Species Of Neotoma Research Articles

Reevaluation of the phylogenetic relationships among Neotomini rodents (Hodomys, Neotoma, and Xenomys) and comments on the woodrat classification.

The woodrats or packrats of the genus Neotoma have been the subject of a wide array of research including paleoecology, physiology, morphological evolution, systematics, speciation, and hybridization. In recent years, much work has been done to elucidate evolutionary relationships within and between closely related species of the genus; in particular the addition of newly collected specimens from critical geographic regions has provided new opportunities for taxonomic assessment. Given these new data and their potential, parsimony (PARS), maximum likelihood (ML), and Bayesian inference (BI) analyses were conducted on DNA sequences obtained from nine individual genes (four mitochondrial loci: 12S, 16S, CoII, and Cytb; five nuclear loci: AdhI2, BfibI7, En2, Mlr, and Myh6) to estimate the phylogenetic relationships among 23 species of Neotoma. Results of these analyses depicted a wide array of phylogenetic relationships among taxa; with substantial nodal support recovered in both the ML and PARS analyses at some mid-level and terminal positions. Several individual genes, particularly 12S, AdhI2, BfibI7, CoII, and Cytb, provided support at several basal positions; however, phylogenetic resolution was limited in the other genes. A final BI analysis where the nine genes were concatenated into a single data set produced several supported clades that corresponded to previously recognized species groups (floridana, micropus, mexicana, and lepida) and the subgenus Homodontomys. Levels of genetic divergence for within-species comparisons (estimated from the Cytb data set) ranged from 0.88% (N. magister) to 6.82% (N. fuscipes); for between sister species comparisons ranged from 4.68% (N. devia and N. lepida) to 12.70% (N. angustapalata and N. nelsoni); and for members within closely related clades ranged from 8.70% (N. bryanti and N. lepida) to 12.57% (N. goldmani and N. magister). Evaluations of generic, subgeneric, and species group boundaries were explored using phylogenetic principles on the DNA sequence data presented herein, as well as morphological findings from previous studies. Results obtained suggest that the most conservative taxonomic interpretation involves the abandonment of subgeneric delineations and relies on the recognition of eight species groups (cinerea, floridana, fuscipes, lepida, mexicana, micropus, phenax, and stephensi) as the backbone of the woodrat classification.

Phylogenetic positions of Paronychomys Jacobs and Basirepomys Korth and De Blieux relative to the tribe Neotomini (Rodentia, Cricetidae)

AbstractA recent study on the fossil history of North American woodrats and their relatives suggested that the Neotomini includes two subtribes: the Neotomina (woodrats; Tsaphanomys, Neotoma, Hodomys, Xenomys) and Galushamyina (reprats: Protorepomys, Galushamys, Miotomodon, Repomys, Nelsonia). The extinct Miocene Lindsaymys was proposed as a possible early neotominan, but not formally included in the Neotomini. In other studies, two extinct genera, Basirepomys and Paronychomys, occasionally have been treated as related to neotominans, but their ancestry had not been formally explored in detail. We performed a phylogenetic analysis on representatives of all genera with 40 dental and mandibular characters likely to be preserved in fossil material. The analysis resulted in a single most parsimonious tree supporting a neotominan-galushamyinan tribal classification of the Neotomini, and securely placed Lindsaymys within the Neotomina. None of the Basirepomys and Paronychomys species or Protorepomys bartlettensis nested within the Neotomini. The three Basirepomys species, possibly a paraphyletic group, are not closely related to Repomys, and Paronychomys (minus P. shotwelli = Tsaphanomys shotwelli) is not closely related to Onychomys, but is a possible sister group to the Neotomini. With the understanding that further study may remove it from Protorepomys, P. bartlettensis is tentatively retained within the genus, representing a relatively underived species possibly ancestral to both neotominan clades. Neotoma species of the extinct subgenus Paraneotoma and extant Neotoma may be paraphyletic at the generic level, but that determination will require further study.

