Spiny Pocket Mouse Research Articles

Identification of a novel polyomavirus in wild Sonoran Desert rodents of the family Heteromyidae.

Rodents are the largest and most diverse group of mammals. Covering a wide range of structural and functional adaptations, rodents successfully occupy virtually every terrestrial habitat, and they are often found in close association with humans, domestic animals, and wildlife. Although a significant amount of research has focused on rodents' prominence as known reservoirs of zoonotic viruses, there has been less emphasis on the viral ecology of rodents in general. Here, we utilized a viral metagenomics approach to investigate polyomaviruses in wild rodents from the Baja California peninsula, Mexico, using fecal samples. We identified a novel polyomavirus in fecal samples from two rodent species, a spiny pocket mouse (Chaetodipus spinatus) and a Dulzura kangaroo rat (Dipodomys simulans). These two polyomaviruses represent a new species in the genus Betapolyomavirus. Sequences of this polyomavirus cluster phylogenetically with those of other rodent polyomaviruses and two other non-rodent polyomaviruses (WU and KI) that have been identified in the human respiratory tract. Through our continued work on seven species of rodents, we endeavor to explore the viral diversity associated with wild rodents on the Baja California peninsula and expand on current knowledge of rodent viral ecology and evolution.

A new species of Epichernes (Pseudoscorpiones: Chernetidae) associated with rodents in Costa Rica

ABSTRACT The genus Epichernes Muchmore, 1982 has three Neotropical species with specific rodent hosts. Epichernes vickeryae sp. nov. is here described from Monteverde, Puntarenas, Costa Rica: the specimens were collected from a spiny pocket mouse Heteromys nubicolens. The new species, named E. vickeryae, is closer to E. navarroi by the position of trichobothria setae ist and isb, which are adjacent and the number of teeth on the movable finger, known from Mexico. The new species is characterized by trichobothrium ist adjacent to isb, femur L/B 1.71–1.85, it has 22–31 external accessory teeth, 58 teeth on fixed finger and 62 on movable finger. The carapace ranging from 1.12 mm to 1.33 mm in length, central tergites with 21–22 setae, chelicera with five setae on the hand, sb and b denticulate. The new species represents the second known species of Epichernes from Costa Rica.

Molecular data suggest that Heteromys irroratus bulleri should be recognized as a species-level taxon

Recent collecting surveys in the Sierra de Manantlán Biosphere Reserve, Jalisco (México), uncovered the existence of a new population of the Mexican spiny pocket mouse, Heteromys irroratus. Because the subspecies H. i. bulleri and H. i. jaliscensis occur nearby, our objective was to properly determine the taxonomic identity of the novel sample. Also, we evaluate its distinctiveness, both in terms of genetic divergence and phylogenetic placement, relative to other members of H. irroratus. Preliminary, we compared external and cranial measurements of recently collected individuals to those reported for representatives of the subspecies of H. irroratus occurring close by. In addition, we examined levels of genetic differentiation and phylogenetic relationships, based on sequence data of the Cytochrome b, among this population and other members of H. irroratus, including an individual from Sierra de Juanacatlán, Jalisco, the type locality of H. i. bulleri. Phylogenetic relationships were estimated using Maximum Likelihood and Bayesian Inference methods and levels of genetic divergence were assessed employing Kimura-2-parameters genetic distances. Samples from Sierra de Manantlán and Sierra de Juanacatlán were grouped together in a well-supported haplogroup and genetic distances between them were lower than < 1.02 %. Our phylogenetic hypothesis shows that H. i. bulleri represents the sister group to all other samples of H. irroratus but that, genetically, is a very divergent lineage. Distances values between H. i. bulleri to any of the other groups were > 10.05 %. Comparison of external and cranial measurements showed that, in average, individuals from Sierra de Manantlán are larger than those of H. i. jaliscensis, but more similar in size to H. i. bulleri. Our results show that the new population of the Mexican spiny pocket mouse from Sierra de Manantlán belongs to H. i. bulleri. In addition, the phylogenetic separation and the high levels of genetic divergence of H. i. bulleri, relative to other members of H. irroratus, suggest that the first should be recognized as a species-level taxon. Considering the scarce collecting records of H. i. bulleri and the known area of occurrence, that is very restricted, this taxon may warrant special conservation status.

