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).

For my Spring 2022-23 Barrett Honors College creative project, I designed and created my own analog game. The created game is a tile-management game for 2-4 players called Plash. Players collect tiles and manipulate the board to complete goals and win the game. The paper for this project details the inspirations and research done for the game’s design, the game's design journey, and detailed instructions on how to play.

For my creative project thesis, I have designed and developed a video game called Amity Academy. Amity Academy is a strategic resource management simulator that aims to subvert genre expectations and challenge generally accepted definitions of success and leadership both in-game and in the real world. It does so by moving the focus away from amassing large amounts of in-game currencies and becoming politically or militarily dominant towards caring for the denizens of the social unit the player controls. The player acts as an administrator at a school where they must make decisions on how to best run the institution. Although they are allowed to lead the school however they see fit, the emphasis is on prioritizing strong interpersonal and intracommunity relationships and connections and the wellbeing and happiness of those under their ward. Amity Academy is also part of the newly-emerging “wholesome” or “comfy” game genre. Unlike serious strategy games that can be stressful, Amity Academy presents a self-paced, low-stakes situation. This mood is further encouraged by calming environmental noises and music, a gentle color palette, and a charming art style. The game feels domestic and quaint, almost reminiscent of a Jane Wooster Scott or Mary Singleton painting. You can download and play Amity Academy here: https://mvaughn8.itch.io/amity-academy