Many relationships exist between humans and their animal companions. Regardless of the relationship, the costs of pet ownership are more than just veterinary bills and the purchase of pet food. The purpose of this study is to examine the environmental impacts associated with ownership of canus lupus familiaris, more commonly known as the domesticated dog. Since dogs are carnivorous by nature, there has already been significant interest in the ecological ‘pawprint’ of pet food, or the pressure that dog food production exerts on the environment.

This study utilizes Life Cycle Assessment (LCA) to determine the environmental impacts of industrial pet food production and furthermore, pet ownership through nutritional requirements. Additionally, this study aims to examine how pet food type—beef or lamb—can influence greenhouse gas (GHG) emissions. The approach taken by this study is that of a hybrid input-output LCA, combining Economic Input Output (EIO-LCA) data and process-level data to examine how supply chain decisions made by pet food manufactures can affect the ecological ‘pawprint’ of the domestic dog. The EIO-LCA provides an economy-wide lens, whereas, process-based LCAs provide data relevant to specific materials and processes. This approach was used to compare the environmental impacts associated with environmentally friendly supply chain decisions compared to the typical environmental impact of dog food.

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).