Improving Area of Occupancy Estimates for Parapatric Species Using Distribution Models and Support Vector Machines

As geographic range estimates for the IUCN Red List guide conservation actions, accuracy and ecological realism are crucial. IUCN's extent of occurrence (EOO) is the general region including the species' range, while area of occupancy (AOO) is the subset of EOO occupied by the species. Data-poor species with incomplete sampling present particular difficulties, but species distribution models (SDMs) can be used to predict suitable areas. Nevertheless, SDMs typically employ abiotic variables (i.e., climate) and do not explicitly account for biotic interactions that can impose range constraints. We sought to improve range estimates for data-poor, parapatric species by masking out areas under inferred competitive exclusion. We did so for two South American spiny pocket mice: Heteromys australis (Least Concern) and Heteromys teleus (Vulnerable due to especially poor sampling), whose ranges appear restricted by competition. For both species, we estimated EOO using SDMs and AOO with four approaches: occupied grid cells, abiotic SDM prediction, and this prediction masked by approximations of the areas occupied by each species' congener. We made the masks using support vector machines (SVMs) fit with two data types: occurrence coordinates alone; and coordinates along with SDM predictions of suitability. Given the uncertainty in calculating AOO for low-data species, we made estimates for the lower and upper bounds for AOO, but only make recommendations for H. teleus as its full known range was considered. The SVM approaches (especially the second one) had lower classification error and made more ecologically realistic delineations of the contact zone. For H. teleus, the lower AOO bound (a strongly biased underestimate) corresponded to Endangered (occupied grid cells), while the upper bounds (other approaches) led to Near Threatened. As we currently lack data to determine the species' true occupancy within the post-processed SDM prediction, we recommend that an updated listing for H. teleus include these bounds for AOO. This study advances methods for estimating the upper bound of AOO and highlights the need for better ways to produce unbiased estimates of lower bounds. More generally, the SVM approaches for post-processing SDM predictions hold promise for improving range estimates for other uses in biogeography and conservation.

Improving area of occupancy estimates for parapatric species using distribution models and support vector machines.

As geographic range estimates for the IUCN Red List guide conservation actions, accuracy and ecological realism are crucial. IUCN’s extent of occurrence (EOO) is the general region including the species’ range, while area of occupancy (AOO) is the subset of EOO occupied by the species. Data‐poor species with incomplete sampling present particular difficulties, but species distribution models (SDMs) can be used to predict suitable areas. Nevertheless, SDMs typically employ abiotic variables (i.e., climate) and do not explicitly account for biotic interactions that can impose range constraints. We sought to improve range estimates for data‐poor, parapatric species by masking out areas under inferred competitive exclusion. We did so for two South American spiny pocket mice: Heteromys australis (Least Concern) and Heteromys teleus (Vulnerable due to especially poor sampling), whose ranges appear restricted by competition. For both species, we estimated EOO using SDMs and AOO with four approaches: occupied grid cells, abiotic SDM prediction, and this prediction masked by approximations of the areas occupied by each species’ congener. We made the masks using support vector machines (SVMs) fit with two data types: occurrence coordinates alone; and coordinates along with SDM predictions of suitability. Given the uncertainty in calculating AOO for low‐data species, we made estimates for the lower and upper bounds for AOO, but only make recommendations for H. teleus as its full known range was considered. The SVM approaches (especially the second one) had lower classification error and made more ecologically realistic delineations of the contact zone. For H. teleus, the lower AOO bound (a strongly biased underestimate) corresponded to Endangered (occupied grid cells), while the upper bounds (other approaches) led to Near Threatened. As we currently lack data to determine the species’ true occupancy within the post‐processed SDM prediction, we recommend that an updated listing for H. teleus include these bounds for AOO. This study advances methods for estimating the upper bound of AOO and highlights the need for better ways to produce unbiased estimates of lower bounds. More generally, the SVM approaches for post‐processing SDM predictions hold promise for improving range estimates for other uses in biogeography and conservation.

Do island populations differ in size and shape compared to mainland counterparts?

