Reference: Dodge, T. O., Farquharson, K. A., Ford, C., Cavanagh, L., Schubert, K., Schumer, M., Belov, K, & Hogg, C. J. (2022). Genomes of two Extinct‐in‐the‐Wild reptiles from Christmas Island reveal distinct evolutionary histories and conservation insights. Molecular Ecology Resources. doi:10.1111/1755-0998.13780
Abstract
Genomics can play important roles in biodiversity conservation, especially for Extinct-in-the-Wild species where genetic factors greatly influence risk of total extinction and probability of successful reintroductions. The Christmas Island blue-tailed skink (Cryptoblepharus egeriae) and Lister’s gecko (Lepidodactylus listeri) are two endemic reptile species that went extinct in the wild shortly following the introduction of a predatory snake. After a decade of management, captive populations have expanded from 66 skinks and 43 geckos to several thousand individuals; however, little is known about patterns of genetic variation in these species. Here, we use PacBio HiFi long-read and Hi-C sequencing to generate highly contiguous reference genomes for both reptiles, including the XY chromosome pair in the skink. We then analyze patterns of genetic diversity to infer ancient demography and more recent histories of inbreeding. We observe high genome-wide heterozygosity in the skink (0.007 heterozygous sites per base-pair) and gecko (0.005), consistent with large historical population sizes. However, nearly 10% of the blue-tailed skink reference genome falls within long (>1Mb) runs of homozygosity (ROH), resulting in homozygosity at all major histocompatibility complex (MHC) loci. In contrast, we detect a single ROH in Lister’s gecko. We infer from the ROH lengths that related skinks may have established the captive populations. Despite a shared recent extinction in the wild, our results suggest important differences in these species’ histories and implications for management. We show how reference genomes can contribute evolutionary and conservation insights, and we provide resources for future population-level and comparative genomic studies in reptiles.
Reference: Stojanovic, D., Hogg, C. J., Alves, F., Baker, G. B., Biggs, J. R., Bussolini, L., Carey, M. J., Crates, R., Magrath, M. J. L., Pritchard, R., Troy, S., Young, C. M., & Heinsohn, R. (2023). Conservation management in the context of unidentified and unmitigated threatening processes. Biodiversity and Conservation, 1-17. doi: 10.1007/s10531-023-02568-0
Abstract
The decision to intervene in endangered species management is often complicated. Migratory species exemplify this difficulty because they experience diverse threats at different times and places that can act cumulatively and synergistically on their populations. We use population viability analysis (PVA) to compare potential conservation interventions on the critically endangered, migratory Orange-bellied Parrot Neophema chrysogaster. This species suffers high juvenile mortality, but it is not clear why this is so. Given uncertainty about the best recovery strategy, we compare PVA scenarios that simulate various ways of utilizing captive-bred parrots to support the wild population in the context of unresolved threatening processes. Increasing the number of juveniles entering the population each year had the greatest benefit for population growth rate and size. Directly lowering juvenile mortality rates is difficult given uncertainty about the drivers of mortality in the wild. In lieu of this, releasing 100 juveniles from captivity to the wild population each autumn (either as a stand-alone action, or in combination with other interventions) was the most feasible and straightforward intervention of the options we tested. However, our PVAs also show that unless substantial and sustainable reductions can be made to juvenile mortality rates, Orange-bellied Parrots will remain dependent on intensive conservation management. This study highlights the utility of PVAs for answering practical questions about how to implement species conservation. PVAs provide a way to incorporate the best available information in a replicable modelling framework, and to identify impacts of parameter uncertainty on demographic trends.
Reference: Smith, D., Abeli, T., Beckman Bruns, E., Dalrymple, S. E., Foster, J., Gilbert, T.C., Hogg, C. J., Lloyd, N. A., Meyer, A., Moehrenschlager, A., Murrell, O., Rodriguez, J. P., Smith, P. P., Terry, A. & Ewen, J. G. (2023) Extinct in the wild: The precarious state of Earth’s most threatened group of species. Science 379, eadd2889(2023).
Extinct in the Wild (EW) species are placed at the highest risk of extinction under the International Union for Conservation of Nature Red List, but the extent and variation in this risk have never been evaluated. Harnessing global databases of ex situ animal and plant holdings, we report on the perilous state of EW species. Most EW animal species—already compromised by their small number of founders—are maintained at population sizes far below the thresholds necessary to ensure demographic security. Most EW plant species depend on live propagation by a small number of botanic gardens, with a minority secured at seed bank institutions. Both extinctions and recoveries are possible fates for EW species. We urgently call for international effort to enable the latter.
