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"Chipmunks."
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To model or not to model
Occupancy models are commonly used with motion-sensitive camera data to estimate patterns of species occurrence while accounting for false negative detection error (i.e., the species is present but not detected). False positive detection error (i.e., the species is not present but is detected) is present in camera data sets, especially when morphologically similar species co-occur. Researchers use different approaches to address this problem: ignore the potential for false positive detections, remove all ambiguous detections and treat them as non-detections, or model false positive detection error by dividing detections into ambiguous detections (could be true or false positives) and unambiguous detections (true positives). We performed a simulation study to compare these 3 strategies. To implement these modeling strategies, detections must be classified as ambiguous or unambiguous, or all ambiguous detections must be re-classified as non-detections. We also performed a simulation study to assess the impact of researcher confidence in the designation of ambiguous and unambiguous detections. Ignoring false positive detection error resulted in biased parameter estimates, whereas removing ambiguous detections and modeling false positive detections resulted in similar estimates of occupancy probability (ψ) in most situations. Researcher over-confidence (i.e., the tendency for observers to overestimate their own ability) positively biased estimates of ψ. Moderate under-confidence did not increase bias or decrease precision in estimates of ψ. Consistent with the patterns observed in simulations, analysis of example data from a chipmunk (Neotamias minimus atristriatus) population in the Sacramento Mountains of south-central New Mexico during 2019 indicated that removing ambiguous detections and modeling false positives resulted in similar estimates of ψ and that over-confidence biased estimates of ψ. Our results expand on previous literature, suggesting that removing ambiguous detections provides similar estimates of occupancy compared to modeling false positives in many scenarios, and emphasizing the importance of the designation of ambiguous and unambiguous detections. We provide guidance on simple methods to define ambiguous and unambiguous detections, thus mitigating the chances for erroneous inferences.
Journal Article
Chipmunks
\"Developed by literacy experts for students in kindergarten through grade three, this book introduces chipmunks to young readers through leveled text and related photos\"--Provided by publisher.
Book
No evidence for phylosymbiosis in western chipmunk species
ABSTRACT
Phylosymbiosis refers to a congruent pattern between the similarity of microbiomes of different species and the branching pattern of the host phylogeny. Phylosymbiosis has been detected in a variety of vertebrate and invertebrate hosts, but has only been assessed in geographically isolated populations. We tested for phylosymbiosis in eight (sub)species of western chipmunks with overlapping ranges and ecological niches; we used a nuclear (Acrosin) and a mitochondrial (CYTB) phylogenetic marker because there are many instances of mitochondrial introgression in chipmunks. We predicted that similarity among microbiomes increases with: (1) increasing host mitochondrial relatedness, (2) increasing host nuclear genome relatedness and (3) decreasing geographic distance among hosts. We did not find statistical evidence supporting phylosymbiosis in western chipmunks. Furthermore, in contrast to studies of other mammalian microbiomes, similarity of chipmunk microbiomes is not predominantly determined by host species. Sampling site explained most variation in microbiome composition, indicating an important role of local environment in shaping microbiomes. Fecal microbiomes of chipmunks were dominated by Bacteroidetes (72.2%), followed by Firmicutes (24.5%), which is one of the highest abundances of Bacteroidetes detected in wild mammals. Future work will need to elucidate the effects of habitat, ecology and host genomics on chipmunk microbiomes.
Gut microbiomes of western chipmunks species did not show the same pattern as would be expected based on their species phylogeny
Journal Article
Chipmunks
\"Carefully leveled text and vibrant photographs explore the world of a chipmunk as it searches for food in preparation of winter. Includes picture glossary and index.\"-- Provided by publisher.
