Rodentia comprises 42 % of living mammalian species. The taxonomic identification can be difficult, the number of species currently known probably being underestimated, since many species show only slight morphological variations. Few studies surveyed the biodiversity of species, especially in the Amazon region. Cytogenetic studies show great chromosomal variability in rodents, with diploid numbers ranging from 10 to 102, making it difficult to find chromosomal homologies by comparative G banding. Chromosome painting is useful, but only a few species of rodents have been studied by this technique. In this study, we sorted whole chromosome probes by fluorescence-activated cell sorting from two Hylaeamys megacephalus individuals, an adult female (2n = 54) and a fetus (2n = 50). We made reciprocal chromosome painting between these karyotypes and cross-species hybridization on Cerradomys langguthi (2n = 46). Both species belong to the tribe Oryzomyini (Sigmodontinae), which is restricted to South America and were collected in the Amazon region. Twenty-four chromosome-specific probes from the female and 25 from the fetus were sorted. Reciprocal chromosome painting shows that the karyotype of the fetus does not represent a new cytotype, but an unbalanced karyotype with multiple rearrangements. Cross-species hybridization of H. megacephalus probes on metaphases of C. langguthi shows that 11 chromosomes of H. megacephalus revealed conserved synteny, 10 H. megacephalus probes hybridized to two chromosomal regions and three hybridized to three regions. Associations were observed on chromosomes pairs 1-4 and 11. Fluorescence in situ hybridization with a telomeric probe revealed interstitial regions in three pairs (1, 3, and 4) of C. langguthi chromosomes. We discuss the genomic reorganization of the C. langguthi karyotype.

Oil palm monoculture comprises one of the most financially attractive land-use options in tropical forests, but cropland suitability overlaps the distribution of many highly threatened vertebrate species. We investigated how forest mammals respond to a landscape mosaic, including mature oil palm plantations and primary forest patches in Eastern Amazonia. Using both line-transect censuses (LTC) and camera-trapping (CT), we quantified the general patterns of mammal community structure and attempted to identify both species life-history traits and the environmental and spatial covariates that govern species intolerance to oil palm monoculture. Considering mammal species richness, abundance, and species composition, oil palm plantations were consistently depauperate compared to the adjacent primary forest, but responses differed between functional groups. The degree of forest habitat dependency was a leading trait, determining compositional dissimilarities across habitats. Considering both the LTC and CT data, distance from the forest-plantation interface had a significant effect on mammal assemblages within each habitat type. Approximately 87% of all species detected within oil palm were never farther than 1300 m from the forest edge. Our study clearly reinforces the notion that conventional oil palm plantations are extremely hostile to native tropical forest biodiversity, which does not bode well given prospects for oil palm expansion in both aging and new Amazonian deforestation frontiers.

Sigmodontinae rodents show great diversity and complexity in morphology and ecology. This diversity is accompanied by extensive chromosome variation challenging attempts to reconstruct their ancestral genome. The species Hylaeamys megacephalus–HME (Oryzomyini, 2n = 54), Necromys lasiurus—NLA (Akodontini, 2n = 34) and Akodon sp.–ASP (Akodontini, 2n = 10) have extreme diploid numbers that make it difficult to understand the rearrangements that are responsible for such differences. In this study we analyzed these changes using whole chromosome probes of HME in cross-species painting of NLA and ASP to construct chromosome homology maps that reveal the rearrangements between species. We include data from the literature for other Sigmodontinae previously studied with probes from HME and Mus musculus (MMU) probes. We also use the HME probes on MMU chromosomes for the comparative analysis of NLA with other species already mapped by MMU probes. Our results show that NLA and ASP have highly rearranged karyotypes when compared to HME. Eleven HME syntenic blocks are shared among the species studied here. Four syntenies may be ancestral to Akodontini (HME2/18, 3/25, 18/25 and 4/11/16) and eight to Sigmodontinae (HME26, 1/12, 6/21, 7/9, 5/17, 11/16, 20/13 and 19/14/19). Using MMU data we identified six associations shared among rodents from seven subfamilies, where MMU3/18 and MMU8/13 are phylogenetic signatures of Sigmodontinae. We suggest that the associations MMU2entire, MMU6proximal/12entire, MMU3/18, MMU8/13, MMU1/17, MMU10/17, MMU12/17, MMU5/16, MMU5/6 and MMU7/19 are part of the ancestral Sigmodontinae genome.

The Neacomys genus (Rodentia, Sigmodontinae) is distributed in the Amazon region, with some species limited to a single endemic area, while others may occur more widely. The number of species within the genus and their geographical boundaries are not known accurately, due to their high genetic diversity and difficulties in taxonomic identification. In this work we collected Neacomys specimens from both banks of the Tapajós River in eastern Amazon, and studied them using chromosome painting with whole chromosome probes of Hylaeamys megacephalus (HME; Rodentia, Sigmodontinae), and molecular analysis using haplotypes of mitochondrial genes COI and Cytb. Chromosome painting shows that Neacomys sp. A (NSP-A, 2n = 58/FN = 68) and Neacomys sp. B (NSP-B, 2n = 54/FN = 66) differ by 11 fusion/fission events, one translocation, four pericentric inversions and four heterochromatin amplification events. Using haplotypes of the concatenated mitochondrial genes COI and Cyt b, Neacomys sp. (2n = 58/FN = 64 and 70) shows a mean divergence of 6.2% for Neacomys sp. A and 9.1% for Neacomys sp. B, while Neacomys sp. A and Neacomys sp. B presents a medium nucleotide divergence of 7.4%. Comparisons were made with other published Neacomys data. The Tapajós and Xingu Rivers act as geographic barriers that define the distribution of these Neacomys species. Furthermore, our HME probes reveal four synapomorphies for the Neacomys genus (associations HME 20/[13,22]/4, 6a/21, [9,10]/7b/[9,10] and 12/[16,17]) and demonstrate ancestral traits of the Oryzomyini tribe (HME 8a and 8b, 18 and 25) and Sigmodontinae subfamily (HME 15 and 24), which can be used as taxonomic markers for these groups.

