Octomys Research Articles

Evolution of the Largest Mammalian Genome.

The genome of the red vizcacha rat (Rodentia, Octodontidae, Tympanoctomys barrerae) is the largest of all mammals, and about double the size of their close relative, the mountain vizcacha rat Octomys mimax, even though the lineages that gave rise to these species diverged from each other only about 5 Ma. The mechanism for this rapid genome expansion is controversial, and hypothesized to be a consequence of whole genome duplication or accumulation of repetitive elements. To test these alternative but nonexclusive hypotheses, we gathered and evaluated evidence from whole transcriptome and whole genome sequences of T. barrerae and O. mimax. We recovered support for genome expansion due to accumulation of a diverse assemblage of repetitive elements, which represent about one half and one fifth of the genomes of T. barrerae and O. mimax, respectively, but we found no strong signal of whole genome duplication. In both species, repetitive sequences were rare in transcribed regions as compared with the rest of the genome, and mostly had no close match to annotated repetitive sequences from other rodents. These findings raise new questions about the genomic dynamics of these repetitive elements, their connection to widespread chromosomal fissions that occurred in the T. barrerae ancestor, and their fitness effects—including during the evolution of hypersaline dietary tolerance in T. barrerae.

Small mammal remains recovered from two archaeological sites in northwestern Mendoza (Late Holocene, Argentina): Taxonomic composition, taphonomic issues and paleoenvironmental implications

We present the results of the extensive analysis on the taxonomic composition, the taphonomic characteristics, and the possible paleoenvironmental implications of the small mammal assemblages in two archaeological sites located in northwestern Mendoza, Argentina: Vaquería Gruta 1 and Rincón de los Helados. Such sites have been radiocarbon dated for the Late Holocene. The taphonomic characteristics of these remains, which were accumulated in VQG1 and RH by raptor Strigiformes and Falconiformes birds respectively, were analyzed by means of digestive corrosion on the bones, breakage patterns and relative abundances. In order to evaluate the changes in the composition between past and current assemblages, zooarchaeological and current small mammal assemblages were compared. The taxonomic composition and abundance of small mammals in archaeological assemblages suggest the existence of greater environmental heterogeneity than the current during the Late Holocene, as would suggest the presence of Reithrodon auritus and Octomys mimax, currently extinct species in the region. The co-occurrence of these species currently with allopatric distributions, lead us to consider these archaeological sets as non-analogue communities. In relation with the changes detected between past and current assemblages, some factors need to be considered. Among them, the relevance of the anthropic activities that have negatively affected the diversity, richness and abundance of flora and fauna since the XVI century, and the possible mixture of taxa due to the predation by owls in different altitudinal levels of vegetation.

Remote sensing variables as predictors of habitat suitability of the viscacha rat (Octomys mimax), a rock-dwelling mammal living in a desert environment

Identifying high-quality habitats across large areas is a central goal in biodiversity conservation. Remotely sensed data provide the opportunity to study different habitat characteristics (e.g., landscape topography, soil, vegetation cover, climatic factors) that are difficult to identify at high spatial and temporal resolution on the basis of field studies. Our goal was to evaluate the applicability of remotely sensed information as a potential tool for modeling habitat suitability of the viscacha rat (Octomys mimax), a rock-dwelling species that lives in a desert ecosystem. We fitted models considering raw indices (i.e., green indices, Brightness Index (BI) and temperature) and their derived texture measures on locations used by and available for the viscacha rat. The habitat preferences identified in our models are consistent with results of field studies of landscape use by the viscacha rat. Rocky habitats were well differentiated by the second-order contrast of BI, instead of BI only, making an important contribution to the global model by capturing the heterogeneity of the substratum. Furthermore, rocky habitats are able to maintain more vegetation than much of the surrounding desert; hence, their availability might be estimated using SATVI (Soil Adjusted Total Vegetation Index) and its derived texture measures: second-order contrast and entropy. This is the first study that evaluates the usefulness of remotely sensed data for predicting and mapping habitat suitability for a small-bodied rock dwelling species in a desert environment. Our results may contribute to conservation efforts focused on these habitat specialist species by using good predictors of habitat quality.

