The Biodiversity Genomics conference took place virtually, October 2-7, 2022. The event was hosted by the Earth BioGenome Project and was open and free for all to attend. Carolyn Hogg, from the University of Sydney, talks about Australian Biodiversity Genomics:
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Reproductive skew in a Vulnerable bird favors breeders that monopolize nest cavities
Type: Journal Article
Reference: Stojanovic, D., McLennan, E., Olah, G., Cobden, M., Heinsohn, R., Manning, A. D., Alves, F., Hogg, C. & Rayner, L. (2023). Reproductive skew in a Vulnerable bird favors breeders that monopolize nest cavities. Animal Conservation. doi: 10.1111/acv.12855
Abstract
Reproductive skew occurs when a few individuals monopolize breeding output, which can act as a mechanism of natural selection. However, when population sizes become small, reproductive skew can depress effective population size and worsen inbreeding. Identifying the cause of reproductive skew is important for mitigating its effect on conservation of small populations. We hypothesized that superb parrots Polytelis swainsonii, which strongly select for the morphology of tree cavity nests, may be reproductively skewed toward pairs that monopolize access to nests. We use SNP genotyping to reconstruct a pedigree, estimate molecular relatedness and genetic diversity of wild superb parrot in the Australian Capital Territory. We successfully genotyped 181 nestlings (a census between 2015–2019) and showed they were the progeny of 34 monogamous breeding pairs. There was a strong reproductive skew – 21 pairs bred only once producing 40% of the nestlings, whereas 13 pairs bred two to four times, producing 60% of the total nestlings. Five of these repeat-breeders produced 28% of all nestlings, which was nearly triple the productivity of one-time breeders. Repeat breeders usually monopolized access to their nest cavities, but the few pairs that switched nests did not differ in fecundity from those that stayed. The cause of nest switching was unknown, but uninterrupted access to a suitable nest (not minor variations in morphology between nests) better predicted fitness of breeding superb parrots. Pedigrees offer powerful insights into demographic processes, and identifying reproductive skew early provides opportunities to proactively avoid irreversible loss of genetic diversity via conservation management. We identify new research questions based on our results to clarify the relationship between access to resources and breeding success.
See all our publications HERE!
Luke Silver
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
Kate Farquharson
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

Holidays in the Sun
by Patra Petrohilos (PhD Student)
I am not a seasoned traveller.
I can count the number of times I have been on a plane on my fingers. The only time one of those planes took me overseas was 20 years ago.
Then I heard about a summer school that was being held in Cambridge on the evolutionary biology and ecology of cancer. When my supervisors suggested I apply to attend, I reacted pretty much as if they’d suggested I apply for the first manned mission to Mars. That’s the kind of amazing thing you fantasise about. Not the kind of thing you get to do in real life.
Despite my unworldliness, I had heard of Cambridge. I knew it was home to the third oldest university in the world – one so old that it predated the Aztec Empire. And I knew it was “a long way away”. But it wasn’t until I was sitting on a plane for fourteen hours straight (and then a second plane for an additional seven hours) that I appreciated what “a long way away” actually meant.
“How long was your flight?” a European PhD student asked me soon after I arrived.
“Well, the first one was fourteen hours.”
I’m not sure what shocked her more – the fact that I’d had to endure a fourteen-hour flight, or the fact that after such obscene amount of time I was still only partway to my destination. Either way – it was reassuring to not be the only one who hadn’t realised just how far “a long way away” can actually be.
And so began one of the best weeks of my entire life:
There were morning walks through the lush forest.


There were squirrels frolicking in the greenery. Like an Enid Blyton book come to life!
There were fancy meals in even fancier dining halls. I basically spent my days pretending to be a rich character in a Jane Austen novel.


