roedor Proechimys no bioma Amazônia. Pudica wandiquei n. sp. é diferente das outras espécies de Pudica pela distância entre os raios 6 e 8 e pelo tipo da bolsa caudal, que é 1-3-1 em ambos os lados.

Locomotion, as a fundamental function in mammals directly associated with the use of ecological resources, is expected to have anatomical structures functionally committed that evolved under intense selective pressure, possibly carrying specializations for different locomotor habits. Among caviomorph rodents, the family Echimyidae stands out for having the greatest species richness, with relatively well-resolved phylogenetic relationships, wide variation in body mass, and remarkable diversity of locomotor habits, including arboreal, scansorial, semi-aquatic, semifossorial, and terrestrial forms. Thus, Echimyidae constitutes a promising model for understanding how phylogenetic, allometric, and ecological factors affect the evolution of postcranial structures directly linked to locomotor function. We investigated the influence of these three factors on scapular and humeral morphological variation in 38 echimyid species using two-dimensional geometric morphometry and phylogenetically informed comparative methods. Scapular and humeral shape variation had a low correlation with body mass and structure size, conveying a small or negligible allometric effect. Conversely, a significant moderate to strong phylogenetic signal was detected in both structures, suggesting that an important part of their morphometric variation results from shared evolutionary history. Notably, morphological variation of the scapula was extensively structured by phylogeny, without the marked influence of locomotor habits, suggesting that its shape may be a suitable taxonomic marker. Finally, locomotor habits were important in structuring the morphological variation of the humerus. Our results suggest that the morphologies of the scapula and humerus, despite being anatomically and functionally interconnected, were differentially shaped by ecological factors associated with locomotor habits.