Matching Items (9)

The Agassiz’s desert tortoise genome provides a resource for the conservation of a threatened species

Description

Agassiz’s desert tortoise (Gopherus agassizii) is a long-lived species native to the Mojave Desert and is listed as threatened under the US Endangered Species Act. To aid conservation efforts for

Agassiz’s desert tortoise (Gopherus agassizii) is a long-lived species native to the Mojave Desert and is listed as threatened under the US Endangered Species Act. To aid conservation efforts for preserving the genetic diversity of this species, we generated a whole genome reference sequence with an annotation based on deep transcriptome sequences of adult skeletal muscle, lung, brain, and blood. The draft genome assembly for G. agassizii has a scaffold N50 length of 252 kbp and a total length of 2.4 Gbp. Genome annotation reveals 20,172 protein-coding genes in the G. agassizii assembly, and that gene structure is more similar to chicken than other turtles. We provide a series of comparative analyses demonstrating (1) that turtles are among the slowest-evolving genome-enabled reptiles, (2) amino acid changes in genes controlling desert tortoise traits such as shell development, longevity and osmoregulation, and (3) fixed variants across the Gopherus species complex in genes related to desert adaptations, including circadian rhythm and innate immune response. This G. agassizii genome reference and annotation is the first such resource for any tortoise, and will serve as a foundation for future analysis of the genetic basis of adaptations to the desert environment, allow for investigation into genomic factors affecting tortoise health, disease and longevity, and serve as a valuable resource for additional studies in this species complex.

Data Availability: All genomic and transcriptomic sequence files are available from the NIH-NCBI BioProject database (accession numbers PRJNA352725, PRJNA352726, and PRJNA281763). All genome assembly, transcriptome assembly, predicted protein, transcript, genome annotation, repeatmasker, phylogenetic trees, .vcf and GO enrichment files are available on Harvard Dataverse (doi:10.7910/DVN/EH2S9K).

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Agent

Created

Date Created
  • 2017-05-31

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New Sonoran: A Graphic Novel

Description

In the event of a climate disaster, everything changes, but the places we’ve romanticized as a frontier will become new to us once again. New Sonoran is, in essence, an

In the event of a climate disaster, everything changes, but the places we’ve romanticized as a frontier will become new to us once again. New Sonoran is, in essence, an American story on a global problem. It draws on American pioneer/Old West/cowboy culture, the lasting effects of climate change denial, and the individualism that pervades American culture. I want to use this project to underscore the actual isolation of individualism, as well as create a new story that speaks to a problematic but evocative cultural history while accessing an uncertain future. For this project, I drew from a varied palette of media: comics, video games, and the pervasive cultural malaise that surrounds my current generation.
The work is based in anxieties, but its media influences are a strong indicator of tone and concept. At the very least, they helped me articulate why I wanted to work on a graphic novel on a post-climate change Sonoran. This desert that I’ve grown used to will change irrevocably, but it will be a new frontier to explore while the old will become a loss to mourn. This cycle of change is something I want to highlight in my work: we can worry, mourn, and fear, but there’s going to be something new.
New Sonoran is a graphic novel based upon the journey of Sage, a cartographer and anthropologist who travels the desert, annotating maps and studying a desert irrevocably affected by global climate change. As she catalogues the changes and losses in this new landscape, she learns how residents have adapted, and how people may still relate to the land.

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Agent

Created

Date Created
  • 2020-05

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Urban Forestry as a Carbon Offset Method at ASU West Campus

Description

As part of Arizona State University’s net-zero carbon initiative, 1000 mesquite trees were planted on a vacant plot of land at West Campus to sequester carbon from the atmosphere. Urban

As part of Arizona State University’s net-zero carbon initiative, 1000 mesquite trees were planted on a vacant plot of land at West Campus to sequester carbon from the atmosphere. Urban forestry is typically a method of carbon capture in temperate areas, but it is hypothesized that the same principle can be employed in arid regions as well. To test this hypothesis a carbon model was constructed using the pools and fluxes measured at the Carbon sink and learning forest at West Campus. As an ideal, another carbon model was constructed for the mature mesquite forest at the Hassayampa River Preserve to project how the carbon cycle at West Campus could change over time as the forest matures. The results indicate that the West Campus plot currently functions as a carbon source while the site at the Hassayampa river preserve currently functions as a carbon sink. Soil composition at both sites differ with inorganic carbon contributing to the largest percentage at West Campus, and organic carbon at Hassayampa. Predictive modeling using biomass accumulation estimates and photosynthesis rates for the Carbon Sink Forest at West Campus both predict approximately 290 metric tons of carbon sequestration after 30 years. Modeling net ecosystem exchange predicts that the West Campus plot will begin to act as a carbon sink after 33 years.

