Furtress of solitude

In the Pilbara region of Western Australia lives the western pebble mouse (Pseudomys

chapmani), a rarely seen rodent that excavates a complex subterranean burrow system in the rocky substrate. These tunnels are topped with distinctive “fortress-style” pebble mounds composed of thousands of excavated pebbles that likely persist on this arid landscape for hundreds to thousands of years. Although their exact function remains unknown, they are thought to protect the mice from extreme desert conditions, including both intense heat and freezing temperatures.

Photo: A western pebble mound mouse (Pseudomys chapmani) next to a mound burrow entrance;

provided by Aline Gibson Vega.

Western pebble mice are typically solitary, however in the rare instances when outback conditions become hospitable during good years following major cyclonic activity, multiple females will live communally in a mound to cooperatively rear their offspring.

The western pebble mouse was only first discovered in 1980, 16 years after the first mines were established in the iron-rich Pilbara region. As mining activity has increased, so has the concern for this elusive species. Today, the Western Australian Department of Biodiversity, Conservation and Attractions declares the western pebble mouse to be a Priority 4 (taxa in need of monitoring) species.

Today, we release the chromosome-length genome of the western pebble mouse created using a combination of PacBio HiFi and Hi-C sequencing from a male sample collected at the Western Australian Museum.

This work was funded by an Australian Research Council to Renée Firman (University of Western Australia) and Dustin Rubenstein (Columbia University).

Explore the interactive Hi-C contact map for the western pebble mouse below, and check out the assembly page for more details and fasta links.

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.