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).

The goal of this research project was to examine how different messaging techniques, and especially expressions of emotionality surrounding the loss and recovery of biodiversity, can differently influence public attitudes about conservation and the environment. This question was explored using the case of de-extinction, an emerging and controversial conservation technology. De-extinction claims to “resurrect” extinct species, challenging widely held notions of extinction as permanent. Yet seeing extinction as reversible may shift how people feel about biodiversity loss and our moral responsibility to stop it.

Revive and Restore is a California-based nonprofit that uses genetic engineering to help solve conservation problems, such as saving endangered species and increasing the biodiversity of ecosystems. To facilitate their solutions, Revive and Restore utilizes genetic engineering, which is the process of making changes to an organism’s DNA, or the set of instructions for how an organism develops and functions. One of their broad solutions is genetic rescue, which involves imbuing populations of endangered species with a wider variety of traits to make them more adaptable to a changing environment. Their other solution is de-extinction, which takes a more radical approach by attempting to recreate extinct species that performed important roles in their ecosystems. While scientists working with Revive and Restore have helped advance genome editing technology on a theoretical and technical level, their research has also prompted practical and ethical concerns over the extent of permissible human interference with nature, even when attempting to conserve it.

In 2015, Revive & Restore launched the Woolly Mammoth Revival Project with a goal of engineering a creature with genes from the woolly mammoth and introducing it back into the tundra to combat climate change. Revive & Restore is a nonprofit in California that uses genome editing technologies to enhance conservation efforts in sometimes controversial ways. In order to de-extinct the woolly mammoth, researchers theorize that they can manipulate the genome of the Asian elephant, which is the mammoth’s closest living evolutionary relative, to make it resemble the genome of the extinct woolly mammoth. While their goal is to create a new elephant-mammoth hybrid species, or a mammophant, that looks and functions like the extinct woolly mammoth, critics have suggested researchers involved in the project have misled and exaggerated the process. As of 2021, researchers have not yet succeeded in their efforts to de-extinct the woolly mammoth, but have expressed that it may become a reality within a decade.