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Agent

Created

Date Created
  • 2021-05

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Examining sound and urban-desert differences in the acoustic properties of Northern Mockingbird (Mimus polyglottus) calls as it relates to species survival

Description

Human activity produces ambient noise that potentially alters species’ abilities to communicate with each other—among other impacts. Given that birds are known to be sensitive to structural changes in

Human activity produces ambient noise that potentially alters species’ abilities to communicate with each other—among other impacts. Given that birds are known to be sensitive to structural changes in habitat and highly communicative through sound, it is beneficial to understand how changing acoustic ecologies and ambient noise impact birds’ ability to communicate in their respective environments. In this study, mockingbird calls from an urban, desert, and intermediate study site were recorded and analyzed for differences in acoustic properties. Acoustic properties such as frequency and amplitude differed significantly across sites as it was determined that mockingbirds in urban areas increase both the peak frequency and amplitude of their calls in order to communicate. This study identifies what these changes in acoustic properties mean in relation to the survival and conservation of birds and concludes with recommendations for novel research.

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Agent

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Date Created
  • 2019-05

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Soil moisture availability and energetic controls on belowground network complexity and function in arid ecosystems

Description

The explicit role of soil organisms in shaping soil health, rates of pedogenesis, and resistance to erosion has only just recently begun to be explored in the last century. However,

The explicit role of soil organisms in shaping soil health, rates of pedogenesis, and resistance to erosion has only just recently begun to be explored in the last century. However, much of the research regarding soil biota and soil processes is centered on maintaining soil fertility (e.g., plant nutrient availability) and soil structure in mesic- and agro- ecosystems. Despite the empirical and theoretical strides made in soil ecology over the last few decades, questions regarding ecosystem function and soil processes remain, especially for arid areas. Arid areas have unique ecosystem biogeochemistry, decomposition processes, and soil microbial responses to moisture inputs that deviate from predictions derived using data generated in more mesic systems. For example, current paradigm predicts that soil microbes will respond positively to increasing moisture inputs in a water-limited environment, yet data collected in arid regions are not congruent with this hypothesis. The influence of abiotic factors on litter decomposition rates (e.g., photodegradation), litter quality and availability, soil moisture pulse size, and resulting feedbacks on detrital food web structure must be explicitly considered for advancing our understanding of arid land ecology. However, empirical data coupling arid belowground food webs and ecosystem processes are lacking. My dissertation explores the resource controls (soil organic matter and soil moisture) on food web network structure, size, and presence/absence of expected belowground trophic groups across a variety of sites in Arizona.

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Agent

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Date Created
  • 2014

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Advancing sustainable urbanism through civic space planning & design

Description

The lack of substantive, multi-dimensional perspectives on civic space planning and design has undermined the potential role of these valuable social and ecological amenities in advancing urban sustainability goals. Responding

The lack of substantive, multi-dimensional perspectives on civic space planning and design has undermined the potential role of these valuable social and ecological amenities in advancing urban sustainability goals. Responding to these deficiencies, this dissertation utilized mixed quantitative and qualitative methods and synthesized multiple social and natural science perspectives to inform the development of progressive civic space planning and design, theory, and public policy aimed at improving the social, economic, and environmental health of cities. Using Phoenix, Arizona as a case study, the analysis was tailored to arid cities, yet the products and findings are flexible enough to be geographically customized to the social, environmental, built, and public policy goals of other urbanized regions. Organized into three articles, the first paper applies geospatial and statistical methods to analyze and classify urban parks in Phoenix based on multiple social, ecological, and built criteria, including landuse-land cover, `greenness,' and site amenities, as well as the socio- economic and built characteristics of park neighborhoods. The second article uses spatial empirical analysis to rezone the City of Phoenix following transect form-based code. The current park system was then assessed within this framework and recommendations are presented to inform the planning and design of civic spaces sensitive to their social and built context. The final paper culminates in the development of a planning tool and site design guidelines for civic space planning and design across the urban-to-natural gradient augmented with multiple ecosystem service considerations and tailored to desert cities.

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Agent

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Date Created
  • 2013

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Curating the Desert Southwest: Distortion as a Way of Knowing

Description

The Desert Southwest has no shortage of representations in literature, art, and film. Its aesthetics—open horizons, strange landscapes, and vast wilderness—inform and saturate the early Western films of John Ford,

The Desert Southwest has no shortage of representations in literature, art, and film. Its aesthetics—open horizons, strange landscapes, and vast wilderness—inform and saturate the early Western films of John Ford, the paintings of Georgia O’Keeffe, Edward Abbey’s Desert Solitaire, and continue in today’s popular imaginations. My work acknowledges such contributions and then it challenges them: why are those names more widely associated with the Southwest than Luis Alberto Urrea, Alicia Gaspar de Alba, or Pat Mora?