AbstractAdaptation and evolution of terrestrial vertebrates inhabiting islands have been the topic of many studies, particularly those seeking to identify trends or patterns in body size in mammals, albeit not necessarily in shape, in relation to mainland populations. The spiny pocket mouse, Chaetodipus spinatus, is distributed in the Baja California peninsula and its surrounding islands. Insular populations became isolated ~12,000 due to changes in sea level; these populations’ matrilinear (mitochondrial) DNA shows minor interpopulation variation. We tested the hypothesis that adaptation and evolution in these island populations involve variation in both skull size and skull shape (using geometric morphometrics) relative to mainland populations, rather than only in size as previously assumed. A total of 363 specimens from 15 insular and peninsular populations were used in analysis of the skull length and geometric morphometric analyses. Our findings revealed significant differences related to skull size among population. The skull shape analyses showed two significantly different morphotypes: one for all island specimens and one for all mainland samples. Our analyses support the hypothesis that insular populations may not only vary in size relative to mainland populations, but may also show variations in shape, regardless of differing conditions across islands.

A New Species of Flea of the Genus Kohlsia Traub, 1950 (Siphonaptera: Ceratophyllidae) from Veracruz, Mexico.

A new flea species, Kohlsia misantlensis, is described from the central mountains of Veracruz, Mexico. The hosts of this new species are the Mexican deer mouse Peromyscus mexicanus (Saussure, 1860) (Mammalia: Rodentia:Muridae) and the Mexican spiny pocket mouse Heteromys sp. (Heteromyidae). This flea species is easily recognized by the great development of sternite VIII with a tuft of seven long bristles near the apex. The new species is included in a taxonomic key for the species of genus Kohlsia occurring in Mexico.

Rediscovery of Heteromys nelsoni in its type locality after over a century

Abstract We rediscovered a population of Nelson’s spiny pocket mouse (Heteromys nelsoni; Merriam, 1902) in the type locality of Pinabeto in the Mexican state of Chiapas, 121 years after it was last collected. We describe five topotype specimens according to their morphology and external measurements, and we confirm its identity at the species level in the Basic Local Alignment Search Tool (BLAST) of GenBank. As the population of H. nelsoni in Pinabeto is isolated, it is likely to be susceptible to extinction. There is a need to carry out additional scientific studies of this microendemic species in order to obtain more information regarding its biology, ecology and evolutionary history, and to be able to influence environmental policy to protect and conserve this species, as well as the region’s cloud forests.

Divergent genetic mechanism leads to spiny hair in rodents.

Spines, or modified hairs, have evolved multiple times in mammals, particularly in rodents. In this study, we investigated the evolution of spines in six rodent families. We first measured and compared the morphology and physical properties of hairs between paired spiny and non-spiny sister lineages. We found two distinct hair morphologies had evolved repeatedly in spiny rodents: hairs with a grooved cross-section and a second near cylindrical form. Compared to the ancestral elliptical-shaped hairs, spiny hairs had higher tension and stiffness, and overall, hairs with similar morphology had similar functional properties. To examine the genetic basis of this convergent evolution, we tested whether a single amino acid change (V370A) in the Ectodysplasin A receptor (Edar) gene is associated with spiny hair, as this substitution causes thicker and straighter hair in East Asian human populations. We found that most mammals have the common amino acid valine at position 370, but two species, the kangaroo rat (non-spiny) and spiny pocket mouse (spiny), have an isoleucine. Importantly, none of the variants we identified are associated with differences in rodent hair morphology. Thus, the specific Edar mutation associated with variation in human hair does not seem to play a role in modifying hairs in wild rodents, suggesting that different mutations in Edar and/or other genes are responsible for variation in the spiny hair phenotypes we observed within rodents.

Identification of Bartonella Species Isolated from Rodents from Yucatan, Mexico, and Isolation of Bartonella vinsonii subsp. yucatanensis subsp. nov.

Bartonella species are highly endemic among wild rodents in many parts of the world. Blood and/or blood clot cultures from 38 rodents, including 27 Yucatan deer mouse (Peromyscus yucatanicus), 7 Gaumer's spiny pocket mouse (Heteromys gaumeri), 2 black rats (Rattus rattus) and 2 big-eared climbing rats (Ototylomys phyllotis) captured near Merida, Yucatan, Mexico, led to the isolation in 3-4 days of small gram-negative bacilli, which were identified as Bartonella spp. based on colony morphology. DNA extraction and PCR testing were also performed from heart samples of 35 of these 38 rodents. Overall, Bartonella spp. were isolated from the blood/blood clots of 22 (58%) rodents. All Bartonella-positive rodents were Yucatán deer mice from San José Pituch. Sequencing of a fragment of the gltA gene showed that all but one rodent isolates were closest to B. vinsonii subsp. vinsonii and one isolate was intermediate between B. vinsonii subsp. berkhoffii and B. vinsonii subsp. arupensis. Further analysis of concatenated housekeeping genes (gltA, ftsZ, rpoB, and 16S rRNA) suggests that this outlier isolate is a new subspecies within the B. vinsonii genogroup, for which we proposed the name B. vinsonii subsp. yucatanensis.

