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.

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.