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).

Institutional factors are rarely examined in disaster risks in the Himalayan region, as much of the focus so far has been on improving the scientific understanding of the natural hazards and risks. This is particularly true for glacial lake outburst floods (GLOFs), which are natural hazards endemic to high mountain ranges such as the Andes, Alps, and Himalayas. While these have put mountain communities at risk for centuries, vulnerability is viewed to be increasing due to climate change. While the science behind the causes and characteristics of these hazards is now better understood, there is an absence of research understanding the social, cultural and institutional drivers behind creating effective strategies to mitigate risks from GLOFs. This is more so for the Himalayan region, where institutions have recently started to address this risk, but contention between local communities and external organizations can hinder mitigation efforts. To better understand how people’s perception towards disaster risk, a study conducted by Sherpa et al. (2019) examined the socio-economic and cultural perceptions surrounding GLOF hazards.

This research highlighted gaps in how scientific knowledge is disseminated to local communities, and the resulting distrust in government mitigation projects such as lake lowering and Early Warning Systems. A clear need developed to conduct an institutional analysis of the governance systems responsible for disaster risk management and their interaction with local communities. This study examines the institutional conditions under which mountain communities create effective adaptation strategies to address climate induced hazards. We use a mixed-methods approach, combining: a) quantitative analysis of household surveys collected in 2016-2017 and b) qualitative analysis that maps out the various factors of institutions that influence the success of community-based adaptation efforts. Additionally, GLOF case studies from Nepal are compared to those in Peru, where institutions have a longer history of managing GLOF risks. The research finds that there are several considerations including: lack of cross-scalar communication networks, lack of local knowledge and participation in policy processes, and ineffective interorganizational coordination of knowledge sharing and funding streams for local projects. This disconnect between external versus local and informal institutions becomes an inherent issue in projects where agenda setting by external organizations plays prevalent roles in project implementation.