The University of Sydney
Holly Nelson (PhD Student) worked on how we can use genomics to revolutionise threatened species management. From genome assembly to downstream analyses using whole-genome data, Holly used her work to answer genetic questions on the Bellinger River Snapping Turtle, Koala, and other threatened species. Her work, in partnership with the NSW Governments Saving Our Species program, aimed to create more robust conservation strategies that can be developed and applied together with wildlife managers.
Silver, L. (2023). Birth, Death and Diversity: Using genomes and genomics to investigate evolution of the marsupial MHC. The University of Sydney.
The major histocompatibility complex (MHC) is an immune gene family involved in the vertebrate immune response. Class I and class II genes have roles in resistance to disease and show high levels of diversity. MHC genes evolve through a birth and death process with class I genes evolving faster than class II genes. Marsupials are an interesting study system as they give birth to highly altricial and immunologically naïve young. The number of reference genomes available for marsupials has increased and it is now possible to bioinformatically annotate and compare the repertoire of MHC genes and investigate functional diversity in a number of species. Koalas are an iconic Australian marsupial threatened by two pathogens, Chlamydia pecorum and koala retrovirus (KoRV) and are currently listed as ‘Endangered’, making research into their immune system imperative for conservation of the species. This thesis investigates the birth, death and diversity of MHC genes in marsupials. This thesis provides a workflow for investigating evolution and diversity of any gene family in any wildlife species. I was able to achieve this by: i) tracing patterns of gene gain and loss in class II MHC genes across the marsupial lineage (29 species), ii) determine the minimum sequence depth required to accurately genotype MHC genes, iii) identify associations between variation in immune genes, and disease progression using koalas and Chlamydia and iv) investigate variation in SNPs and copy number within MHC genes of koalas. Overall, my thesis demonstrates the power of genomic technologies to investigate the birth, death, and diversity of MHC genes. By leveraging existing genomic resources and investigating sequencing and analysis methods, I was able to identify patterns of gene gain and loss, investigate the role of MHC diversity in disease resistance, and measure diversity across the entire range of koalas.
https://sydney.primo.exlibrisgroup.com/permalink/61USYD_INST/1c0ug48/alma991031727098905106
Farquharson, K. A. (2020). Investigating adaptation to captivity: a data-driven approach. The University of Sydney.
Captive breeding programs are an increasingly common tool to prevent extinction and provide a source population for reintroductions to the wild. Breeding programs attempt to ‘halt evolution’ in captivity, however, there will always be differences between captive and wild environments. Genetic adaptation to captivity as a result of artificial or unintended selection is therefore likely. In this thesis, I examined (1) whether there are differences in reproductive success in captive environments between wild-born and captive-born animals, (2) long-term multi-generational changes in reproductive success in captivity and (3) how changes may occur between generations of captive breeding, including through variation in reproductive success and undetected selection. As the consequences of adaptation to captivity are of relevance to all captive breeding programs, I used a data-driven approach to examine the response of multiple species to captive breeding. In captivity, wild-born animals across diverse taxa had higher reproductive success than their captive-born counterparts and fitness changes occurred over multiple generations of captive breeding. The Tasmanian devil was then used as a case study to allow a closer examination of genetic change in captivity. High variation in the reproductive success of Tasmanian devils housed in free-range enclosures may reduce genetic diversity and accelerate adaptation to captivity if unmanaged, however mate choice did not explain the reproductive skew. Undetected early viability selection, where offspring deviate from Mendelian inheritance, was identified as a mechanism for undetected genetic change to occur in captive breeding programs. This thesis provides new information about the consequences and possible mechanisms of adaptation to captivity. Useful recommendations are provided to conservation managers considering the impact of adaptation to captivity in their species.
https://sydney.primo.exlibrisgroup.com/permalink/61USYD_INST/1c0ug48/alma991031727098905106
Brandies, P. A. (2021). Conserving Australia’s iconic marsupials; one genome at a time. The University of Sydney.
