Developing Genomic Tools for the Management of Threatened Species

Abstract

Despite a revolution in DNA sequencing and genotyping technologies in the past decade there still exists a deficit in genomic resources for many threatened species. As a result, these species are not always being managed as effectively as possible. Single nucleotide polymorphisms (SNPs) hold great promise for illuminating the genetic characteristics of mammalian populations and monitoring their genetic health. Unfortunately, many techniques for SNP discovery are still beyond the reach of conservation projects. This thesis describes two cost-effective techniques for identifying SNPs in non-model species - whole-genome genotyping using cross-species array data, and reduced representation sequencing using a universal primer resource. I have designed, implemented, and validated strategies that can be utilized for SNP discovery and genotyping in species with no existing genome resources. These tools will facilitate phylogenetics and high-throughput population genetics in non-model species at a reasonable price point. Practical improvements to the conservation genomics toolkit come at a crucial time, as the genetic management of small and vulnerable populations will play an increasingly important role into the future. The strategies outlined here are achievable in the framework of a conservation management project and will hopefully advance real-world outcomes for threatened species.