Detecting the effects of environmental change on Alaska's small mammal fauna using machine-learning-based geographic and isotopic niche modeling

Thesis (Ph.D.) University of Alaska Fairbanks, 2015As anthropogenic climate change continues to alter biomes, ecosystems, and wildlife communities, determining how the niche spaces of species will respond is vital for determining appropriate conservation policy that promotes biodiversity and species persistence. In Alaska, quantifications of dietary patterns and geographic distributions of small mammals (rodents and shrews) are incomplete. As a result, wildlife managers are often ill-equipped to adequately account for these ecologically important taxa. I used stable isotopes, open-access occurrence records, and machine learning methods to model the dietary and geographic niche spaces of 17 species of small mammals in mainland Alaska. I also calculated the degree of niche overlap among species to estimate potential competition among conspecifics for both food and space. Using `bio-blitz' sampling along two statewide megatransects, I documented small mammal species richness and collected stable isotope samples at 20 locations across Alaska. Stable isotope (δ¹⁵N and δ¹³C) mixing models were used to define proportions of fungi, herbaceous plants, woody plants, lichens, and mosses in the diets of each species and to outline their fundamental and realized foraging niches. I created spatial distribution models for each species for the years 2010 and 2100 by applying machine learning methods to 4,408 unique occurrence records attributed with 27 and 33 environmental predictor variables, respectively. Spatial relationships between co-occurring species helped to determine the dominant structure of small mammal community assemblages for both time periods. Land change analyses identified regions of species loss, persistence, or gain over time. Stable isotopes (δ¹⁵N and δ¹³C) of shrews, rodents, fungi, and herbaceous plants were also modeled spatially to create continuous baseline isoscape predictions for Alaska. Dietary niche models showed a high degree of fundamental niche overlap among species at the statewide scale, whereas realized niches were more segregated at the study area scale. This suggests that species may be plastic in their use of shared resources in order to avoid competition. Isoscape models highlighted mid-elevations in the Yukon-Tanana Uplands, Brooks Range foothills, and the Yukon-Kuskokwim Delta as isotopic `hot-spots.' Isotope values were considerably higher than trophic baselines in these regions, indicating where small mammals may have been consuming more fungi than herbaceous plants. On average, 2010 distribution models accurately predicted the occurrence of species in the field 75% of the time, and a composite species richness model highlighted biodiversity hotspots (11-13 species) across the Yukon-Tanana Uplands and western Brooks Range. Community assemblage analysis for 2010 parsed species into 5 main community groups: northern, cold-climate, interior, continental, and southern, but membership to these communities was predicted to remain largely unchanged by 2100. Individual distributions, however, were predicted to change dramatically by 2100 as members of the northern, cold-climate, and interior communities shifted northward, inland, and upward in elevation following moving climate envelopes. Regions such as southwest Alaska and the Seward Peninsula experienced projected declines in species richness, while the number of species inhabiting the western Brooks Range and Alaska Range were predicted to increase. Results indicated that while species assemblages were robust in their organization over time, evidence of dietary niche plasticity suggests that communities may remain amenable to the addition of new species as shifting distributions overlap in new and unexpected patterns. Mid-elevations in topographically diverse regions such as the Brooks Range, Alaska Range, and the Yukon-Tanana Uplands will likely be centers for increased species richness and contact zones for novel species interactions in the future. These models, intended for public use, describe baseline conditions and future projections of small mammal niche ecology, with far-reaching implications for terrestrial trophic systems. I recommend that wildlife conservation and management decisions consider these models as we seek to describe and conserve biodiversity and the persistence of small mammal species across Alaska in a future altered by climate change

Observations on pulpal response to carbon dioxide laser drilling of dentine in healthy human third molars

