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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).
and local economies. However, the negative impacts of invasive species are not always
immediately visible and may be disregarded by local communities if social benefits of
control efforts are not clear. In this dissertation, I use a mixed-methods approach to
investigate the drivers of invasive plant distribution, potential financially feasible
management techniques to control invasion, and community forest user perceptions of
those techniques. In this work, I aim to incorporate the diverse perspectives of local
people and increase the long-term success of invasive species control activities in socio
economically vulnerable populations.
Integrating a spatially and temporally diverse data set, I explore the social and
ecological drivers of invasive plant abundance across 21 buffer zone community forests
in the Western Chitwan Valley of Nepal. I evaluate to what extent forest user and
collective manager activities, the legacies of historic activities, and ecological properties
influence present-day invasive plant abundance. I built upon this study to identify areas
with critically high levels of invasion then initiated a three-year, community-based
management intervention to evaluate traditional and adaptive land management
approaches to control invasive plants. I found that both approaches reduced invasive
plant abundance relative to the surrounding, untreated forest. I then interviewed focus
groups to investigate their perceived efficacy of the various treatment types and found
that almost all forest users and managers preferred the adaptive approach over the
traditional management approach. Notably, forest users cited the importance of the
availability of forest resources and lack of harmful plants in the plots that had undergone
this method. Understanding how forest users relate to and experience invasive plants has
been relatively understudied but can influence forest user engagement in different
management approaches. For this reason, I performed in-depth ethnoecological
interviews to explore how forest users perceive, how they utilize, and to what extent they
value invasive plants. This mixed-methods approach contributes to a more holistic
understanding of the role that local people play in invasive plant management and
restoration activities.
Located directly south of Pima County, Arizona, there is a culturally rich community known as Santa Cruz County, Arizona. Santa Cruz County is a smaller community being home to an estimated 47,000 people. Santa Cruz County has a rich history given its proximity to the United States-Mexico border. One example of this rich history can be found at the Tumacacori National Historical Park (NHP) with the attractive and unique ruins. The Tumacacori NHP was once an active Spanish mission that oversaw the religious expansion and communal resources. While the Tumacacori NHP no longer operates in this manner, it does serve an important role in providing visitors with a diverse and immersive look into the history of the region and the Tumacacori mission. While the Tumacacori NHP is meant to be a place for all people to visit, most visitors are not from the local community. The reason for this stems from a lack of educational and engagement opportunities between the Tumacacori NHP and the community youth, mainly due to community members being unaware of the park’s existence or the programs that are offered. This project analyzes and uncovers this disconnect as well as the barriers between the Tumacacori NHP and the Santa Cruz County youth through a research study and the use of children’s literature.