The sensitivity of Neotoma to climate change and biodiversity loss over the late Quaternary

AbstractThe late Quaternary in North America was marked by highly variable climate and considerable biodiversity loss including a megafaunal extinction event at the terminal Pleistocene. Here, we focus on changes in body size and diet in Neotoma (woodrats) in response to these ecological perturbations using the fossil record from the Edwards Plateau (Texas) across the past 20,000 years. Body mass was estimated using measurements of fossil teeth and diet was quantified using stable isotope analysis of carbon and nitrogen from fossil bone collagen. Prior to ca. 7000 cal yr BP, maximum mass was positively correlated to precipitation and negatively correlated to temperature. Independently, mass was negatively correlated to community composition, becoming more similar to modern over time. Neotoma diet in the Pleistocene was primarily sourced from C3 plants, but became progressively more reliant on C4 (and potentially CAM) plants through the Holocene. Decreasing population mass and higher C4/CAM consumption was associated with a transition from a mesic to xeric landscape. Our results suggest that Neotoma responded to climatic variability during the terminal Pleistocene through changes in body size, while changes in resource availability during the Holocene likely led to shifts in the relative abundance of different Neotoma species in the community.

The relationship between molar morphology and ecology withinNeotoma

AbstractThe extensive diversity in dental form across mammals and its strong relationship with function provides insights into the diet, habitat, and behavior, of both extant and extinct taxa. Understanding the extent of variation in dental morphology across species allows for more accurate identification of fossils and a better ability to infer relationships between form and function and ecology. We examined variation in the size and shape of the first upper molar among the genus Neotoma. We employed elliptical Fourier analysis to quantify differences in the shape of 2D outlines for 23 populations and six species of Neotoma, varying in body size and habitat preference. As expected, molar length is a strong predictor of body size and is significantly and negatively correlated with temperature, particularly in species whose ranges span large latitudinal gradients. We found that differences in molar shape separate species into three general morpho-groups, with no evidence of a phylogenetic signal. While outline analysis could not robustly classify all molars to the species level, it did perform well for Neotoma cinerea, probably because of the greater degree of folding and more acute angling of molar lophs. In contrast, wider lophs with shallower enamel infolding was characteristic of species specializing on softer, more succulent resources (i.e., Neotoma albigula and Neotoma micropus). Neotoma floridana were inaccurately classified to species in the majority of cases, but were the only molars correctly identified to locality 100% of the time, suggesting that dietary specializations at a local level may drive morphological changes within the species as well as across the genus.

A new species of Sigmodontinae (Rodentia) from the late Hemphillian of central Mexico, and comments on the possible radiation of this group

The Sigmodontinae subfamily represents one of the most diverse groups of mammals in the world; this rodent group evolved in the open and arid ecosystems of the Miocene of North America and was the most successful legion of mammals in the Great American Biotic Interchange. Part of its diversification occurred in the Mexican Pliocene, in the Hemphillian-Blancan boundary, where Prosigmodon and Sigmodon species are very common. Recent molecular phylogenetic systematics research propose that Sigmodon is related to South American sigmodontines, while studies of classical morphometry in isolated molar teeth consider Prosigmodon as synonymy of Sigmodon, which modifies the biogeographic and chronostratigraphic interpretations of this group in America. In this paper, we describe a new species of Prosigmodon from the late Hemphillian (~4.89 Ma) of central Mexico based on jaws, maxillary, and complete isolated teeth. This is the most complete and austral record of the genus in North America. This species was compared with North American species of the Sigmodontinae and Neotominae subfamilies and we defined it as a new Prosigmodon species characterized by having a consistently present minute mesoloph in M1 and M2, in addition, there is an isolated metaconid from the protoconid in the m1 of young individuals. We performed a phylogenetic model focused on understanding the relationship between Prosigmodon (four species) and Sigmodon (eight species), where we included Baiomys (two species), Neotoma (two species), Peromyscus (two species), and Reithrodontomys (two species). Our results indicate that Prosigmodon is a monophyletic group if Sigmodon minor is included within the genus and P. chihuahuensis is excluded. The Mexican Prosigmodon species have more apomorphic characters with respect to S. minor and P. holocuspis. The species of Prosigmodon and Sigmodon are not closely related, Sigmodon is more related to the Neotoma species than the species of Baiomys, Prosigmodon, Reitrhodontomys, and Peromyscus. Based on the topology of our cladogram and the stratigraphic ranges of the species Sigmodontinae and Neotominae, we discuss that Baiomys, Prosigmodon, Reitrhodontomys, and Peromyscus probably diversified in the early Hemphillian, while Sigmodon and Neotoma did so during the late Pliocene.