There were pints of beer in 16th century pubs shared with new friends from all over the world.
New friends with job descriptions I didn’t even know existed! (Exciting and exotic sounding things like “fish vet” and “mathematical oncologist”). I told them excitedly about my project and listened, enthralled, as they told me about theirs. We attended workshops on evolution and mathematical modelling and game theory and applying landscape ecology methods to cancer research.
But back to my favourite part – those 16th century pubs. I was determined to try all the exotic British foods that I only knew from books – toad in the hole, black pudding, pickled eggs. Pickled eggs! Imagine my delight to see an entire jar of them glistening temptingly behind the bar.
“Would you like the full experience?” the bartender asked me.
When someone asks if you want the full experience, the answer is always “yes”. In this case, the full experience turned out to be crushing up a bag of salt and vinegar chips before rolling your pickled egg in the salty, sour, crunchy crumbs of pure deliciousness.

I clutched my English delicacy with glee as I eagerly headed back to our table. For some reason, my new friends looked slightly less excited with my find than I was. Their facial expressions spanned the entire gamut of confusion, from shock to amusement to admiration at my bravery. Evidently, they were fellow foreigners like me, I told myself, unfamiliar with the fineries of traditional English bar snacks.
And then – “I have never in my life seen anyone actually order a pickled egg,” a lovely English doctor announced.
Ok so maybe it was less a British delicacy and more something they tell stupid Australian tourists. It was still delicious.
Cambridge had a magic that I had thought only existed in literature. The entire trip felt like falling into the pages of my favourite childhood books, like I had finally been handed my letter from Hogwarts. I was Alice in a wonderland of history.
I saw baby swans as I went punting down the Cam River.
I was thrilled to drink beer at the Eagle – that famous Cambridge pub where the structure of DNA was first announced. I was even more thrilled to see that someone had the gumption to add Dr Rosalind Franklin’s name to the plaque out the front.

I even loved the charming signs telling me to wash my duvet.
I returned to Sydney, energised and inspired; armed with a
renewed fervour to attack my PhD. I can’t wait to carve out my own tiny sliver
of novelty in the monolith of human knowledge so that I can tentatively place it
upon the shoulders of the giants who came before me. Thank you so much to my
supervisors Professor Kathy Belov, Dr Carolyn Hogg and Dr Emma Peel for making
this happen.
Author:

Patra Petrohilos (PhD Student) is researching the evolution of devil facial tumour disease (DFTD). By investigating anticancer properties of naturally occurring peptides, she is aiming to identify novel agents with therapeutic potential against DFTD.
Assisted Colonisation as a Conservation Tool: Tasmanian Devils and Maria Island
Type: Book Chapter
Reference: Hogg, C., & Wise, P. (2022). Assisted Colonisation as a Conservation Tool: Tasmanian Devils and Maria Island. In M. Gaywood, J. Ewen, P. Hollingsworth, & A. Moehrenschlager (Eds.), Conservation Translocations (Ecology, Biodiversity and Conservation, pp. 476-483). Cambridge: Cambridge University Press. doi:10.1017/9781108638142.029
Summary
Tasmanian devils are endangered due to an infectious clonal cancer that has reduced populations by up to 80 per cent since it first arose in 1996. As part of a management strategy for the species, an island population was established through an assisted colonisation event on Maria Island
National Park. The original scope of the Maria Island population was to establish and maintain a disease-free population of devils. The island is now used as a source site for these trial releases of devils to mainland Tasmania populations. The 2012 release cohort to the island had a high degree of relatedness. However, through dedicated management strategies, including contraception and selective harvesting, this situation has been rectified and the Maria Island population now represents a genetically diverse group. Monitoring, using traditional methods of trapping and camera traps, in addition to genetic monitoring, has been essential to the establishment and maintenance of the Maria
Island population.
See all our publications HERE!
How genomics is saving the Tasmanian Devil and Koala with Dr. Carolyn Hogg
During her stay in Vancouver, Dr. Hogg joined Stu McNish for a “Conversation That Matters” about the role genomics is playing in an all-out effort to save the Tasmanian devil. You can watch that interview below as well as her Don Rix Distinguished Keynote Address below. As an added bonus, listen to our podcast episode “Nice Genes! – The Devil is in the Details.”
Find the full article here: https://www.genomebc.ca/blog/carolynhogg-drdk2022-ctm
NSW Department of Planning and Environment: Keeping up with the Bellinger River snapping turtle
An article about people working to conserve the critically endangered Bellinger River snapping turtle to learn more about the species and what’s being done to try to protect it. Research to assist recovery of the Bellinger River snapping turtle is ongoing. University of Sydney PhD student Holly Nelson is using whole genome and genetic data to help inform and develop tools for the management of the species.
Find the full article here: https://www.environment.nsw.gov.au/news/keeping-up-with-the-bellinger-river-snapping-turtle