Ecología poblacional de Heteromys pictus (Rodentia: Heteromyidae), en un bosque tropical caducifolio con perturbación humana en la costa de Oaxaca, México.

Spiny pocket mice Liomys and Heteromys are forest-dwelling granivorous rodents distributed in seasonally dry forest or thorn scrub along the Pacific lowlands or xeric regions in the Mexican Plateau. We analyzed the population dynamics of the spiny pocket mouse Heteromys pictus, in the coast of Oaxaca, Mexico, in two sites of tropical deciduous forest with different degrees of disturbance: ZPP = less disturbed site, and ZMP = more disturbed site. Two plots were established in each area with 66 trap stations; we used the capture-recapture method and trapping for 12 periods for one year. Population density was estimated using the method of Minimum Number of Individuals Known Alive (MNKA). We captured 706 individuals, 290 for the ZPP and 416 for the ZMP. The population density ranged from 28 to 142 ind./ha for both zones, but it was higher for the ZMP (54 against 142 ind./ha). The population density for both areas increased during the rainy season and coincided with the increased recruitment of adults. Reproductive activity occurred throughout the study period in both areas, but it was higher for the ZMP. The sex ratio in the ZPP was 1:1 while in the ZMP was 1:0.75. In the ZMP we found a higher population density and reproductive activity in females, compared to the ZPP. These results suggest that H. pictus prefers the ZMP, indicating that thespeciesisnot significantly affected by human disturbance in the studied location.

Fleas, Lice, and Epifaunistic Pseudoscorpions of Some Native Mammals in Northwestern Costa Rica

ABSTRACT: Two species of chewing lice (Eutrichophilus mexicanus and Neotrichodectes mephiditis), 4 species of sucking lice (Fahrenholzia fairchildi, Fahrenholzia ferrisi, Fahrenholzia n. sp., and Hoplopleura mendezi), 4 species of fleas (Kohlsia traubi, Polygenis roberti beebei, Rhopalopsyllus australis australis, and Rhopalopsyllus lugubris), and 1 species of epifaunistic pseudoscorpion (Epichernes guanacastensis) were recorded from native mammals in the Area de Conservacion Guanacaste in northwestern Costa Rica during a parasite All Taxa Biodiversity Inventory from 1996 to 2004. All 6 species of lice were host specific. Fleas were less host specific and included a record of a rodent flea (R. a. australis) from a jaguar, Panthera onca. Epifaunistic pseudoscorpions were recorded only from Salvin’s spiny pocket mouse, Liomys salvini, on which they appear to be mutualistic with the host by preying on ectoparasites in the host pelage. Eutrichophilus mexicanis, N. mephiditis, F. ferrisi, H. mendezi, K. traub...

SpThin: an R package for spatial thinning of species occurrence records for use in ecological niche models

Spatial thinning of species occurrence records can help address problems associated with spatial sampling biases. Ideally, thinning removes the fewest records necessary to substantially reduce the effects of sampling bias, while simultaneously retaining the greatest amount of useful information. Spatial thinning can be done manually; however, this is prohibitively time consuming for large datasets. Using a randomization approach, the ‘thin’ function in the spThin R package returns a dataset with the maximum number of records for a given thinning distance, when run for sufficient iterations. We here provide a worked example for the Caribbean spiny pocket mouse, where the results obtained match those of manual thinning.

The endemic insular and peninsular species Chaetodipus spinatus (Mammalia, Heteromyidae) breaks patterns for Baja California.