Preservation of pulpal health is the primary prerequisite for successful application of laser systems in the hard tissue management of vital teeth. The purpose of this study was to investigate the short and long-term pulpal effects to cavity preparations in healthy human teeth using carbon dioxide (CO2) laser. A total of seven, healthy, third molars that were scheduled to be removed due to space problems were used. After the laser drilling, the occlusal cavities were closed temporarily, and the teeth were extracted 7days (n=5) and 3 months (n=2) after the operation. The specimens were fixed, decalcified, subdivided and processed for light and transmission electron microscopy. Seven days postoperatively all the five teeth that had been irradiated with the CO2 laser did not reveal any pathological changes in the pulpo-dentine complex. Three months postoperatively the two teeth that were prepared with the laser showed subtle but distinct apposition of tertiary dentine that was lined with intact odontoblasts. One of the specimens at 3 months revealed the presence of a mild, but very circumscribed, pulpal infiltration of chronic inflammatory cells subjacent to the cavity preparation. The latter is unlikely to be due to a direct effect of the laser irradiation but a possible consequence of microleakage of oral antigens and/or other tissue-irritating molecules through the temporary restoration and the remaining dentine thickness (RDT). Although these preliminary histological results suggest that the CO2 laser under investigation induced only minimal response of the dentine-pulp complex when used as a hard-tissue drilling tool, with specific energy settings, pulse duration within thermal relaxation time and emitting radiations at 9.6μm of wavelength, larger clinical trials involving various types of teeth are necessary to reach definite conclusions for large-scale clinical application of the laser devic

Polar phonons and spin-phonon coupling in HgCr2S4 and CdCr2S4

Polar phonons of HgCr2S4 and CdCr2S4 are studied by far-infrared spectroscopy as a function of temperature and external magnetic field. Eigenfrequencies, damping constants, effective plasma frequencies and Lyddane-Sachs-Teller relations, and effective charges are determined. Ferromagnetic CdCr2S4 and antiferromagnetic HgCr2S4 behave rather similar. Both compounds are dominated by ferromagnetic exchange and although HgCr2S4 is an antiferromagnet, no phonon splitting can be observed at the magnetic phase transition. Temperature and magnetic field dependence of the eigenfrequencies show no anomalies indicating displacive polar soft mode behavior. However, significant effects are detected in the temperature dependence of the plasma frequencies indicating changes in the nature of the bonds and significant charge transfer. In HgCr2S4 we provide experimental evidence that the magnetic field dependence of specific polar modes reveal shifts exactly correlated with the magnetization showing significant magneto-dielectric effects even at infrared frequencies.Comment: 8 pages, 8 figure

Identifying Winter Forage Triticale (×\u3ci\u3eTriticosecale\u3c/i\u3e Wittmack) Strains for the Central Great Plains

Triticale (×Triticosecale Wittmack) is mainly used as a forage crop in the central Great Plains. A successful triticale cultivar should have high forage yield with good quality, and also high grain yield so the seed can be economically produced. The purpose of this study was to evaluate existing triticale cultivars and experimental strains for their relative value in the central Great Plains as an annual hay crop primarily for feeding to beef cattle. Two experiments (one for forage yield and one for grain yield) were planted at two locations (one representing the arid Great Plains and the second representing the or higher rainfall central Great Plains) for 2 yr. Twenty-nine triticale cultivars and strains were evaluated for forage yield and quality, and grain yield. In both experiments, year effects were significant (P \u3c 0.05) for all traits except grain yield; location effects were significant for forage yield, neutral detergent fiber (NDF), and acid detergent fiber. There was no location × strain or year × location × strain interaction for all the quality traits indicating that triticale forage quality was stable across environments. Triticale strains differed significantly for forage yield, grain yield, NDF, acid detergent lignin, and relative feed value. However, forage of all strains had good feed quality. Three strains had high grain and forage yield, and very good relative feed value suggesting that triticale improvement for both grain and forage traits is possible

