DNA Fingerprinting Reveals Low Genetic Diversity in Gunnison\u27s Prairie Dog (Cynomys gunnisoni)

The use of molecular techniques for the assessment of familial relationships among social species of mammals has become relatively commonplace. However, some species represent poor candidates for such studies due to naturally low levels of genetic diversity, leading to unacceptably large standard errors associated with estimates of relatedness. Here, we report on a preliminary study of genetic diversity within two populations of a social species of ground squirrel, Gunnison\u27s prairie dog (Cynomys gunnisoni) using DNA fingerprinting. We observed low levels of diversity in the form of large mean coefficients of genetic similarity among individuals occupying the same population. Overall similarity, determined from the combined data, yielded by three minisatellte probes, ranged from 55 to 61%. These values place Gunnison\u27s prairie dog at the extreme upper end of the range of similarity values reported for outbred species of mammals (ca. 0.20-0.50). As a partial means of explaining these results, and as a means of comparing our results to those of similar studies using allozymes, we determined the level of differentiation between our two study colonies in the form of an F-statistic analog. A value of 0.11 (± 2.26 × 10−3) was obtained and is similar to values reported from allozyme studies (0.07–0.12). A significance test of this value yielded a positive result (D = 5.63, d.f. = 1, P \u3c 0.025), demonstrating that gene flow between populations is limited, a factor that may help to maintain low levels of diversity

DNA Fingerprinting Reveals Low Genetic Diversity in Gunnison\u27s Prairie Dog (Cynomys gunnisoni)

The use of molecular techniques for the assessment of familial relationships among social species of mammals has become relatively commonplace. However, some species represent poor candidates for such studies due to naturally low levels of genetic diversity, leading to unacceptably large standard errors associated with estimates of relatedness. Here, we report on a preliminary study of genetic diversity within two populations of a social species of ground squirrel, Gunnison\u27s prairie dog (Cynomys gunnisoni) using DNA fingerprinting. We observed low levels of diversity in the form of large mean coefficients of genetic similarity among individuals occupying the same population. Overall similarity, determined from the combined data, yielded by three minisatellte probes, ranged from 55 to 61%. These values place Gunnison\u27s prairie dog at the extreme upper end of the range of similarity values reported for outbred species of mammals (ca. 0.20-0.50). As a partial means of explaining these results, and as a means of comparing our results to those of similar studies using allozymes, we determined the level of differentiation between our two study colonies in the form of an F-statistic analog. A value of 0.11 (± 2.26 × 10−3) was obtained and is similar to values reported from allozyme studies (0.07–0.12). A significance test of this value yielded a positive result (D = 5.63, d.f. = 1, P \u3c 0.025), demonstrating that gene flow between populations is limited, a factor that may help to maintain low levels of diversity

Wildfire, climate, and perceptions in northeast Oregon

Wildfire poses a rising threat in the western USA, fueled by synergies between historical fire suppression, changing land use, insects and disease, and shifts toward a drier, warmer climate. The rugged landscapes of northeast Oregon, with their historically forest- and resource-based economies, have been one of the areas affected. A 2011 survey found area residents highly concerned about fire and insect threats, but not about climate change. In 2014 we conducted a second survey that, to explore this apparent disconnect, included questions about past and future summertime (fire season) temperatures. Although regional temperatures have warmed in recent decades at twice the global rate, accompanied by increasing dryness and fire risks, the warming itself is recognized by only 40 % of our respondents. Awareness of recent warming proves unrelated to individual characteristics that might indicate experience on the land: old-timer versus newcomer status, year-round versus seasonal residence, and ownership of forested land. Perceptions of past warming and expectations of future warming are more common among younger respondents and less common among Tea Party supporters. The best-educated partisans stand farthest apart. Perceptions about local temperatures that are important for adaptation planning thus follow ideological patterns similar to beliefs about global climate change

Multidimensional Data Visual Exploration by Interactive Information Segments

Visualization techniques provide an outstanding role in KDD process for data analysis and mining. However, one image does not always convey successfully the inherent information from high dimensionality, very large databases. In this paper we introduce VSIS (Visual Set of Information Segments), an interactive tool to visually explore multidimensional, very large, numerical data. Within the supervised learning, our proposal approaches the problem of classification by searching of meaningful intervals belonging to the most relevant attributes. These intervals are displayed as multi–colored bars in which the degree of impurity with respect to the class membership can be easily perceived. Such bars can be re–explored interactively with new values of user–defined parameters. A case study of applying VSIS to some UCI repository data sets shows the usefulness of our tool in supporting the exploration of multidimensional and very large data

Vertical profile of peroxyacetyl nitrate (PAN) from MIPAS-STR measurements over Brazil in February 2005 and its contribution to tropical UT NOy partitioning

