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Trinomys yonenagae (Rocha, 1995), Yonenaga's Atlantic spiny-rat, is a small caviomorph rodent locally known as “rabo-de-facho” (Portuguese) due to its setiform hairs and long penciled tail. It is endemic to the sand dune field of the arid Brazilian Caatinga, on the west side of the Middle São Francisco River, from Barra to Pilão Arcado (Bahia, Brazil). The long hind feet, the fossorial and colonial habits, and the inflated tympanic bullae are cited as adaptations to the hot and sandy habitat. One of 10 species in the genus, it is listed as “Endangered” by the International Union for Conservation of Nature and Natural Resources because it is found only at a single location of less than 5,000 km2 and its habitat continues to decline due to the extraction of sand.

The XX/XY sex chromosome system is highly conserved across mammals, with rare exceptions where males lack a Y chromosome. Among these is the genus Tokudaia, a group of spiny rats comprising three species with unique sex chromosome systems deviating from the typical XX/XY pattern. While Tokudaia osimensis and Tokudaia tokunoshimensis have completely lost the Y chromosome, they retain some Y-linked genes on the X chromosome. In contrast, Tokudaia muenninki retains large sex chromosomes where both the X and Y chromosomes have fused with an autosome pair, carrying multi-copied Y-linked genes, including Sry. In this study, we generated chromosome-level genome assemblies for male individuals of all three Tokudaia species. By investigating loci typically associated with rodent Y-linked genes, we characterized sequences derived from the Tokudaia Y-chromosomal most recent common ancestor (Tokudaia Y-MRCA) and traced their evolutionary trajectories. Our analyses revealed that an initial X-to-Y translocation of a sequence containing the boundary-associated segmental duplication in a common ancestor of Tokudaia marked the beginning of their unique sex chromosome evolution. The boundary-associated segmental duplication, uniquely multi-copied in Tokudaia, facilitated further rearrangements through nonallelic homologous recombination and duplications. These processes culminated in subsequent Y-to-X translocations and duplications, leading to the complete loss of the Y chromosome as a distinct entity while preserving Y-linked genes in a multicopy state on the X chromosome. These findings highlight Tokudaia's rapid sex chromosome evolution within 3 million years and provide insights into the mechanisms underlying Y chromosome loss, contributing to a broader understanding of sex chromosome evolution in rodents.

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.

Evolutionary constraints and ecological pressures influence species' morphological diversity. The aim of this study was to explore patterns of morphological variation, to investigate the influence of environmental variables on morphological differentiation, and assess the strength of phylogenetic signal for the cranium and mandible in spiny rats of the genus Trinomys. We examined 377 crania and mandibles of all species of the genus Trinomys. We used geometric morphometric methods based on two-dimensional anatomical landmarks to describe cranium and mandible shape and size. Phylogenetic signal was tested using the K statistics and associations between morphology and environmental variables were made using a phylogenetic partial least squares analysis. We found marked differences in size and shape in the synchranium among species, especially in the segregation of T. albispinus and T. yonenagae from the other species, which in turn greatly overlapped both in size and shape spaces. We found a weak phylogenetic signal for size of the synchranium and intermediate phylogenetic signals for shape, a pattern similar to other studies. Differentiation of the synchranium shape in Trinomys was associated largely with precipitation-related variables, while the association between size and environmental variables was weak. Notably, Trinomys species inhabiting xeric environments had relatively larger tympanic bullae.

Terrestrial echimyid rodents typically use subterranean cavities and hollow logs as refuges. We examined habitat characteristics at refuges used by 2 such species of rodents, Proechimys semispinosus and Hoplomys gymnurus, to better understand coexistence of these morphologically similar sympatric species. The study was performed in a lowland moist forest in central Panama from 2009 to 2013. Sewing-bobbin tracking was used to locate refuges. We examined refuge habitat at 2 scales. At a coarser scale (microhabitat), we measured 10 variables within a 5-m radius around each refuge site and an associated random point, which represented available habitat. At a finer scale (refuge entrance), we measured 11 variables within a radius of 0.5 m centered on each refuge and an associated random point. We used discriminant function analysis to search for differences between refuge and available habitats at both scales and for both species separately. We located 70 refuges of both species. Refuges used by P. semispinosus were positively associated with litter depth, canopy openness, numbers and sizes of nearby logs, and proximity to tree-fall gaps, which all indicate forest disturbances. Hoplomys gymnurus refuges did not show any differences from available habitat. Lastly, we found no differences in refuge use between the sexes or age classes for either species. We conclude that interspecific competition for refuges is generally unlikely to be important because small-scale differences in refuge habitats facilitate coexistence.