Spin-driven Phonon Splitting in Bond-frustrated ZnCr2S4

Utilizing magnetic susceptibility, specific heat, thermal expansion and IR spectroscopy we provide experimental evidence that the two subsequent antiferromagnetic transitions in ZnCr_2S_4 at T_N1 = 15 K and T_N2= 8 K are accompanied by significant thermal and phonon anomalies. The anomaly at T_N2 reveals a strong temperature hysteresis typical for a first-order transformation. Due to strong spin-phonon coupling both magnetic phase transitions induce a splitting of phonon modes, where at T_N1 the high-frequency and at T_N2 the low-frequency modes split. The anomalies and phonon splitting observed at T_N2 are strongly suppressed by magnetic field. Regarding the small positive Curie-Weiss temperature Theta= 8 K, we argue that this scenario of two different magnetic phases with concomitant different magneto-elastic couplings results from the strong competition of ferromagnetic and antiferromagnetic exchange of equal strength.Comment: 4 pages, 4 figure

Lattice dynamics and the electron-phonon interaction in Ca2_2RuO4_4

We present a Raman scattering study of Ca$_2$RuO$_4$, in which we investigate the temperature-dependence of the lattice dynamics and the electron-phonon interaction below the metal-insulator transition temperature ({\it T}$_{\rm MI}$). Raman spectra obtained in a backscattering geometry with light polarized in the ab-plane reveal 9 B$_{1g}$ phonon modes (140, 215, 265, 269, 292, 388, 459, 534, and 683 cm$^{-1}$) and 9 A$_g$ phonon modes (126, 192, 204, 251, 304, 322, 356, 395, and 607 cm$^{-1}$) for the orthorhombic crystal structure (Pbca$-$D$_{2h}^{15}$). With increasing temperature toward {\it T}$_{\rm MI}$, the observed phonon modes shift to lower energies and exhibit reduced spectral weights, reflecting structural changes associated with the elongation of the RuO$_6$ octahedra. Interestingly, the phonons exhibit significant increases in linewidths and asymmetries for {\it T} $>$ {\it T}$_{\rm N}$. These results indicate that there is an increase in the effective number of electrons and the electron-phonon interaction strengths as the temperature is raised through {\it T}$_{\rm N}$, suggesting the presence of orbital fluctuations in the temperature regime {\it T}$_{\rm N}$ $<$ {\it T} $<$ {\it T}$_{\rm MI}$.Comment: 6 pages, 4 figure

The Ice Selective Inlet: a novel technique for exclusive extraction of pristine ice crystals in mixed-phase clouds

Climate predictions are affected by high uncertainties partially due to an insufficient knowledge of aerosol-cloud interactions. One of the poorly understood processes is formation of mixed-phase clouds (MPCs) via heterogeneous ice nucleation. Field measurements of the atmospheric ice phase in MPCs are challenging due to the presence of supercooled liquid droplets. The Ice Selective Inlet (ISI), presented in this paper, is a novel inlet designed to selectively sample pristine ice crystals in mixed-phase clouds and extract the ice residual particles contained within the crystals for physical and chemical characterisation. Using a modular setup composed of a cyclone impactor, droplet evaporation unit and pumped counterflow virtual impactor (PCVI), the ISI segregates particles based on their inertia and phase, exclusively extracting small ice particles between 5 and 20 μm in diameter. The setup also includes optical particle spectrometers for analysis of the number size distribution and shape of the sampled hydrometeors. The novelty of the ISI is a droplet evaporation unit, which separates liquid droplets and ice crystals in the airborne state, thus avoiding physical impaction of the hydrometeors and limiting potential artifacts. The design and validation of the droplet evaporation unit is based on modelling studies of droplet evaporation rates and computational fluid dynamics simulations of gas and particle flows through the unit. Prior to deployment in the field, an inter-comparison of the WELAS optical particle size spectrometers and a characterisation of the transmission efficiency of the PCVI was conducted in the laboratory. The ISI was subsequently deployed during the Cloud and Aerosol Characterisation Experiment (CLACE) 2013 – an extensive international field campaign encompassing comprehensive measurements of cloud microphysics, as well as bulk aerosol, ice residual and ice nuclei properties. The campaign provided an important opportunity for a proof of concept of the inlet design. In this work we present the setup of the ISI, including the modelling and laboratory characterisation of its components, as well as a case study demonstrating the ISI performance in the field during CLACE 2013