Habitat selection by the viscacha rat (Octomys mimax, Rodentia: Octodontidae) in a spatially heterogeneous landscape

AbstractThe viscacha rat

Microhabitat selection by Octomys mimax (Rodentia: Octodontidae) in the Monte Desert is affected by attributes and thermal properties of crevices

Fil: Campos, Valeria Evelin. Universidad Nacional de San Juan. Facultad de Ciencias Exactas, Fisicas y Naturales. Instituto y Museo de Ciencias Naturales; Argentina. Consejo Nacional de Investigaciones Cientificas y Tecnicas; Argentina. Universidad Nacional de San Juan. Facultad de Ciencias Exactas Fisicas y Naturales. Departamento de Biologia; Argentina

Phylogenetic analysis and phylogeography of the tetraploid rodentTympanoctomys barrerae(Octodontidae): insights on its origin and the impact of Quaternary climate changes on population dynamics

The allotetraploid Tympanoctomys barrerae has a broad, patchy distribution around salt flats in western Argentina. To gain insights into its phylogenetic relationships, phylogeographical patterns, and origin, seven populations of T. barrerae and its allied taxa were studied through a 1075-bp fragment of cytochrome b and cytochrome oxidase I. Matrilineal phylogenetic relationships were explored with maximum likelihood and Bayesian approaches. The intraspecific genealogy was inferred by median-joining networks. The populational structure was assessed by molecular variance, and the demographic history through coalescence. The tree topology depicted sister-group relationship between Octomys mimax to the pair T. barrerae–Pipanacoctomys aureus, suggesting P. aureus belongs to the maternal lineage that gave rise to T. barrerae. High degrees of intrapopulational variation and the several instances of interpopulational polyphyly suggest range shifts and secondary contact. Consistent with the phylogenetic results, the network analysis revealed two haplotypic lineages depicting genetic admixtures unrelated to the current geographical distribution, and a deep split with the southernmost lineage of Chubut. The origin of T barrerae was estimated at approximately 2.52 Mya, whereas the divergence estimate for Chubut coincides with the end of largest Patagonian glaciation, at 1.47 Mya. Apparently, this population remained isolated during a northward Pleistocenic range shift. The historical demographic patterns of the lineages of T. barrerae fit with a contraction–expansion model coincident with Quaternary cycling events. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 108, 453–469.

Distribution of repetitive DNAs and the hybrid origin of the red vizcacha rat (Octodontidae)

Great genome size (GS) variations described in desert-specialist octodontid rodents include diploid species ( Octomys mimax and Octodontomys gliroides ) and putative tetraploid species ( Tympanoctomys barrerae and Pipanacoctomys aureus ). Because of its high DNA content, elevated chromosome number, and gigas effect, the genome of T. barrerae is claimed to have resulted from tetraploidy. Alternatively, the origin of its GS has been attributed to the accumulation of repetitive sequences. To better characterize the extent and origin of these repetitive DNA, self-genomic in situ hybridization (self-GISH), whole-comparative genomic hybridization (W-CGH), and conventional GISH were conducted in mitotic and meiotic chromosomes. Self-GISH on T. barrerae mitotic plates together with comparative self-GISH (using its closest relatives) discriminate a pericentromeric and a telomeric DNA fraction. As most of the repetitive sequences are pericentromeric, it seems that the large GS of T. barrerae is not due to highly repeated sequences accumulated along chromosomes arms. W-CGH using red-labeled P. aureus DNA and green-labeled O. mimax DNA simultaneously on chromosomes of T. barrerae revealed a yellow-orange fluorescence over a repetitive fraction of the karyotype. However, distinctive red-only fluorescent signals were also detected at some centromeres and telomeres, indicating closer homology with the DNA sequences of P. aureus. Conventional GISH using an excess of blocking DNA from either P. aureus or O. mimax labeled only a fraction of the T. barrerae genome, indicating its double genome composition. These data point to a hybrid nature of the T. barrerae karyotype, suggesting a hybridization event in the origin of this species.

Octomys mimax (Rodentia: Octodontidae)

Octomys mimax O. Thomas, 1920, the viscacha rat, is a surface-dwelling rodent, endemic to the Monte biome of western Argentina. The genus Octomys is monotypic and represents a basal clade within the family Octodontidae. O. mimax is strictly herbivorous and is found in low-elevation arid environments characterized by galleries or rock formations. In these environments, O. mimax nests within rock crevices located inside ravines with relatively low vegetation cover. O. mimax is solitary and mostly nocturnal. Nocturnal activity coupled with a basal metabolic rate and thermal conductance lower than expected for body mass of O. mimax probably represent strategies for water conservation in this species. DOI: 10.1644/853.1.