BackgroundProechimys is the most diverse genus in family Echimyidae, comprising 25 species (two of which are polytypic) and 39 taxa. Despite the numerous forms of this rodent and their abundance in nature, there are many taxonomic problems due to phenotypic similarities within the genus and high intraspecific variation. Extensive karyotypic variation has been noted, however, with diploid numbers (2n) ranging from 14 to 62 chromosomes. Some heteromorphism can be found, and 57 different karyotypes have been described to date.ResultsIn the present work, we describe a cytotype with a very low 2n. Specimens of Proechimys cf. longicaudatus were collected from two different places in northern Mato Grosso state, Brazil (12°54″S, 52°22″W and 9°51′17″S, 58°14′53″W). The females and males had 16 and 17 chromosomes, respectively; all chromosomes were acrocentric, with the exception of the X chromosome, which was bi-armed. The sex chromosome system was found to be XY1Y2, originating from a Robertsonian rearrangement involving the X and a large acrocentric autosome. Females had two Neo-X chromosomes, and males had one Neo-X and two Y chromosomes. NOR staining was found in the interstitial region of one autosomal pair.ConclusionsComparison of this karyotype with those described in the literature revealed that Proechimys with similar karyotypes had previously been collected from nearby localities. We therefore suggest that this Proechimys belongs to a different taxon, and is either a new species or one that requires reassessment.

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Background The Neacomys genus is predominantly found in the Amazon region, and belongs to the most diverse tribe of the Sigmodontinae subfamily (Rodentia, Cricetidae, Oryzomyini). The systematics of this genus and questions about its diversity and range have been investigated by morphological, molecular (Cytb and COI sequences) and karyotype analysis (classic cytogenetics and chromosome painting), which have revealed candidate species and new distribution areas. Here we analyzed four species of Neacomys by chromosome painting with Hylaeamys megacephalus (HME) whole-chromosome probes, and compared the results with two previously studied Neacomys species and with other taxa from Oryzomyini and Akodontini tribes that have been hybridized with HME probes. Maximum Parsimony (MP) analyses were performed with the PAUP and T.N.T. software packages, using a non-additive (unordered) multi-state character matrix, based on chromosomal morphology, number and syntenic blocks. We also compared the chromosomal phylogeny obtained in this study with molecular topologies (Cytb and COI) that included eastern Amazonian species of Neacomys, to define the phylogenetic relationships of these taxa. Results The comparative chromosome painting analysis of the seven karyotypes of the six species of Neacomys shows that their diversity is due to 17 fusion/fission events and one translocation, pericentric inversions in four syntenic blocks, and constitutive heterochromatin (CH) amplification/deletion of six syntenic autosomal blocks plus the X chromosome. The chromosomal phylogeny is consistent with the molecular relationships of species of Neacomys. We describe new karyotypes and expand the distribution area for species from eastern Amazonia and detect complex rearrangements by chromosome painting among the karyotypes. Conclusions Our phylogeny reflects the molecular relationships of the Akodontini and Oryzomyini taxa and supports the monophyly of Neacomys. This work presents new insights about the chromosomal evolution of this group, and we conclude that the karyotypic divergence is in accord with phylogenetic relationships.

The persistent high deforestation rate and fragmentation of the Amazon forests are the main threats to their biodiversity. To anticipate and mitigate these threats, it is important to understand and predict how species respond to the rapidly changing landscape. The short-eared dog Atelocynus microtis is the only Amazon-endemic canid and one of the most understudied wild dogs worldwide. We investigated short-eared dog habitat associations on two spatial scales. First, we used the largest record database ever compiled for short-eared dogs in combination with species distribution models to map species habitat suitability, estimate its distribution range and predict shifts in species distribution in response to predicted deforestation across the entire Amazon (regional scale). Second, we used systematic camera trap surveys and occupancy models to investigate how forest cover and forest fragmentation affect the space use of this species in the Southern Brazilian Amazon (local scale). Species distribution models suggested that the short-eared dog potentially occurs over an extensive and continuous area, through most of the Amazon region south of the Amazon River. However, approximately 30% of the short-eared dog's current distribution is expected to be lost or suffer sharp declines in habitat suitability by 2027 (within three generations) due to forest loss. This proportion might reach 40% of the species distribution in unprotected areas and exceed 60% in some interfluves (i.e. portions of land separated by large rivers) of the Amazon basin. Our local-scale analysis indicated that the presence of forest positively affected short-eared dog space use, while the density of forest edges had a negative effect. Beyond shedding light on the ecology of the short-eared dog and refining its distribution range, our results stress that forest loss poses a serious threat to the conservation of the species in a short time frame. Hence, we propose a re-assessment of the short-eared dog's current IUCN Red List status (Near Threatened) based on findings presented here. Our study exemplifies how data can be integrated across sources and modelling procedures to improve our knowledge of relatively understudied species.