On the ancestry of woodrats

Abstract We evaluated the fossil record of extinct and extant woodrats, and generated a comprehensive phylogenetic hypothesis of woodrat origins and relationships based on these data. The galushamyinin cricetines are redefined and reclassified as a subtribe of the Neotomini, including Repomys, Miotomodon, Galushamys, Nelsonia, and a new extinct genus with two new species. The geographic distribution of Nelsonia, restricted to montane coniferous forests of western Mexico, suggests that this subtribe was mostly confined to western coniferous ecosystems or similar ecosystems at lower elevation during glacial advances. A second subtribe of the Neotomini includes a new archaic genus and species, Neotoma, Hodomys, and Xenomys. Lindsaymys, a possible neotominin from the late Clarendonian (late Miocene) of California, demonstrates an occlusal morphology consistent with ancestry for the Neotomini, but the presence of a fourth root on M1 is problematic and may preclude the known populations from filling that role. Molars identified as Neotoma sp. from the Hemphillian (latest Miocene or early Pliocene) Rancho el Ocote assemblage of Guanajuato, Mexico, may represent the earliest Xenomys. Extant Neotoma species with a bilobed m3 appear to have originated subsequent to about 2.0 Ma, whereas Hodomys alleni and Xenomys nelsoni likely originated earlier from one or more extinct ancestors with an S-shaped m3.

Molecular phylogenetics of an endangered species: the Tamaulipan woodrat (Neotoma angustapalata)

Neotoma angustapalata (Tamaulipan woodrat) is a large cricetid rodent found only in southwestern Tamaulipas and northeastern San Luis Potosi, Mexico. This species currently is listed as endangered due to habitat alteration, its restricted distribution, and relative rarity. Previous taxonomic assessments have allied N. angustapalata with N. albigula (now encompassing N. leucodon), N. mexicana or N. micropus. We sequenced portions of the mitochondrial cytochrome b gene from two skin samples of the Tamaulipan woodrat, including one of two topotypes. We estimated genealogical relationships between N. angustapalata and other species of Neotoma using maximum likelihood and Bayesian inference. In general, our results confirm the phylogeny of woodrats as proposed previously but we also recovered major genetic differentiation within what currently is recognized as N. mexicana and N. albigula. Our data document that the Tamaulipan woodrat is genetically indistinguishable from geographically adjacent haplotypes of N. leucodon. However, mitochondrial introgression from N. leucodon cannot be ruled out inasmuch as we were not able to obtain nuclear sequence data for N. angustapalata. Morphological analyses document that both male and female Tamaulipan woodrats differ morphologically from N. leucodon. Given that the Tamaulipan woodrat is diagnosable morphologically and occurs in habitat that differs from N. leucodon, we recognize N. angustapalata as a species-level entity.

A longitudinal study of Bartonella infection in populations of woodrats and their fleas

Rodent-borne bartonellae have been identified as human pathogens. Little is known about Bartonella infections in woodrat hosts and their fleas and how woodrat-flea associations may affect the dynamics of Bartonella infections. We collected blood samples and fleas from two species of woodrats (Neotoma micropus and N. albigula) from Santa Fe County, NM, from 2002-2005. The most predominant flea species were Orchopeas sexdentatus and O. neotomae. Bartonella prevalence in woodrats was 64% overall, with a lower prevalence occurring in the pre-reproductive period compared to the early and late reproductive periods. A negative correlation between Bartonella prevalence in N. micropus and weight of N. micropus was observed. Flea load in Neotoma species was highest in the early reproductive period compared to the pre- and late reproductive periods and was higher in N. micropus compared to N. albigula. Bartonella prevalence in fleas was highest in the early reproductive period and lowest in the late reproductive period, and it was higher in fleas collected from N. micropus than in fleas collected from N. albigula. Abundance of O. sexdentatus was significantly higher in N. micropus compared to N. albigula, and abundance of O. sexdentatus and O. neotomae was highest in the early reproductive period. No direct correlations were found either between Bartonella prevalence in woodrats and in fleas or between Bartonella prevalence in woodrats and flea loads. Out of 25 partially characterized Bartonella isolates from Neotoma woodrats, 24 belonged to one genogroup based on sequencing of the gltA gene.

