Putting genomics to work in threatened species management

Abstract

Earth’s sixth mass extinction event threatens over one million species. Small populations are most at risk of extinction due to genomic erosion and decreased adaptive potential. Conservation genetic management of threatened populations is pivotal to species recovery, yet implementation of genetic data into recovery programs lags behind ecological and biological disciplines, making genetic initiatives more crucial than ever. Here, I generate and utilise a high-quality reference genome. In combination with a variety of bioinformatic and sequencing approaches, I use the genome to produce a suite of downstream genomic resources that can be applied by threatened species recovery programs. I used the critically endangered and disease susceptible Bellinger River turtle (Myuchelys georgesi) as my case study species. My thesis aims to (i) generate a high-quality reference genome for a critically endangered species, (ii) use the reference genome in combination with existing genetic datasets to answer important conservation questions relating to genetic diversity and relatedness in captive and wild populations, (iii) develop an eDNA assay for species detection using a bioinformatic approach, and (iv) undertake high-resolution immune gene investigations to better understand adaptive potential in a disease susceptible species. Bridging the gap between geneticists and conservation action is crucial for maximising the uptake of genomic resources for the management of threatened species. My thesis showcases the implementation of reference genomes and other genome-wide data into conservation recovery programs. By leveraging cutting-edge genomic technologies alongside existing genomic resources, I demonstrate the power of large datasets in identifying molecular information that can be transformed into practical conservation recommendations and tools.