My Journey to a Wildlife Conservation Degree
by Lucy Ockert (2022 Honours Student)
Are you thinking about enrolling in a Bachelor of Science/Bachelor of Advanced Studies (Taronga Wildlife Conservation) but not sure if it’s the right degree for you? Two years ago, I was in a similar situation. I had originally enrolled in a Bachelor of Science at USYD, majoring in ‘Ecology & Evolutionary Biology’ and ‘Immunology & Pathology’. I always knew that I wanted to pursue science, yet there are so many different fields to choose from, being forced to decide straight after high school after being exposed to a tiny piece of the scientific puzzle. I enrolled in these two majors to give myself the opportunity to learn about two opposing fields of biological science and discover which one I wanted to pursue. While I found all my subjects incredibly interesting, halfway through my degree I realised that I wanted to contribute to conservation science and help remedy the ecological damage caused by humans over the past few centuries. I wanted to transfer into a major which was more focused on conservation than just biology or ecology – that’s when I found out about the Wildlife Conservation major in partnership with the Taronga Conservation Society Australia. Despite being a new degree, only starting the year I first enrolled in University, I knew it was the perfect degree for me. Many of my credit points transferred over from my Ecology & Evolutionary Biology major which was a bonus. I overloaded on subjects in my third year to catch up, and while challenging, it was worth it. The amazing teaching staff and small cohort form a tight-knit community of avid conservationists and creates an amazing environment to learn about all the skills needed to assist in wildlife conservation. We recently went to Taronga Western Plains Zoo for a week to learn about their conservation programs. It was a great opportunity to see first-hand the theories we have been learning about throughout the degree. We also recently completed a unit surrounding the health and welfare of wildlife where we learnt how to conduct diagnostic tests for stress and disease. We also were able to conduct a post-mortem on a (opportunistically collected) kangaroo. I’ve been able to gain a combination of experiences that would not have been possible in another degree and feel very fortunate because of it.
This year I started honours with AWGG, characterising the pouch microbiome of an extremely threatened and iconic species – the Tasmanian devil. I found this degree to be a perfect mix of theory and practice, providing me with the skills to eventually work in a field I am truly passionate about. I hope to continue with research, aiming to start a PhD next year after conducting some conservation volunteering in biodiversity hotspots around the world! If you’re not sure what you want to do but are interested in science and wildlife, I would recommend looking into the degree. Either way, you can always transfer if you change your mind!
Author:

Lucy Ockert (2022 Honours Student) is characterising the pouch microbiome in lactating and non-lactating Tasmanian devils to understand the immunological protection of marsupial pouch young provided by cathelicidins.
Conversations That Matter: Can genomics save the ‘devil’
For the past 12 years, Dr. Carolyn Hogg has been working with the Save the
Tasmanian devil Program utilizing genomics as a vital tool to save this
endangered marsupial. Carolyn joined a Conversation That Matters about the role genomics is playing in an all-out effort to save the Tasmanian devil.
Listen to the whole interview here: https://vancouversun.com/news/conversations-that-matter-can-genomics-save-the-devil