Book
Linking camera‐trap data to taxonomy: Identifying photographs of morphologically similar chipmunks
Remote cameras are a common method for surveying wildlife and recently have been promoted for implementing large‐scale regional biodiversity monitoring programs. The use of camera‐trap data depends on the correct identification of animals captured in the photographs, yet misidentification rates can be high, especially when morphologically similar species co‐occur, and this can lead to faulty inferences and hinder conservation efforts. Correct identification is dependent on diagnosable taxonomic characters, photograph quality, and the experience and training of the observer. However, keys rooted in taxonomy are rarely used for the identification of camera‐trap images and error rates are rarely assessed, even when morphologically similar species are present in the study area. We tested a method for ensuring high identification accuracy using two sympatric and morphologically similar chipmunk (Neotamias) species as a case study. We hypothesized that the identification accuracy would improve with use of the identification key and with observer training, resulting in higher levels of observer confidence and higher levels of agreement among observers. We developed an identification key and tested identification accuracy based on photographs of verified museum specimens. Our results supported predictions for each of these hypotheses. In addition, we validated the method in the field by comparing remote‐camera data with live‐trapping data. We recommend use of these methods to evaluate error rates and to exclude ambiguous records in camera‐trap datasets. We urge that ensuring correct and scientifically defensible species identifications is incumbent on researchers and should be incorporated into the camera‐trap workflow. Misidentification of animals in camera‐trap data can be high even among experts, compromising its utility. We tested a method for ensuring high identification accuracy using two sympatric and morphologically similar chipmunk (Neotamias) species as a case study. We recommend use of these methods to evaluate error rates and to remove ambiguous records in camera‐trap datasets, and we urge that ensuring correct and scientifically defensible species identifications is incumbent on researchers and should be incorporated into the camera‐trap workflow.
Journal Article
Directional selection effects on patterns of phenotypic (co)variation in wild populations
Phenotypic (co)variation is a prerequisite for evolutionary change, and understanding how (co)variation evolves is of crucial importance to the biological sciences. Theoretical models predict that under directional selection, phenotypic (co)variation should evolve in step with the underlying adaptive landscape, increasing the degree of correlation among co-selected traits as well as the amount of genetic variance in the direction of selection. Whether either of these outcomes occurs in natural populations is an open question and thus an important gap in evolutionary theory. Here, we documented changes in the phenotypic (co)variation structure in two separate natural populations in each of two chipmunk species (Tamias alpinus and T. speciosus) undergoing directional selection. In populations where selection was strongest (those of T. alpinus), we observed changes, at least for one population, in phenotypic (co)variation that matched theoretical expectations, namely an increase of both phenotypic integration and (co)variance in the direction of selection and a re-alignment of the major axis of variation with the selection gradient.
Journal Article
Molecular characterization and new genotypes of Enterocytozoon bieneusi in pet chipmunks (Eutamias asiaticus) in Sichuan province, China
Background
Enterocytozoon bieneusi
, the most commonly identified microsporidian species in humans, is also identified in livestock, birds, rodents, reptiles, companion animals, even wastewater. However, there is no information available on occurrence of
E. bieneusi
in pet chipmunks. The aim of the present study was to determine the genotypes, molecular characterization of
E. bieneusi
in pet chipmunks, and assess the zoonotic potential.
Results
A total of 279 fecal specimens were collected from chipmunks from seven pet shops and one breeding facility in Sichuan province, China. The prevalence for
E. bieneusi
was 17.6% (49/279) based on nested PCR targeting the internal transcribed spacer (
ITS
) region
.
The prevalence of
E. bieneusi
in chipmunks < 90 days of age was significantly higher than that in older chipmunks; however, differences among different sources and between genders were not significant. Eight genotypes of
E. bieneusi
were identified, including four known genotypes (D, Nig7, CHG9, and CHY1) and four novel genotypes (SCC-1 to 4). Phylogenetic analysis classified these genotypes into four distinct groups as follows: genotypes D and CHG9 clustered into group 1 of zoonotic potential; genotypes Nig7 and CHY1 clustered into group 6 and a new group, respectively; the four novel genotypes (SCC-1 to 4) formed a separate group named group 10.
Conclusions
To the best of our knowledge, this is the first study reporting the prevalence and genotypes of
E. bieneusi
in pet chipmunks in China. Genotypes D and Nig7, found in chipmunks in this study, have also been previously identified in humans, which suggests that chipmunks might play a role in the transmission of this pathogen to humans.
Journal Article