The Baja California peninsula is the second longest, most geographically isolated peninsula on Earth. Its physiography and the presence of many surrounding islands has facilitated studies of the underlying patterns and drivers of genetic structuring for a wide spectrum of organisms. Chaetodipus spinatus is endemic to the region and occurs on 12 associated islands, including 10 in the Gulf of California and two in the Pacific Ocean. This distribution makes it a model species for evaluating natural historical barriers. We test hypotheses associated with the relationship between the range of the species, patterns in other species, and its relationship to Pleistocene-Holocene climatic changes. We analyzed sequence data from mtDNA genes encoding cytochrome b (Cytb) and cytochrome c oxidase subunits I (COI) and III (COIII) in 26 populations including all 12 islands. The matrilineal genealogy, statistical parsimony network and Bayesian skyline plot indicated an origin of C. spinatus in the southern part of the peninsula. Our analyses detected several differences from the common pattern of peninsular animals: no mid-peninsula break exists, Isla Carmen hosts the most divergent population, the population on an ancient southern Midriff island does not differ from peninsular populations, and a mtDNA peninsular discordance occurs near Loreto.

Influence of kangaroo rat burrows in the spatial organization of the San Jose Island rodent community

Knowledge of the spatial distribution of rodents around kangaroo rat burrows may help us to understand the role that kangaroo rats play in the spatial organization of small desert rodent communities. In this study we analyzed the pattern of proximity between capture locations of desert rodents and burrows of Dipodomys merriami insularis, and describe the reproductive characteristics of these rodents. Captures and recaptures of individuals were carried out in an area of 79.8 ha on Isla San José in the Gulf of California, Mexico, during March to May and October to November of 2008. In order of decreasing frequency, Chaetodipus spinatus bryanti, D. m. insularis, Peromyscus fraterculus cinereus, and Neotoma bryanti bryanti were captured during both periods. The results provide evidence that the spatial distribution of these rodents around D. m. insularis burrows varies with sex and reproductive activity of the kangaroo rats. They suggest that female and male kangaroo rats have a different influence on the spatial organization of the rodent community on Isla San José. Furthermore, this study provides information that should improve our understanding of the island rodent community, and hence should help to improve conservation management of this endangered population of kangaroo rats.

Association between Small Rodents and Forest Patch and Landscape Structure in the Fragmented Lacandona Rainforest, Mexico

Identifying the main factors that shape biological communities in human-modified tropical landscapes has key ecological and conservation implications. In these emerging landscapes, the maintenance of biodiversity may depend on both forest patch and landscape attributes, but this topic has been poorly investigated. Here we assessed the landscape (forest cover, degree of fragmentation, and matrix composition) and patch metrics (tree basal area, patch size, and isolation) that best predicted the abundance and diversity of small terrestrial rodents in the Lacandona rainforest, Mexico. In 2011 and 2012, we sampled rodent communities in 12 sites (9 patches and 3 areas within a continuous forest). We assessed the landscape characteristics within a 100-ha buffer from the center of each site. In total, we captured 78 individuals in 2011 and 82 individuals in 2012 from four species: Desmarest's Spiny Pocket Mouse ( Heteromys desmarestianus), Rice Rat ( Oryzomys sp.), Mexican Deermouse ( Peromyscus mexicanus), and Toltec Cotton Rat ( Sigmodon toltecus). Only the abundance of rodents was strongly associated with forest patch and landscape attributes, but the best predictors differed between years. The degree of fragmentation, matrix composition, and patch isolation showed the lowest impact on rodents, probably because the region is dominated by a highly heterogeneous anthropogenic matrix. Community composition was weakly related to patch and landscape attributes in both years. Overall, our findings suggest that almost a half-century of land use in the region has not led to significant changes at the community level, but additional long-term studies including arboreal species are needed before a strong conclusion can be drawn.

The effect of spatially marginal localities in modelling species niches and distributions