MOLECULAR SYSTEMATICS OF THE GENUS NEOTOMA BASED ON DNA SEQUENCES FROM INTRON 2 OF THE ALCOHOL DEHYDROGENASE GENE.

Phylogenetic relationships were evaluated among 13 species of Neotoma based on DNA sequences from intron 2 of the nuclear alcohol dehydrogenase gene 1 (Adh1-I2). Sequences were analyzed using parsimony, likelihood, and Bayesian methods. Three major clades (I-III) consistently were recovered and relationships among taxa within 2 of the clades remained unchanged between analyses; however, relationships within clade III were largely unresolved. Average genetic divergence values were 2.12% among species, 4% between subgenera (Teonoma and Neotoma), and 5.1% between genera (Hodomys and Neotoma). Adh1-I2 sequences were concatenated with mitochondrial cytochrome-b sequences generated from the same individuals. Examination of the combined data resulted in a phylogeny whose topology was similar to that based only on cytochrome-b sequences.

SHORT REPORT: A DISSEMINATED INFECTION OF LEISHMANIA MEXICANA IN AN EASTERN WOODRAT, NEOTOMA FLORIDANA, COLLECTED IN TEXAS

An eastern woodrat (Neotoma floridana) collected in January 2001 near Bedias, Grimes County, Texas, had extensive lesions of both ears and swollen feet. Impression smears and histologic sections demonstrated the presence of Leishmania in both ears and the one foot that was screened. Polymerase chain reaction screening using species-specific primers detected parasites in both ears and all four feet and indicated the parasites were L. mexicana. The detection of L. mexicana in N. floridana represents a new host record in a new ecologic region and may help explain a human infection acquired outside the previously-known range of the disease. Given the geographic distribution of N. floridana and the two other species of Neotoma found naturally infected, enzootic foci of Leishmania could be present over much of the southern United States.

Ecologic niche modeling and potential reservoirs for Chagas disease, Mexico.

Ecologic niche modeling may improve our understanding of epidemiologically relevant vector and parasite-reservoir distributions. We used this tool to identify host relationships of Triatoma species implicated in transmission of Chagas disease. Associations have been documented between the protracta complex (Triatoma: Triatominae: Reduviidae) with packrat species (Neotoma spp.), providing an excellent case study for the broader challenge of developing hypotheses of association. Species pairs that were identified coincided exactly with those in previous studies, suggesting that local interactions between Triatoma and Neotoma species and subspecies have implications at a geographic level. Nothing is known about sylvatic associates of T. barberi, which are considered the primary Chagas vector in Mexico; its geographic distribution coincided closely with that of N. mexicana, suggesting interaction. The presence of the species was confirmed in two regions where it had been predicted but not previously collected. This approach may help in identifying Chagas disease risk areas, planning vector-control strategies, and exploring parasite-reservoir associations for other emerging diseases.

Geographic distribution and genetic diversity of Whitewater Arroyo virus in the southwestern United States.

The purpose of this study was to extend our knowledge of the geographic distribution and genetic diversity of the arenavirus(es) associated with Neotoma species (woodrats) in the southwestern United States. Infectious arenavirus was recovered from 14 (3.3%) of 425 woodrats. The virus-positive species included N. albigula in New Mexico and Oklahoma, N. cinerea in Utah, N. mexicana in New Mexico and Utah, and N. micropus in Texas. Analyses of viral nucleocapsid protein gene sequence data indicated that all the isolates were strains of the Whitewater Arroyo virus, an arenavirus previously known only from northwestern New Mexico. Analyses of the sequence data also indicated that there can be substantial genetic diversity among strains of Whitewater Arroyo virus from conspecific woodrats collected from different localities and substantial genetic diversity among strains from different woodrat species collected from the same locality.

