The Use of Conservation Genomics To Inform Law and Policy

Abstract

Over the last decade, there have been incredible leaps forward in sequencing technology and bioinformatic tools for dealing with large genomic datasets. This genomics revolution has allowed us to ask and answer questions about the natural world that would have remained tantalizingly out of reach using traditional genetic methods. While genomics quickly gained widespread use in academia, traction has been much slower in more applied settings. Much of the emphasis has been on generating basic knowledge, rather than answering questions related specifically to management and policy. In this dissertation, I give examples, from my own research, of how we can use genomics to inform wildlife management, conservation, and law and policy. In Appendix A, I describe the development of PumaPlex100: a tool for genotyping pumas (Puma concolor) at over 100 SNP markers. This marker set allows managers, and other puma researchers, to use non-invasive scat samples to monitor puma abundance, population structure, and genetic diversity. This tool will hopefully be used to inform on-the-ground management. In Appendix B, I used pedigree reconstruction and relatedness analyses to examine the effects of sport hunting on a population of pumas from the Uncompahgre Plateau in southwest Colorado. This study suggests that hunting reduced the average age of male breeders, increased relatedness among males, and decreased relatedness among females, thus altering the sexual structure of the population. This study also suggests that genetic diversity, across multiple metrics, increased when there was no hunting and decreased each year when hunting was present. This study highlights how genomics can be used in adaptive management and for use in setting scientifically supported hunting regulations. In Appendix C, I describe the use of genomics to determine subspecies in black-tailed prairie dogs (Cynomys ludovicianus) and to inform a translocation of prairie dogs into Arizona. I found strong evidence for at least two subspecies within C. ludovicianus, as well as a possible third. Determining taxonomic groups is of vital importance legally, especially when it comes to potential protection under the Endangered Species Act. I also highlight the utility of genomics for informing management actions like translocations; I was able to recommend that prairie dogs in Sonora or New Mexico be used for future translocations into the populations in Arizona. Finally, in Appendix D, I discuss how changes in our understanding of the biological process of hybridization should lead to changes in our legal system of protection for endangered populations under the Endangered Species Act (ESA). New findings from genomic studies could make many of the species we are currently protecting legally unsuitable for protection. As such, I proposed a 2-step policy that would take into consideration the twin aims of protecting genetic lineages and protecting ecosystems: (1) will protecting hybrids benefit the continued persistence of the endangered taxon and (2) will protecting hybrids benefit the ecosystem as a whole.