We report on the retrieval of PAN (CH₃C(O)OONO₂) in the upper tropical troposphere from limb measurements by the remote-sensor MIPAS-STR on board the Russian high altitude research aircraft M55-Geophysica. The measurements were performed close to Araçatuba, Brazil, on 17 February 2005. The retrieval was made in the spectral range 775–820 cm^&minus;1 where PAN exhibits its strongest feature but also more than 10 species interfere. Especially trace gases such as CH₃CCl₃, CFC-113, CFC-11, and CFC-22, emitting also in spectrally broad not-resolved branches, make the processing of PAN prone to errors. Therefore, the selection of appropriate spectral windows, the separate retrieval of several interfering species and the careful handling of the water vapour profile are part of the study presented. <br><br> The retrieved profile of PAN has a maximum of about 0.14 ppbv at 10 km altitude, slightly larger than the lowest reported values (&lt;0.1 ppbv) and much lower than the highest reported in the literature (0.65 ppbv). Besides the NO_y constituents measured by MIPAS-STR (HNO₃, ClONO₂, HO₂NO₂, PAN), the in situ instruments aboard the Geophysica provide simultaneous measurements of NO, NO₂, and the sum NO_y. Comparing the sum of in-situ and remotely derived NO+NO₂+HNO₃+ClONO₂+HO₂NO₂+PAN with total NO_y a deficit of 30–40% (0.2–0.3 ppbv) in the troposphere remains unexplained whereas the values fit well in the stratosphere

Validation and data characteristics of methane and nitrous oxide profiles observed by MIPAS and processed with Version 4.61 algorithm

The ENVISAT validation programme for the atmospheric instruments MIPAS, SCIAMACHY and GOMOS is based on a number of balloon-borne, aircraft, satellite and ground-based correlative measurements. In particular the activities of validation scientists were coordinated by ESA within the ENVISAT Stratospheric Aircraft and Balloon Campaign or ESABC. As part of a series of similar papers on other species [this issue] and in parallel to the contribution of the individual validation teams, the present paper provides a synthesis of comparisons performed between MIPAS CH4 and N2O profiles produced by the current ESA operational software (Instrument Processing Facility version 4.61 or IPF v4.61, full resolution MIPAS data covering the period 9 July 2002 to 26 March 2004) and correlative measurements obtained from balloon and aircraft experiments as well as from satellite sensors or from ground-based instruments. In the middle stratosphere, no significant bias is observed between MIPAS and correlative measurements, and MIPAS is providing a very consistent and global picture of the distribution of CH4 and N2O in this region. In average, the MIPAS CH4 values show a small positive bias in the lower stratosphere of about 5%. A similar situation is observed for N2O with a positive bias of 4%. In the lower stratosphere/upper troposphere (UT/LS) the individual used MIPAS data version 4.61 still exhibits some unphysical oscillations in individual CH4 and N2O profiles caused by the processing algorithm (with almost no regularization). Taking these problems into account, the MIPAS CH4 and N2O profiles are behaving as expected from the internal error estimation of IPF v4.61 and the estimated errors of the correlative measurements

Partial clustering prevents global crystallization in a binary 2D colloidal glass former

A mixture of two types of super-paramagnetic colloidal particles with long range dipolar interaction is confined by gravity to a flat interface of a hanging water droplet. The particles are observed by video microscopy and the dipolar interaction strength is controlled via an external magnetic field. The system is a model system to study the glass transition in 2D, and it exhibits partial clustering of the small particles. This clustering is strongly dependent on the relative concentration $\xi$ of big and small particles. However, changing the interaction strength $\Gamma$ reveals that the clustering does not depend on the interaction strength. The partial clustering scenario is quantified using Minkowski functionals and partial structure factors. Evidence that partial clustering prevents global crystallization is discussed

Population Structure and Genetic Diversity among Isolates of Coccidioides posadasii in Venezuela and Surrounding Regions

Coccidioides posadasii is a pathogenic fungus that causes coccidioidomycosis in many arid regions of the Americas. One of these regions is bordered by the Caribbean Sea, and the surrounding landscape may play an important role in the dispersion of C. posadasii across South America through southeastern Mexico, Honduras, Guatemala, and Venezuela. Comparative phylogenomic analyses of C. posadasii reveal that clinical strains from Venezuela are genetically distinct from the North American populations found in (i) Arizona and (ii) Texas, Mexico, and the rest of South America (TX/MX/SA). We find evidence for admixture between the Venezuela and the North American populations of C. posadasii in Central America. Additionally, the proportion of Venezuelan alleles in the admixed population decreases as latitude (and distance from Venezuela) increases. Our results indicate that the population in Venezuela may have been subjected to a recent bottleneck and shows a strong population structure. This analysis provides insight into potential for Coccidioides spp. to invade new regions.IMPORTANCE Valley Fever is a fungal disease caused by two species of fungi: Coccidioides immitis and C. posadasii These fungi are found throughout the arid regions of North and South America; however, our understanding of genetic diversity and disease in South America is limited. In this report, we analyze 10 new genomes of Coccidioides posadasii from regions bordering the Caribbean Sea. We show that these populations are distinct and that isolates from Venezuela are likely a result of a recent bottleneck. These data point to patterns that might be observed when investigating recently established populations.NIH/NIAIDUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of Allergy & Infectious Diseases (NIAID) [R21AI28536]; NIH/NIGMSUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of General Medical Sciences (NIGMS) [R01GM121750]Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Historical Distribution and Molecular Diversity of Bacillus anthracis, Kazakhstan

This study provides useful baseline data for guiding future disease control programs