ASU Scholarship Showcase

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).

Communicating climate risks is crucial when engaging the public to support climate action planning and addressing climate justice. How does evidence-based communication influence local residents’ risk perception and potential behavior change in support of climate planning? Built upon our previous study of Climate Justice maps illustrating high scores of both social and ecological vulnerability in Michigan’s Huron River watershed, USA, a quasi-experiment was conducted to examine the effects of Climate Justice mapping intervention on residents’ perceptions and preparedness for climate change associated hazards in Michigan. Two groups were compared: residents in Climate Justice areas with high social and ecological vulnerability scores in the watershed (n=76) and residents in comparison areas in Michigan (n=69). Measurements for risk perception include perceived exposure, sensitivity, and adaptability to hazards. Results indicate that risk information has a significant effect on perceived sensitivity and level of preparedness for future climate extremes among participants living in Climate Justice areas. Findings highlight the value of integrating scientific risk assessment information in risk communication to align calculated and perceived risks. This study suggests effective risk communication can influence local support of climate action plans and implementation of strategies that address climate justice and achieve social sustainability in local communities.

Accessibility is increasingly used as a metric when evaluating changes to public transport systems. Transit travel times contain variation depending on when one departs relative to when a transit vehicle arrives, and how well transfers are coordinated given a particular timetable. In addition, there is necessarily uncertainty in the value of the accessibility metric during sketch planning processes, due to scenarios which are underspecified because detailed schedule information is not yet available. This article presents a method to extend the concept of "reliable" accessibility to transit to address the first issue, and create confidence intervals and hypothesis tests to address the second.

Hundreds of thousands of archaeological investigations in the United States conducted over the last several decades have documented a large portion of the recovered archaeological record in the United States. However, if we are to use this enormous corpus to achieve richer understandings of the past, it is essential that both CRM and academic archaeologists change how they manage their digital documents and data over the course of a project and how this information is preserved for future use. We explore the nature and scope of the problem and describe how it can be addressed. In particular, we argue that project workflows must ensure that the documents and data are fully documented and deposited in a publicly accessible, digital repository where they can be discovered, accessed, and reused to enable new insights and build cumulative knowledge.

Cientos de miles de investigaciones arqueológicas en los Estados Unidos realizado en las últimas décadas han documentado una gran parte del registro arqueológico recuperado en los Estados Unidos. Sin embargo, si vamos a utilizar este enorme corpus para lograr entendimientos más ricos del pasado, es esencial que CRM y los arqueólogos académicos cambian cómo administran sus documentos digitales y los datos en el transcurso de un proyecto y cómo se conserva esta información para uso en el futuro. Exploramos la naturaleza y el alcance del problema y describimos cómo se pueden abordarse. En particular, sostenemos que los flujos de trabajo de proyecto deben asegurarse que los documentos y datos son totalmente documentados y depositados en un repositorio digital de acceso público, donde puede ser descubiertos, acceder y reutilizados para activar nuevos conocimientos y construir conocimiento acumulativo.