Habitat selection by two sympatric rodent species in the Monte desert, Argentina. First data for Eligmodontia moreni and Octomys mimax

Habitat selection in deserts is mainly modulated by the availability of resources. The basic hypotheses regarding coexistence of species in arid environments offer two possibilities: 1) coexisting species partition available resources (each species acting as a specialist) and 2) generalists coexist with specialists because the former use habitats which are underused or not selected by the latter. This study presents the first data on macro- and microhabitat selection by Eligmodontia moreni (Cricetidae) and Octomys mimax (Octodontidae), two rodent species which coexist in the most arid part of the Monte desert of Argentina. In order to evaluate both hypotheses, animals were trapped during two seasons (humid and dry) in six macrohabitats of the arid Monte (creosote bush scrub, mesquite woodlands, columnar cactus slopes, barrens, chical and saltbush). A multivariate analysis of variance was used to evaluate differences in PCA components of microhabitat (floristic composition and vegetation structure) among capture and control points. The resulting models suggest E. moreni to be described as a fine-grained generalist species, which would be segregated from the specialist O. mimax in shared macrohabitats by resource partitioning, basically related to substrate type and vegetation cover. Our findings accord with theories of community assembly involving generalist and specialist species.

Epigenetic processes in a tetraploid mammal

Polyploidy has played a most important role in speciation and evolution of plants and animals. It is thought that low frequency of polyploidy in mammals is due to a dosage imbalance that would interfere with proper development in mammalian polyploids. The first tetraploid mammal, Tympanoctomys barrerae (Octodontidae), appears to be an exception to this rule. In this study we investigated X chromosome inactivation (XCI) and genomic imprinting in T. barrerae, two epigenetic processes usually involved in dosage control in mammalian genomes. The imprinting status of the Peg1 gene was determined by Peg1 allelic expression studies. The inactive X chromosome was identified on interphase nuclei by immunofluorescence using specific antisera raised against Met3H3K27 and macroH2A1. Quantitative PCR was used to compare the Peg1/Dmd ratio in T. barrerae and in its most closely related diploid species, Octomys mimax. Our data demonstrate that parental-specific silencing of at least one gene and normal X chromosomal dosage mechanism are conserved in the tetraploid genome. We hypothesize a concerted action of genetic and epigenetic mechanisms during the process of functional diploidization of this tetraploid genome.

Activity, range areas, and nesting patterns in the viscacha rat, Octomys mimax

Several rodent species engage in group living, meaning that individuals share nests, resting places, and range areas. Establishing how group living varies across species is critical for comparative studies to examine the origin and the adaptive value of this behavior. Comparative approaches are more powerful when a diverse array of taxonomic groups is included. We used telemetry techniques to monitor patterns of activity, resting places, and range areas at night to examine the extent of sociality of the scarcely known viscacha rats, Octomys mimax. Seven individuals were live trapped and fitted with radio-collars. Viscacha rat activity, as measured from distance moved between consecutive telemetry scans, took place mostly during the nighttime. During day, animals used from 2 to 6 putative nest places, but one was used more frequently. The sharing of resting locations by two or more radio-collared animals was never recorded. Viscacha rats showed relatively large range areas and low-to-moderate spatial overlap with neighbors. Male rats had larger range areas than females, but spatial overlap with neighbors was similar. Results suggest that viscacha rats are solitary living animals. This study supported a solitary-to-social trend from basal to more derivate forms across Octodontidae.

Whole-genome duplications in South American desert rodents (Octodontidae)

The discovery of tetraploidy in the red viscacha rat, Tympanoctomys barrerae (4 n = 102) has emphasized the evolutionary role of genome duplication in mammals. The tetraploid status of this species is corroborated here by in situ PCR and Southern blot analysis of a single-copy gene. The species meiotic configuration strongly suggests a hybrid derivation. To investigate the origin of T. barrerae further, the recently described Pipanacoctomys aureus was studied. This 92-chromosome species also has a duplicated genome size, redundant gene copy number and diploid-like meiotic pairing, consistent with an event of allotetraploidization. Phylogenetic analysis of mitochondrial sequences indicates sister-group relationships between these two tetraploid rodents. The new karyotypic data and the phylogenetic relationships suggest the participation of the ancestral lineages of Octomys mimax in the genesis of P. aureus . The high overall DNA similarity and shared band homology revealed by genomic Southern hybridization as well as matching chromosome numbers between O. mimax and the descendant tetraploid species support the notion of introgressive hybridization between these taxa. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 443‐451. ADDITIONAL KEYWORDS: allotetraploidy ‐ genome size ‐ hybridization ‐ octodontids ‐ polyploidy ‐ Tympanoctomys barrerae .