Reference: Hogg, C. J., Silver, L., McLennan, E. A., & Belov, K. (2023). Koala Genome Survey: An Open Data Resource to Improve Conservation Planning. Genes, 14(3), 546. doi: 10.3390/genes14030546
Summary
Genome sequencing is a powerful tool that can inform the management of threatened species. Koalas (Phascolarctos cinereus) are a globally recognized species that captured the hearts and minds of the world during the 2019/2020 Australian megafires. In 2022, koalas were listed as ‘Endangered’ in Queensland, New South Wales, and the Australian Capital Territory. Populations have declined because of various threats such as land clearing, habitat fragmentation, and disease, all of which are exacerbated by climate change. Here, we present the Koala Genome Survey, an open data resource that was developed after the Australian megafires. A systematic review conducted in 2020 demonstrated that our understanding of genomic diversity within koala populations was scant, with only a handful of SNP studies conducted. Interrogating data showed that only 6 of 49 New South Wales areas of regional koala significance had meaningful genome-wide data, with only 7 locations in Queensland with SNP data and 4 locations in Victoria. In 2021, we launched the Koala Genome Survey to generate resequenced genomes across the Australian east coast. We have publicly released 430 koala genomes (average coverage: 32.25X, range: 11.3–66.8X) on the Amazon Web Services Open Data platform to accelerate research that can inform current and future conservation planning.
I began my PhD in July 2021, and in May 2022 I sat down with my panel to confirm my candidature. Although I found the lead up to my confirmation unnecessarily daunting, I am glad I have ticked this major milestone off. Now fully immersed into my research project, I want to share a couple of the big lessons I’ve learnt over the past year.
Read. I came in with no prior knowledge of population genetics, which is an integral part of my project. So having the first four months stuck at home in a COVID lockdown had some perks, it allowed me to buckle down and start reading. I read everything, from theoretical concepts to current literature, I stalked experts in the field on google scholar and sought out the publications of my other lab members (a MUST DO when starting in a new lab), and within a month I had filled an entire notebook. Reading the current literature is a constant practise and I have slowly learnt to be more systematic about it to save time, this is important as other tasks continuously pile up.
Record everything. I like to draw out my ideas and process them on paper, leaving the more stringent writing for my laptop. But whether you prefer the “old school” way of pen and paper or use only the computer, get it down. When I got further along with my research, I found the most essential part of developing my project (with reminders from my supervisors), was not the writing up of the experimental design, codes, or analyses I was using but recording the decisions I was making along the way. This has saved me so much headache in the long run, especially when I’m asked why I chose to go in a certain direction.
Sometimes doing nothing at all is progress. One of the best pieces of advice my supervisors gave me early on was to take what I have learnt from my readings and with the broad objectives of my project go and sit quietly to think. I started to implement this by stepping away from computer, and with just my pen and paper I’d spend hours thinking of how I could apply these grand concepts to my project. Sometimes the better half of a day would go by with the feeling that I hadn’t accomplished anything. This is when I’d take whatever ideas I had back to my supervisors to discuss and flesh out actionable steps, and sometimes those ideas never panned out or weren’t feasible, whereas others really caught on and I am currently implementing them.
Admin chores. Finally, those pesky administrative tasks and online modules that everyone hates doing, rip the band aid off from the beginning and get them over and done with.
Author:
Andrea Schraven (PhD Student; co-supervised with Dr Catherine Grueber) is projecting the long-term impacts of supplementation to improve the status of wild Tasmanian devil populations with the ongoing threat of DFTD. By evaluating population genetic and fitness data before and after translocations, she is comparing how populations change over a few generations, and then feeding the data into computational models to simulate “evolutionary time”. The results will directly inform conservation management decisions for the species long-term recovery.
Reference: Dalrymple, S.E., Abeli, T., Ewen, J.G., Gilbert, T.C., Hogg, C.J., Lloyd, N.A., Moehrenschlager, A., Rodríguez, J.P., & Smith, D. (2023). Addressing Threats and Ecosystem Intactness to Enable Action for Extinct in the Wild Species. Diversity15, 268. doi.org/10.3390/d15020268
Abstract
The species listed as Extinct in the Wild (EW) in the IUCN Red List of Threatened Species consist of 84 plants and animals that have been lost from their indigenous range. EW species are therefore restricted to ex situ conservation facilities and often have populations founded with few individuals. Our analysis demonstrates that 60% of EW species are associated with ecoregions that have very low proportions of intact habitat. Furthermore, threats such as invasive species, pollution, and climate change affect just over half of EW species and compound the obstacles facing their reinstatement to the wild. Despite these bleak assessments, there are various options for EW recovery. We present five scenarios that encapsulate the circumstances facing EW species and suggest potential conservation action for each of these situations. We illustrate these scenarios using case studies of EW species that demonstrate how the various options of ex situ management, reintroduction, and assisted colonisation to new habitat can be used to address the very exacting requirements of EW species. Our aim is to present a broad review of the obstacles facing the recovery of EW species whilst inspiring action to prevent the extinction of the most imperilled species on the planet.
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.
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.
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.
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.
