Scale-able defense

Fish-scale geckos, Geckolepis spp., are small and arboreal lizards endemic to Madagascar and the Comoro Islands. The base coloration of the fish-scaled gecko is generally chestnut-cream with darker/black bands or mottling. Their appearance may vary by locality and individual, allowing excellent camouflage on tree bark and rocky surfaces. Its scales are large, overlapping, and partially ossified, giving the lizard a distinctive “fish scale” appearance.

First described more than 150 years ago, Geckolepis maculata (Peters, 1880), is

commonly known as Peters’s spotted gecko or fish-scale gecko. Five species of Geckolepis are

currently recognized: G. typica (Grandidier, 1867), G. maculata (Peters, 1880), G. polylepis

(Boettger, 1893), G. humbloti (Vaillant, 1887), and G. megalepis (Scherz et al., 2017). However, morphological features (scale counts, pattern, size) show variation among populations and from animals in different localities, and molecular analyses suggest that several additional cryptic species may be hidden within the genus (Lemme et al., 2013).

Photo: Fish-scaled gecko (Geckolepis spp.) Provided by Marina Saito, DVM, PhD and George Eisenhoffer, PhD

Today, we share the chromosome-length genome assembly and Hi-C data for Geckolepis

maculata. This genome assembly was done in collaboration with Dr. George Eisenhoffer and team at the Department of Genetics at the MD Anderson Cancer Center using PacBio HiFi data and Hi-C.

Unlike most lizards, which are best known for their ability to drop and regenerate their tails, fish-scale geckos take autotomy to the next level. When threatened by predators—such as birds, snakes or larger lizards—they can shed large patches of skin to facilitate escape and avoid being consumed. This skin loss leaves much of the body surface exposed and unprotected (Scherz et al., 2017).

A unique attribute of the integument (a tough outer protective layer) of G. maculata is the presence of osteoderms, which are mineralized dermal deposits that are embedded in the scales (Paluh et al., 2017). The presence of osteoderms gives G. maculata a kind of protective dermal ossification, which is unusual among geckos. These osteoderms within scales likely contribute to both physical protection and may influence how scales detach. The ability to create a protective layer and then rapidly lose it has lead to the concept of “sheddable armor” (Paluh et al., 2017).

The genome of fish-scaled geckos stands to provide new insights into their striking appearance, unique defensive strategies, and taxonomy uncertainties.

Explore the interactive Hi-C contact map for the fish-scale gecko below, and check out more details about the assembly here.

References:

• A.M. Bauer & A. P. Russell (1992) The evolutionary significance of regional integumentary loss in island geckos: a complement to caudal autotomy, Ethology Ecology & Evolution, 4:4, 343-358, DOI: 10.1080/08927014.1992.9523127

• Lemme, I., Erbacher, M., Kaffenberger, N. et al. Molecules and morphology suggest cryptic species diversity and an overall complex taxonomy of fish scale geckos, genus Geckolepis . Org Divers Evol 13, 87–95 (2013). https://doi.org/10.1007/s13127-012-0098-y

• Paluh, D. J., Griffing, A. H., & Bauer, A. M. (2017). Sheddable armour: identification of osteoderms in the integument of Geckolepis maculata (Gekkota). African Journal of Herpetology, 66(1), 12–24. https://doi.org/10.1080/21564574.2017.1281172

• Scherz MD, Daza JD, Köhler J, Vences M, Glaw F. 2017. Off the scale: a new species of fish-scale gecko (Squamata: Gekkonidae: Geckolepis) with exceptionally large scales. PeerJ 5:e2955. https://doi.org/10.7717/peerj.2955

• Uetz, P.; Freed, P.; Hošek, J. The Reptile Database. 2022. Available online: http://www.reptile-database.org

Unburying the secrets of the American burying beetle

The American burying beetle, Nicrophorus americanus (Coleoptera: Staphylinidae), is the largest burying beetle in North America. The American burying beetle (ABB) has lost nearly 90% of its original habitat range and now only resides in three populations (Rhode Island, Nebraska extending into South Dakota, and Oklahoma extending into Kansas and Arkansas). ABB was listed as endangered in 1989 but, in 2020, was reclassified as threatened. These beetles are important decomposers, and as the largest species in their subfamily, are able handle larger vertebrate carcasses than other related species. ABB are also unique in the fact that they practice biparental care, which is not found in many other species.

Photo: American burying beetle (Nicrophorus americanus), Photo credits: Samantha Hittson (Oklahoma State University)

Today, we generate the chromosome-length genome assembly for the American burying beetle, see https://www.dnazoo.org/assemblies/nicrophorus_americanus. The HiFi draft for this work was generated by Samantha Hittson, Manpreet Kohli, Ethan Tolman, Paul Frandsen, Jessica Ware, and W. Wyatt Hoback, which was upgraded using Hi-C data generated by the DNA Zoo Consortium. Funding for the draft was from Ware Lab start-up funding from American Museum of Natural History. Funding was also provided by grant # 0259007642 to WW Hoback from the U.S. Army, with additional support from Hatch Project accession No. 1019561 from the USDA National Institute of Food and Agriculture. Work was conducted under permit # # TE045150-3 held by Hoback.

Explore the interactive Hi-C contact map for ABB below, and visit the assembly page for more details.

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!