Trinomys Thomas (1921) is a terrestrial genus of spiny rats endemic to the Brazilian areas of Atlantic Forest and the transitional areas of Cerrado and Caatinga. Although most species have been already karyotyped, the available cytogenetic information is mostly restricted to diploid and fundamental numbers. We analyzed the chromosomes of two Trinomys species: Trinomys moojeni (2 n  = 56, FN  = 106) and Trinomys setosus setosus (2 n  = 56, FN  = 106 and 2 n  = 56, FN  = 108). Our analyses included GTG- and CBG-banding, silver-staining of the nucleolar organizer regions, and chromosome mapping of telomeres and 45S rDNA by fluorescent in situ hybridization (FISH). Comparative GTG- and CBG-banding suggested that the interspecific variation may be due to rearrangements such as pericentric inversions, centromere repositioning, and heterochromatin variation. We report two new karyotypes for T. s. setosus and describe for the first time the banding patterns of the two Trinomys species.

Small mammals, particularly rodents, are often important seed-dispersal agents in Neotropical forests. Directional seed dispersal into tree-fall gaps may enhance seedling survival of light-demanding species and thus influence forest regeneration. To examine this proposition, we tracked seeds of a light-demanding palm ( Attalea butyracea ), with a focus on spiny rats ( Proechimys semispinosus ), the most-likely seed-removal agents. We established seed-removal stations at three distances relative to 28 gaps (gap center, gap edge, and intact forest 10 m from a gap edge) in a lowland forest in Central Panama. We placed five fresh fruits (with their seed) in semi-permeable exclosures to exclude larger mammals at each station and tracked the directions in which seeds were moved and deposited intact. More seeds were moved toward or into gaps when removed from gap center or edge stations; however, seeds dispersed from intact forest stations showed no such directionality. Small mammals may have dispersed seeds into and within tree-fall gaps because they favored caching seeds in areas that offered increased cover, which is typical of gaps, and consequently protection from predation. The lack of directional dispersal from intact forest stations may have been because spiny rats were able to find sufficient cover in the young intact forest that was closer than the gaps. In older forest, the contrast between intact forest and gaps may be greater, resulting in directed dispersal into gaps.

Seed predation and dispersal by scatter-hoarding rodents are important for plant population dynamics and forest structure. In this study, the potential of red spiny rats (Maxomys surifer) as predators, dispersers and scatter-hoarders of Parah (Elateriospermum tapos) seeds was examined in Khao Nan National Park, Thailand. One thousand Parah seeds and 100 rats were used in this experiment. Ten seeds with one rat were set inside a cage. Infrared videos of seed predation and dispersal by the rats were made from 9:00-10:00 p.m. afterwards, the numbers of seeds predated (predated, undamaged, and partially predated), dispersed (non-removed, displaced and removed) and scatter-hoarded were recorded. The percentage of undamaged, predated and partially predated seeds, as well as of removed, non-removed, and displaced seeds differed significantly. In both males and females, most of the seeds were undamaged, followed by those predated and partially predated. Additionally, most of the seeds were not removed, followed by those removed and displaced. Both males (35%) and females (37%) scatter-hoarded seeds, and the seed numbers did not differ between sexes. Body weight of rats was positively correlated with the percentage of predated seeds and negatively correlated with the percentage of undamaged seeds, but notwith the potentially viable, non-removed, displaced, or removed seeds. Red spiny rats act as predators, dispersers and scatter-hoarders of Parah seeds. It indicates that these rats may play an important role in Parah population dynamics.

Proechimys pattoni da Silva, 1998 is one of the 3 small-bodied species of Proechimys and its geographic range is only known in western Brazil and eastern and southern Peru. However, based on morphological and molecular analyses, we report P. pattoni from the lowland forest of Bolivia (Pando: Rio Madre de Dios, near San Rosa). This is the first report of P. pattoni in Bolivia and extends its distributional range 315 km to the southeast in the Amazon biogeographic region of Bolivia, representing the southeastern most record. Furthermore, we document the karyotype (2n = 40 / FN = 56) and morphological variation in diagnostic characters.

We studied the removal of seeds of three species of large-seeded tree (Astrocaryum standleyanum, Attalea butyracea and Dipteryx oleifera) from three different heights within six study plots in a lowland forest in central Panama. Fresh fruits with intact seeds fitted with industrial sewing bobbins were placed within semi-permeable exclosures. Removed seeds were tracked to deposition sites, and seed fate was determined. Removals were likely perpetrated by two small rodents, the strictly terrestrial Proechimys semispinosus and the scansorial Sciurus granatensis, because they were the most abundant small rodents in the study site during the study period and were of sufficient size to remove large seeds. Rodent abundance and fruit availability were estimated by conducting censuses. Nine microhabitat variables were measured at each deposition site to determine if these two rodents were preferentially depositing seeds in sites with certain characteristics or were randomly depositing seeds. During the study, rodents handled 98 seeds, 85 of which were not predated upon and could potentially germinate. Removal rates were not influenced by rodent abundance or fruit availability. Seeds were most frequently moved <3 m and deposited with the fruit eaten and the seed intact. However, some seeds did experience relatively long-distance dispersal (>10 m). Rodents preferentially deposited seeds in locations with large logs (>10 cm diameter), dense herbaceous cover, and an intact canopy. The number of large logs was different from random locations. Despite not being able to determine long-term fate (greater than c. 1 y), we show that these small rodents are not primarily seed predators and may in fact be important mutualists by dispersing seeds relatively long distances to favourable germination sites.