Measured and predicted aerosol light scattering enhancement factors at the high alpine site Jungfraujoch

Ambient relative humidity (RH) determines the water content of atmospheric aerosol particles and thus has an important influence on the amount of visible light scattered by particles. The RH dependence of the particle light scattering coefficient (&amp;sigma;&lt;sub&gt;sp&lt;/sub&gt;) is therefore an important variable for climate forcing calculations. We used a humidification system for a nephelometer which allows for the measurement of &amp;sigma;&lt;sub&gt;sp&lt;/sub&gt; at a defined RH in the range of 20–95%. In this paper we present measurements of light scattering enhancement factors &lt;i&gt;f&lt;/i&gt;(RH)=&amp;sigma;&lt;sub&gt;sp&lt;/sub&gt;(RH)/&amp;sigma;&lt;sub&gt;sp&lt;/sub&gt;(dry) from a 1-month campaign (May 2008) at the high alpine site Jungfraujoch (3580 m a.s.l.), Switzerland. Measurements at the Jungfraujoch are representative for the lower free troposphere above Central Europe. For this aerosol type hardly any information about the &lt;i&gt;f&lt;/i&gt;(RH) is available so far. At this site, &lt;i&gt;f&lt;/i&gt;(RH=85%) varied between 1.2 and 3.3. Measured &lt;i&gt;f&lt;/i&gt;(RH) agreed well with &lt;i&gt;f&lt;/i&gt;(RH) calculated with Mie theory using measurements of the size distribution, chemical composition and hygroscopic diameter growth factors as input. Good &lt;i&gt;f&lt;/i&gt;(RH) predictions at RH&amp;lt;85% were also obtained with a simplified model, which uses the Ångström exponent of &amp;sigma;&lt;sub&gt;sp&lt;/sub&gt;(dry) as input. RH influences further intensive optical aerosol properties. The backscatter fraction decreased by about 30% from 0.128 to 0.089, and the single scattering albedo increased on average by 0.05 at 85% RH compared to dry conditions. These changes in &amp;sigma;&lt;sub&gt;sp&lt;/sub&gt;, backscatter fraction and single scattering albedo have a distinct impact on the radiative forcing of the Jungfraujoch aerosol

Existence of orbital polarons in ferromagnetic insulating La1−x_{1-x}Srx_xMnO3_{3} (0.11<x<<x<0.14) evidenced by giant phonon softening

We present an inelastic light scattering study of single crystalline (La$_{1-y}$Pr$_y$)$_{1-x}$Sr$_{x}$MnO$_3$ ($0\leq x\leq0.14$,$y=0$ and $x=1/8$,$0\leq y\leq0.5$). A giant softening up to 20 - 30 cm$^{-1}$ of the Mn-O breathing mode has been observed only for the ferromagnetic insulating (FMI) samples ($0.11\leq x \leq 0.14$) upon cooling below the Curie temperature. With increasing Pr-doping the giant softening is gradually suppressed. This is attributed to a coupling of the breathing mode to orbital polarons which are present in the FMI phase.Comment: 4 pages, 5 figure

Anomalous optical phonons in FeTe pnictides: spin state, magnetic order, and lattice anharmonicity

Polarized Raman-scattering spectra of non-superconducting, single-crystalline FeTe are investigated as function of temperature. We have found a relation between the magnitude of ordered magnetic moments and the linewidth of A1g phonons at low temperatures. This relation is attributed to the intermediate spin state (S=1) and the orbital degeneracy of the Fe ions. Spin-phonon coupling constants have been estimated based on microscopic modeling using density-functional theory and analysis of the local spin density. Our observations show the importance of orbital degrees of freedom for the Fe-based superconductors with large ordered magnetic moments, while small magnetic moment of Fe ions in some iron pnictides reflects the low spin state of Fe ions in those systems.Comment: 17 pages, 3 figure