The project intersects the environmental humanities, critical theory, and cultural studies with the Desert Southwest. It explores the fullness of desert places with regard to cultures, borders, and languages, as well as nonhuman forces and intensities like heat, light, and distance. Dispelling the dominant notion of desert as void or wasteland, it sets a stage to suit the polyvocality of desert place. My work is interdisciplinary because the desert demands it. It begins with Cormac McCarthy’s Blood Meridian in order to reorient readers towards the rupture of the US War With Mexico which helped set the national and cultural borders in effect today. I then explore Denis Villeneuve’s film Sicario to emphasize the correlation between political hierarchy and verticality; those who can experience the desert from above are exempt from the conditions below, where Urrea’s The Devil’s Highway and Gaspar de Alba’s Desert Blood take place. The novels expose the immanence and violence of being on the ground in the desert and at the lower end of said hierarchies. Analyzing Yuri Herrera’s Signs Preceding the End of the World and Mora’s Encantado enables what I term a desert hauntology to produce a desert full of memory, myth, ancestors, and enchantment. Finally, the project puts visual artists James Turrell and Rafa Esparza in conversation to discover a desert phenomenology. The result is an instigation of how far is too far when decentering the human, and what role does place-based art play in creating and empowering community.

John Ford was from Maine. Georgia O’Keeffe, from Wisconsin. Edward Abbey, Pennsylvania. As someone born and raised in the Desert Southwest, I’ve written the project I have yet to encounter.

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Agent

Created

Date Created
  • 2020

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Spatial and temporal patterns in insectivorous bat activity in river-riparian landscapes

Description

River and riparian areas are important foraging habitat for insectivorous bats. Numerous studies have shown that aquatic insects provide an important trophic resource to terrestrial consumers, including bats, and

River and riparian areas are important foraging habitat for insectivorous bats. Numerous studies have shown that aquatic insects provide an important trophic resource to terrestrial consumers, including bats, and are key in regulating population size and species interactions in terrestrial food webs. Yet these studies have generally ignored how structural characteristics of the riverine landscape influence trophic resource availability or how terrestrial consumers respond to ensuing spatial and temporal patterns of trophic resources. Moreover, few studies have examined linkages between a stream's hydrologic regime and the timing and magnitude of aquatic insect availability. The main objective of my dissertation is to understand the causes of bat distributions in space and time. Specifically, I examine how trophic resource availability, structural components of riverine landscapes (channel confinement and riparian vegetation structure), and hydrologic regimes (flow permanence and timing of floods) mediate spatial and temporal patterns in bat activity. First, I show that river channel confinement determines bat activity along a river's longitudinal axis (directly above the river), while trophic resources appear to have stronger effects across a river's lateral (with distance from the river) axis. Second, I show that flow intermittency affects bat foraging activity indirectly via its effects on trophic resource availability. Seasonal river drying appears to have complex effects on bat foraging activity, initially causing imperfect tracking by consumers of localized concentrations of resources but later resulting in disappearance of both insects and bats after complete river drying. Third, I show that resource tracking by bats varies among streams with contrasting patterns of trophic resource availability and this variation appears to be in response to differences in the timing of aquatic insect emergence, duration and magnitude of emergence, and adult body size of emergent aquatic insects. Finally, I show that aquatic insects directly influence bat activity along a desert stream and that riparian vegetation composition affects bat activity, but only indirectly, via effects on aquatic insect availability. Overall, my results show river channel confinement, riparian vegetation structure, flow permanence, and the timing of floods influence spatial and temporal patterns in bat distributions; but these effects are indirect by influencing the ability of bats to track trophic resources in space and time.

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Agent

Created

Date Created
  • 2010

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Behavioral and nutritional regulation of colony growth in the desert leafcutter ant Acromyrmex versicolor

Description

Like individual organisms, complex social groups are able to maintain predictable trajectories of growth, from initial colony foundation to mature reproductively capable units. They do so while simultaneously responding flexibly

Like individual organisms, complex social groups are able to maintain predictable trajectories of growth, from initial colony foundation to mature reproductively capable units. They do so while simultaneously responding flexibly to variation in nutrient availability and intake. Leafcutter ant colonies function as tri-trophic systems, in which the ants harvest vegetation to grow a fungus that, in turn, serves as food for the colony. Fungal growth rates and colony worker production are interdependent, regulated by nutritional and behavioral feedbacks. Fungal growth and quality are directly affected by worker foraging decisions, while worker production is, in turn, dependent on the amount and condition of the fungus. In this dissertation, I first characterized the growth relationship between the workers and the fungus of the desert leafcutter ant Acromyrmex versicolor during early stages of colony development, from colony foundation by groups of queens through the beginnings of exponential growth. I found that this relationship undergoes a period of slow growth and instability when workers first emerge, and then becomes allometrically positive. I then evaluated how mass and element ratios of resources collected by the ants are translated into fungus and worker population growth, and refuse, finding that colony digestive efficiency is comparable to digestive efficiencies of other herbivorous insects and ruminants. To test how colonies behaviorally respond to perturbations of the fungus garden, I quantified activity levels and task performance of workers in colonies with either supplemented or diminished fungus gardens, and found that colonies adjusted activity and task allocation in response to the fungus garden size. Finally, to identify possible forms of nutrient limitation, I measured how colony performance was affected by changes in the relative amounts of carbohydrates, protein, and phosphorus available in the resources used to grow the fungus garden. From this experiment, I concluded that colony growth is primarily carbohydrate-limited.

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Agent

Created

Date Created
  • 2011