Prevalence of Hantavirus in Four Species of Neotoma from Arizona and Utah

Sin Nombre virus (SNV), a hantavirus, can cause severe respiratory illness and death in humans. The primary carrier is the deer mouse, Peromyscus maniculatus , but other species of rodents may be infected with the virus. We screened four species of woodrats ( Neotoma ) for hantavirus using both enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) tests. Woodrats were collected from a variety of habitats in Arizona and Utah. Only Neotoma lepida tested serologically positive in an ELISA assay for hantavirus and also contained SNV RNA. Moreover, across three distinct populations of N. lepida , individuals that tested serum positive were restricted to one population near Jericho, Utah. The prevalence of hantavirus in this population was 27% (4 of 15).

Scaling of Digestive Efficiency with Body Mass in Neotoma

1. Previous authors have suggested that larger animals are more efficient at extracting energy and nutrients from food resources because of their more favourable metabolic rate to gut capacity ratio (MR/GC). For herbivores in particular, the utilization of low quality vegetation becomes progressively more difficult with decreasing size because of the time-dependent nature of the microbial fermentation of plant fibre. 2. The relationship between fibre digestibility, a measure of digestive efficiency important to herbivores, and body size was investigated for three species of Neotoma. Animals ranged in mass from 80 to 400 g. A diagram was constructed which reflected allometric predictions, but also incorporated several mediating factors, such as intake and food sorting behaviour. Because of the high correlations between the variables, path analysis was utilized to evaluate the relative importance of each factor in affecting fibre digestibility. 3. Overall, a low correlation (0.105) was found between fibre digestibility and body mass. Path analysis revealed that this low correlation could be partitioned into a relatively strong direct influence of body mass (0.761) and opposing indirect effects through intake and food sorting (-0.563 and -0.094, respectively). 4. While it is clear from the analysis that body mass is of critical importance in influencing fibre fermentation, actual ecological or evolutionary implications are more difficult to assess. It is plausible, for example, that the apparent propensity towards insular gigantism common among small herbivores is at least partially the result of selection acting on digestive efficiency

Three sympatric species of Neotoma: dietary specialization and coexistence.

Three sympatric species of Neotoma occur in the southern Great Basin Desert in northern Arizona. Observations and experiments from 1980-1984 focused on diet and den selection to determine to what extent woodrats partition available food and shelter. Analyses included microscopic inspection of feces from live-trapped animals, forage moisture content, and seasonal habitat utilization. Each species of woodrat was found to selectively forage on a different genus of the three evergreens on the study site: N. albigula was the only species to eat appreciable amounts of Yucca, while N. devia, specialized on Ephedra epidermis, and N. stephensi on Juniperus. Observations in the laboratory showed a linear dominance hierarchy where the larger species dominated smaller ones, i.e., N. albigula>N. stephensi>N. devia. To determine if such a hierarchy existed in the field, the behaviorally dominant species (N. albigula and N. stephensi) were continually removed (from a 25 ha experimental plot) over a 12-month period leaving only the subordinate species (N. devia) in the area. In these experiments, 40% of the "dominant"-species dens became occupied by 20 of the "subordinate"-species on the removal plot, whereas there were no interspecific den site (n=39) changes among species on the control plot. Removal of the two dominant Neotoma spp resulted in an increase of N. devia from a pre-removal high of 16 to a post-removal population of 26 individuals. These data suggest that while these woodrats may not compete for food, the subordinate species compete with the dominant species for den sites, prime dens being sequestered by the behaviorally dominant species.

Two New Species of Late Pleistocene Woodrats (Cricetidae: Neotoma) from New Mexico

Two new species of Neotoma are described from New Mexican cave deposits older than late Wisconsinan full-stadial time. One of these species, morphologically similar to N. cinerea , N. fuscipes , and N. mexicana , is tentatively hypothesized to be a descendent of Neotoma cinerea populations isolated in the southeastern New Mexican highlands since early Wisconsinan stadial events; the other is most similar to the living Neotoma goldmani of north-central Mexico, and likely is ancestral to that species.