In the midst of a global sixth mass extinction event, conservation initiatives are now more crucial than ever. Australia houses the most diverse range of marsupial species in the world; however, the number that are threatened is growing every year. Genetic management of threatened populations is vital in species recovery, yet incorporation of genetic data in conservation management is currently limited. International and national genome sequencing consortia are currently producing reference genomes for a large variety of species, though there is currently a gap between the creation of these genomic resources and their downstream applications, particularly in conservation contexts. One of the major drivers of this gap is due to the bioinformatic expertise and resources that are required to analyse genomic datasets and to translate the findings into conservation management. This PhD employs a variety of bioinformatic and sequencing approaches to develop genomic resources for threatened Australian Marsupials and demonstrates how these resources can be used as a tool to assist species conservation. The value of genomic data for conservation is demonstrated for a range of species under varying scenarios including: i) using existing genomic datasets for the endangered Tasmanian devil to answer new conservation questions relating to reproduction, ii) creating a reference genome for the common brown antechinus, to act as a model species for its threatened congeneric counterparts and iii) generating and uniting a suite of genomic resources to assist in the management of the vulnerable greater bilby. In addition, ten simple rules for getting started with command-line bioinformatics are presented to facilitate the use of genomic data in wildlife conservation. Bridging the research-implementation gap is essential for harnessing the power of genomic resources for the conservation of threatened species. The findings from this PhD provide crucial steps into bridging this gap.
https://sydney.primo.exlibrisgroup.com/permalink/61USYD_INST/1c0ug48/alma991032543896605106
McLennan, E. A. (2020). To move or not to move? A genetic toolkit for monitoring assisted colonisations. University of Sydney.
Worldwide there are over one million species threatened with extinction. Assisted colonisations are becoming increasingly relevant as in situ threat mitigation fails to keep pace with population declines. Human-mediated movement of species to habitats beyond their native range has been used to protect species against prevailing disease threats, invasive species and climate change. To be successful, scientifically derived principles for planning and implementation of assisted colonisations are needed. Recent technological advancements have increased our capacity to monitor wildlife. With genetic methods we can assess a myriad of population processes such as diet, interindividual relationships, shifts in genetic diversity profiles and ultimately a population’s capacity to adapt to new challenges. Here I demonstrate that a “toolkit” of genetic monitoring techniques can be used to critically examine an assisted colonisation and inform adaptive management. Through the compilation of large genetic datasets, my work has helped identify a toolkit of genetic monitoring protocols most appropriate for monitoring an assisted colonisation and performing adaptive management. I recommend careful monitoring of the inter- and intraspecific interactions that occur following an assisted colonisation with the most appropriate sampling regime and marker type for a given question. Doing so will enable appropriate remedial management such as protection of vulnerable native species at the release site or identification of genetically overrepresented individuals. The work presented here provides a genetic toolkit for global conservation managers who are using assisted colonisation to prevent the extinction of threatened species.
https://sydney.primo.exlibrisgroup.com/permalink/61USYD_INST/1c0ug48/alma991032033232205106
Peel, E. J. (2018). Peptides from the Pouch: Marsupial and Monotreme Cathelicidins. The University of Sydney.
The rise in antimicrobial resistance and paucity of new antimicrobial compounds calls for alternatives to traditional antibiotics. Antimicrobial peptides (AMPs) have emerged as potential candidates. Cathelicidins are a major family of AMPs in mammals which form part of innate immunity through antimicrobial and immunomodulatory functions. Marsupial and monotreme cathelicidins are of particular interest due to their involvement in protecting immunologically naive young during development in the pouch via expression in the pouch lining and milk where they modulate microbial flora and provide passive immunity. As such, the cathelicidin gene family has expanded in marsupials and monotremes, with a high number of cathelicidins in the tammar wallaby, gray short-tailed opossum and platypus. However our knowledge is limited to these species and functional studies involving antimicrobial activity are lacking. This thesis describes the characterisation of cathelicidins in the Tasmanian devil, koala and echidna, and investigates the antimicrobial function of all marsupial and monotreme cathelicidins. As expected, cathelicidins have expanded in the Tasmanian devil and koala, resulting in a high number of cathelicidins which were widely expressed throughout the body, including in pouch lining and milk. Only a single cathelicidin was identified in the echidna due to the quality of the genome. Out of 26 cathelicidins tested, six displayed broad-spectrum antibacterial activity against gram-negative and positive bacteria, including methicillin-resistant Staphylococcus aureus. One koala cathelicidin rapidly inactivated C. pecorum and significantly reduced the number of chlamydial inclusions in vitro. Activity was reduced in the presence of serum and whole blood, and peptides displayed varying levels of haemolytic and cytotoxic activity. Many cathelicidins did not display antimicrobial activity and future work is required to explore their potential immunomodulatory properties. The results presented in this thesis have advanced our understanding of cathelicidins in marsupials and monotremes on a genetic and functional level, and highlights their potential as novel therapeutics in the future.
https://sydney.primo.exlibrisgroup.com/permalink/61USYD_INST/1c0ug48/alma991032033232205106