AbstractAimWe introduce and evaluate the potential effect of spatially marginal localities (specifically those protruding into unsuitable regions), in overestimating species niches and distributions when using ecological niche models (ENMs).LocationNorth‐western South America.MethodsWe built anENMfor the Caribbean spiny pocket mouse (Heteromys anomalus) usingMaxEntand climatic variables. This species typically inhabits extensive tropical forests but can also range into drier habitats through patches of mesic vegetation. We ranked occurrence records according to the suitability value they received, and retrieved habitat information from collectors' field notes and the literature to determine whether those receiving lower values correspond to spatially marginal localities protruding into unsuitable regions. We then built a model excluding a subset of such localities and compared its geographic and environmental prediction with that of the original model.ResultsModels differed substantially in their estimates of suitability. The original model resulted in an overly extensive prediction, considering as suitable hot and dry regions dominated by xerophytic vegetation. Records receiving the lowest suitability values in this model corresponded mainly to captures in patches of mesic forest surrounded by thorn scrub or savannas. The model calibrated without such records restricted suitability mostly to regions characterized by the typical habitat of the species.Main conclusionsWhen it is not possible to use variables that are more proximal or have finer resolutions, we recommend building complementary models that, together, can provide a more realistic estimate of the species' niche and corresponding geographic distribution. Jointly interpreting these models, researchers may better differentiate between areas harbouring typical habitat and those where the species can be found only if locally favourable conditions exist. Such a distinction is of relevance for a wide range of applications relying on inferences obtained fromENMs.

Albinismo platinado en Liomys pictus (Mammalia: Heteromyidae)

Albinism is a genetic abnormality, it can manifest as hypopigmentation or absence of color in skin, fur and eyes. The survival rate of wild animals with albinism is usually low. This paper reports the record of a platinum albino female of painted spiny pocket mouse Liomys pictus from Guerrero state, Mexico. Keywords: Albinism, oak forest, pigmentation, Rodentia, small mammals

Making better Maxent models of species distributions: complexity, overfitting and evaluation

AbstractAimModels of species niches and distributions have become invaluable to biogeographers over the past decade, yet several outstanding methodological issues remain. Here we address three critical ones: selecting appropriate evaluation data, detecting overfitting, and tuning program settings to approximate optimal model complexity. We integrate solutions to these issues for Maxent models, using the Caribbean spiny pocket mouse, Heteromys anomalus, as an example.LocationNorth‐western South America.MethodsWe partitioned data into calibration and evaluation datasets via three variations of k‐fold cross‐validation: randomly partitioned, geographically structured and masked geographically structured (which restricts background data to regions corresponding to calibration localities). Then, we carried out tuning experiments by varying the level of regularization, which controls model complexity. Finally, we gauged performance by quantifying discriminatory ability and overfitting, as well as via visual inspections of maps of the predictions in geography.ResultsPerformance varied among data‐partitioning approaches and among regularization multipliers. The randomly partitioned approach inflated estimates of model performance and the geographically structured approach showed high overfitting. In contrast, the masked geographically structured approach allowed selection of high‐performing models based on all criteria. Discriminatory ability showed a slight peak in performance around the default regularization multiplier. However, regularization levels two to four times higher than the default yielded substantially lower overfitting. Visual inspection of maps of model predictions coincided with the quantitative evaluations.Main conclusionsSpecies‐specific tuning of model parameters can improve the performance of Maxent models. Further, accurate estimates of model performance and overfitting depend on using independent evaluation data. These strategies for model evaluation may be useful for other modelling methods as well.

Food Habits of Ocelots and Potential for Competition With Bobcats In Southern Texas

Recovery efforts for the endangered ocelot (Leopardus pardalis) would be aided by knowledge of its feeding ecology in the affected region. We analyzed scat of ocelots and bobcats (Lynx rufus) from southern Texas. As has been found for most other populations of ocelots, rodents were the primary prey, but the principal species of rodent, the Mexican spiny pocket mouse (Liomys irroratus), is smaller than the principal prey reported for other populations of ocelots. Lagomorphs were more common prey than has been reported in other studies of ocelots, and birds more common prey than in all but one previous study. The diet of bobcats appeared similar overall to the diet of ocelots, but lagomorphs occurred in a significantly higher proportion of scats from bobcats. The data suggest that bobcats also preyed more heavily on the largest rodents and less on the medium-sized rodents than ocelots did. There was no clear division by type of habitat; both felids preyed approximately equally on species that are found primarily in grassland and those that are found in thornscrub. Near the United States-Mexico border, where the ranges of these felids overlap, there is the potential for substantial competition for resources between the two species. An important component of efforts to restore the population of ocelots in this region, therefore, will be a thorough investigation of this possibility. Studies of the dietary differences when both or only one of the felid species is present in an area, use of foraging habitat by both species, and the relationship between densities of prey and felids would allow the likelihood of negative impacts of competition to be fully evaluated.