A desert octodontid rodent, Tympanoctomys barrerae, uses modified hairs for stripping epidermal tissue from leaves of halophytic plants.

Desert rodents that consume halophytic plants must have adaptations for coping with the high salt content of the leaves. A kidney capable of excreting very concentrated urine is one method. Another is removal of the hypersaline epidermis by means of chisel-like incisors prior to ingestion of the leaves. Tympanoctomys barrerae has evolved a unique refinement of the latter adaptation. It possesses two bundles of stiffened hairs on either side of the palate just caudal to the incisors. The bundles vibrate against the lower incisors, removing the epidermis from the leaves. The efficiency of the operation is significantly greater than with the use of incisors alone. Such a device has not been described in any other mammal. The facial muscles associated with the lips, the cheek vibrissae, and the oral cavity are described in T. barrerae and the nonhalophilic octodontid Octomys mimax. M. buccinatorius pars intermaxillaris is the only muscle in direct contact with the bristle bundles. Other anatomical features found in T. barrerae that may be associated with this feeding device are: 1) a much enlarged and mobile lower labial pad operated by Mm. buccinatorius pars orbicularis oris, pars longitudinalis profunda, and mandibularis cranialis profunda; 2) two oral glands not described in other rodents; and 3) a shortened tongue. Although, taken as a whole, this epidermal stripping device is unique to T. barrerae, most of its features have evolved by modification of structures present in the facial region of more generalized rodents.

Molecular Relationships Among Octodontidae (Mammalia: Rodentia: Caviomorpha)

We examined ten species of octodontid rodents and representatives of three outgroups in a complete 13 × 13 DNA-hybridization matrix. The results were indexed as differences in median melting-point depressions (ΔT,ms), symmetrized, subjected to phylogenetic analysis using FITCH, bootstrapped, and exhaustively taxon-jackknifed. Within Octodontidae, four clades were recovered with 100% bootstrap and complete jackknife support: Tympanoctomys barrerae with Octomys mimax, Octodontomys gliroides alone, Octodon spp., and Aconaemys spp. with Spalacopus cyanus; the latter two clades were closer to each other than either was to Octodontomys or Octomys-Tympanoctomys, but were slightly nearer to and united with Octodontomys, with 89% bootstrap support. However, relationships among the three Aconaemys species and Spalacopus were not completely resolved by our experiments. Ctenomys coyhaiquensis, Abrocoma bennetti, and Lagostomus maximus represented successive outgroups to Octodontidae, while one-way comparisons with Cavia porcellus and Microcavia australis suggested that these caviids are almost as distant from octodontoids as is the chinchilloid Lagostomus. When the data were suitably corrected for percentage hybridization and saturation, division of the distances by the rate previously determined for most amniotes (∼0.48%/myr) suggested that the basal divergence among the caviomorph rodents examined occurred about 59 myrbp, and that Octodontidae originated 40 myrbp and diversified into extant lineages beginning 14 myr ago. Calibration against the date of the earliest known caviomorph (late Eocene or about 37.5 myrbp) gave a rate of 0.75%/myr, which would suggest later dates for subsequent caviomorph cladogenesis. It is notable that, based respectively on the slower or faster rates, the tetraploid Tympanoctomys barrerae must have diverged from its sister-taxon Octomys mimax ∼10 or 6.5 myr ago.

Chromosomes of Octomys mimax and Octodontomys gliroides and Relationships of Octodontid Rodents

Octomys mimax possesses a chromosomal complement of 2n = 56, FN = 108, with heterochromatin restricted to the pericentric regions in all chromosomes except one autosomal pair and the X chromosome. One chromosome also has heterochromatin in a secondary constriction. C-bands of Octodontomys gliroides reveal the clear presence of pericentric heterochromatin on the X chromosome and six autosomal pairs. Lightly stained, pericentric C-bands also were present in five other autosomes. A satellite-bearing chromosome did not band. In both species, two active nucleolar organizing regions (AgNOR) were located at secondary constrictions. Based on chromosomal differences found among O. mimax and other octodontids, we hypothesize that the identical or similar 2n and FN observed for O. mimax , Aconaemys fuscus , and some other octodontid species is a result of parallel evolution.