Macrofossil analysis of wood rat ( Neotoma) middens as a key to the quaternary vegetational history of arid America

Wood rat ( Neotoma) deposits preserved in dry rock shelters have radiocarbon ages extending from close to the present to >40,000 BP, thus providing elaborate samples of changing vegetation during the climatic shifts of the late Pleistocene and Holocene. The established record extends geographically from Oregon and Wyoming (at 45°N) south to Baja California, Sonora, and to Tehuacan (at 18°N) in southern Mexico. Several hundred ancient middens have been uncovered, and over 130 have been radiocarbon-dated. There are about 20 extant species of Neotoma with a combined range extending from the Yukon and New England to Nicaragua and Florida. Hence, a wider application for the method seems likely, wherever dry caves favor preservation. The acquisitive rats accumulate an incredibly detailed inventory of the local flora and fauna within a small home range, measured at about 100 m or less in radius. The biomass spectrum of a modern wood rat deposit was compared with associated pollen spectra and source vegetation. The most dominant arborescent species, as determined by a quantitative study of the local vegetation, were proportionately represented in the midden, but not in the pollen rain. Less dominant species were variable in proportionality. A novel approach to the comparative ecological physiology of long-dead plants has been demonstrated with macrofossils from ancient wood rat deposits. The ratio of the stable isotopes of carbon ( 13C/ 12C) is more altered from the atmospheric proportion during CO 2 fixation by C 3 plants than it is by the different (PEP) carboxylating enzyme of heliophile or xerophytic, C 4 or CAM plants. Mass spectrometry of the carbon of macrofossils enables the distinction to be made in the past. The desiccated, allelochemic urine, or amberat, indurates and preserves the middens by cementing the loose debris of macrofossils into a tough, coherent mass of surprising strength and rigidity, that adheres tenaciously to rock surfaces. Water softens the most indurated middens by dissolving the crystallized urine, causing them to dislodge and to fall apart; it also removes the osmotic and allelochemic deterrent to decay by fungi, or to consumption by termites, crickets, or other decomposing herbivores. A secure position in a dry rock shelter is therefore essential to preservation of the macrofossils for time periods on the order of 10 4 years. Attrition with time is seen in the frequency distribution of radiocarbon dates obtained on 132 Neotoma middens. The distribution is skewed toward the end of the Wisconsin glacial and the Holocene, and there is a decline in frequency with age. Cave erosion, including destructive rockfalls and new crevices that admit seepage and cause deterioration and dislodgement of the middens, is probably the main factor in the progressive attrition with increasing age.

Notes on Two Species of Wood Rats in Captivity

A small colony of each of two species of Neotoma was maintained at the Laboratory of Vertebrate Genetics, University of Michigan, Ann Arbor, during 1928, 1929, 1930, 1931, and 1932. One stock was derived from an adult female and two male hoary wood rats, Neotoma micropus canescens, caught three miles north of Carlsbad, New Mexico. The other originated from six female and nine male white-throated wood rats, N. albigula albigula, caught at points near Oracle and Tucson, Arizona. The writer is indebted to Dr. Lee R. Dice and Mr. Philip Blossom for securing and identifying the foundation animals. Grants from the Faculty Research Fund, University of Michigan, supported this work during 1928 and 1929. We maintained these wood rats in the laboratory under the conditions successfully used for members of the Old World genus Rattus. They were confined in wire cages, which had a floor space of 15 x 16 inches and which provided a total space of about 2100 cubic inches. Their diet consisted of one of the uncooked commercial dog foods; a mixture of wheat, corn, and sunflower seeds; rolled oats; and lettuce leaves. In addition, they received cod-liver oil equal in quantity to five-tenths of one per cent by weight of the total food consumed. A small bundle of shredded paper in each cage provided a scanty substitute for their habitually large nests. Each week the sawdust bedding was replaced with clean material. Fresh water was available to the rats at all times. The temperature of the laboratory was maintained within five degrees of 70?F. except on occasional days in July and August. The rats were handled at intervals when weighed or transferred to new cages. There was no indication that they became tame during several years of life in the laboratory. They always struggled violently when handled and sometimes broke their incisor teeth by biting the forceps that held them. In the cages they were timid but not extremely nervous and excitable. When the cage was disturbed they retreated to the rear and thumped the floor with their hind feet in the manner of rabbits. Those individuals born and reared in the cages were not perceptibly tamer than those that were caught in the field.

On a new species of Neotoma (N. ferruginea) from Guatemala

<i>On a new species of</i> Neotoma (N. ferruginea) <i>from Guatemala</i>