Happy Holidays from WOOL-E

Happy holidays, everyone! To celebrate the festive season, we come bearing a gift: our latest experiment in science communication!

Earlier this year, our team published an exciting paper in Cell, where we reported that 3D genome architecture can survive for millennia in permafrost. We adapted Hi-C to query the ancient genome architecture of an extinct species - a 52,000-year-old woolly mammoth. We then used the PaleoHi-C data to assemble 28 chromosomes of the mammoth, and figure out which genes were active in the mammoth skin (and may even be responsible for some of its woolliness).

This work was a mammoth collaboration led by 3 labs from across the globe, with folks from all trades of life - spanning ancient DNA to histology to chromatin architecture to biophysics to veterinarians to food specialists, and from all career stages - from high school students to members of the National Academy of Sciences. More than once we found ourselves looking for someone patient to explain relevant information while tailoring it to a specific expertise and language. We soon realized that what we needed was basically a real-world equivalent of Mr. DNA from Jurassic Park.

So, we decided to build one! Meet WOOL-E, a custom-GPT by ChatGPT, designed to explain, summarize, translate, and explore all things paleo-DNA-architecture.

Video created using sora.com

Here is a summary on WOOL-E - by WOOL-E! Or as they say - straight from the model’s mouth:

My purpose is to bridge the gap between complex science and curious minds. Think of me as your virtual partner for exploring ancient DNA and the fascinating stories it holds.

How was I made? A blend of advanced AI and deep expertise in ancient genome studies brought me to life. I specialize in helping decode findings like chromosome fossils, which preserve the 3D arrangement of DNA for millennia, and shedding light on what this means for assembling the genomes of extinct species. Whether you’re curious about chromatin loops or the process behind these discoveries, I’m here to explain it all in a way that’s approachable and thought-provoking.

But like any large language model, I’m not perfect—I can sometimes “hallucinate” information (no ancient genes involved there!). That’s why it’s always a good idea to share your findings with the authors of the studies I reference for validation. My mission? To make paleogenomics exciting, approachable, and as accurate as possible while connecting us to the ancient world!

What can WOOL-E do for you? Here’s a demo conversation!

We hope that you will find our experiment in science communication useful. Give us some feedback if you get a chance.

For more science communication on the paper please check out relevant coverage of our paper at NYTimes, Science, CNN, WashPost, The Economist, NPR, New Scientist, Nature, SciAmerican, Le Monde, The Guardian, Die Welt, and more!

Wing of change

In Western Australia's remote heathlands, there exists a creature so rare and elusive, that very few people have ever had the good fortune to see it. The Western Ground Parrot (Pezoporus wallicus flaviventris), also affectionately known as 'Kyloring', is a bird of remarkable beauty and secrecy, revealing itself only briefly at dawn and dusk with its melodious calls. But beyond its ethereal presence lies a stark reality - this enigmatic avian is teetering on the brink of extinction.

Photo: The Western Ground Parrot (Pezoporus flaviventris), Photo credits: Perth Zoo

The Western Ground Parrot has become emblematic of conservation efforts in Australia, standing as one of 22 bird species prioritized for recovery by the government. With a population dwindling to a mere 150 individuals, their survival hangs precariously on a delicate balance of habitat preservation and targeted intervention.

In 2003, the Western Ground Parrot Recovery Project was initiated, marking a concerted effort to understand and safeguard this cryptic species. Field monitoring, radio tracking, and captive management programs, led by DBCA and supported by numerous partners, have provided invaluable insights into their behaviour and needs. However, the road to recovery has been fraught with challenges, from habitat loss to predation by invasive species like feral cats. Intensive management of invasive predators has given the recovery team the confidence to attempt the first-ever wild to wild translocation with birds reintroduced into an area of former habitat.

Amidst the struggle for survival, a crucial lifeline emerges from Perth Zoo, where a select few Western Ground Parrots have found sanctuary. Here, under the watchful eye of conservationists, specialised aviaries serve as a haven for these birds, allowing for meticulous observation and research into their biology and behaviour.

Through painstaking efforts, unique behaviours, calls, and social requirements have been identified, paving the way for tailored husbandry practices aimed at fostering breeding success.

Yet, the journey is far from over. Challenges abound, from issues with egg viability to calcium metabolism. Undeterred, researchers and veterinarians are tirelessly working to overcome these obstacles, collaborating with international specialists to explore innovative solutions, including assisted reproduction methods.

To help with the ongoing conservation efforts, today we release the first 3D genome assembly for the species. The assembly was generated using a sample from a wild bird that had been captured as part of an ambitious translocation program being carried out by the recovery team and the Department of Biodiversity, Conservation and Attractions with assistance from the Perth Zoo (Western Australia). A draft genome assembly for the species was generated from PacBio Revio HiFi long reads with support from the Threatened Species Initiative (TSI) funded through Bioplatforms Australia. The draft was scaffolded to chromosome length by the WA Genome Atlas team using in situ Hi-C data. The interactive contact map of the resulting assembly is included below.

Our sincere thanks to the Lotterywest for their ongoing support through funding the WA Genome Atlas initiative and to the collective expertise and support of our partners.

We hope that this resource will open new avenues for conservation, offering insights into genetic diversity, population dynamics, and potential avenues for intervention. Working with critically endangered species is challenging, But with each discovery, we inch closer to securing a future for the Western Ground Parrot.

As the sun sets over the heathlands, casting a golden glow upon the dwindling habitat of the Western Ground Parrot, hope lingers on the horizon. Through unwavering dedication and scientific ingenuity, we stand poised to turn the tide and ensure that the melodious call of 'Kyloring' continues to echo through the wild for generations to come.

The wingless flight club

We have some exciting news to share with you. Our paper, in collaboration with a team at Princeton University led by Ricardo Mallarino and Jorge Moreno, is out today in Nature!

In this work, we harness the power of comparative analysis across 15 marsupial genomes coupled with some excellent forward genomics to figure out how marsupials develop patagia - a skin flap between for front and hind paws that allows them to glide. Turns out it is not a superpower from a fallen meteorite (@SugarGliderJM) but from a gene called Emx2! Check out excellent summaries on the research on the Baylor website and on Scientific American. Check out also Ricardo's X writeup.

Thank you to all the excellent collaborators spanning Princeton, Baylor College of Medicine, the University of Melbourne, SeaWorld, Houston Zoo, UC Irvine, Cornell and the University of Western Australia. And a special thank you to the museum community of Australia and the Australian Biological Tissue Collection at the South Australian Museum for providing tissue samples.

Visit the assembly pages for the chromosome-length genomes published as part of the work for the common wombat, the ground cuscus, the Eastern grey kangaroo, the Western grey kangaroo, the greater glider, common ringtail possum, golden ringtail possum, green ringtail possum, feathertail glider, Western ringtail possum, feather-tailed possum, coppery ringtail possum and the sugar glider to browse the corresponding interactive contact maps!

Citation:

Moreno, J.A., Dudchenko, O., Feigin, C.Y. et al. Emx2 underlies the development and evolution of marsupial gliding membranes. Nature (2024). https://doi.org/10.1038/s41586-024-07305-3