Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial

Ninu (greater bilby, Macrotis lagotis) are desert-dwelling, culturally and ecologically important marsupials. In collaboration with Indigenous rangers and conservation managers, we generated the Ninu chromosome-level genome assembly (3.66 Gbp) and genome sequences for the extinct Yallara (lesser bilby, Macrotis leucura). We developed and tested a scat single-nucleotide polymorphism panel to inform current and future conservation actions, undertake ecological assessments and improve our understanding of Ninu genetic diversity in managed and wild populations. We also assessed the beneficial impact of translocations in the metapopulation (N = 363 Ninu). Resequenced genomes (temperate Ninu, 6; semi-arid Ninu, 6; and Yallara, 4) revealed two major population crashes during global cooling events for both species and differences in Ninu genes involved in anatomical and metabolic pathways. Despite their 45-year captive history, Ninu have fewer long runs of homozygosity than other larger mammals, which may be attributable to their boom-bust life history. Here we investigated the unique Ninu biology using 12 tissue transcriptomes revealing expression of all 115 conserved eutherian chorioallantoic placentation genes in the uterus, an XY1Y2 sex chromosome system and olfactory receptor gene expansions. Together, we demonstrate the holistic value of genomics in improving key conservation actions, understanding unique biological traits and developing tools for Indigenous rangers to monitor remote wild populations.

Keeping an ear out: size relationship of the tympanic bullae and pinnae in bandicoots and bilbies (Marsupialia: Peramelemorphia)

Bandicoots and bilbies (Order Peramelemorphia) occupy a broad range of habitats across Australia and New Guinea, from open, arid deserts to dense forests. This once diverse group has been particularly vulnerable to habitat loss and introduced eutherian predators, and numerous species extinctions and range retractions have occurred. Understanding reasons for this loss requires greater understanding of their biology. Morphology of the pinnae and tympanic bullae varies markedly among species. As hearing is important for both predator avoidance and prey location, the variability in ear morphology could reflect specialization and adaptation to specific environments, and therefore be of conservation relevance. We measured 798 museum specimens representing 29 species of Peramelemorphia. Controlling for phylogenetic relatedness and head length, pinna surface area was weakly negatively correlated with average precipitation (rainfall being our surrogate measure of vegetation productivity/complexity), and there were no environmental correlates with effective diameter (pinna width). Controlling for phylogenetic relatedness and skull length, tympanic bulla volume was negatively correlated with precipitation. Species that inhabited drier habitats, which would be open and allow sound to carry further with less obstruction, had relatively larger pinnae and tympanic bullae. In contrast, species from higher rainfall habitats, where sounds would be attenuated and diffused by dense vegetation, had the smallest pinnae and bullae, suggesting that low-frequency hearing is not as important in these habitats. Associations with temperature did not reach statistical significance. These findings highlight linkages between hearing traits and habitat that can inform conservation and management strategies for threatened species.

The external ear morphology and presence of tragi in Australian marsupials

Multiple studies have described the anatomy and function of the external ear (pinna) of bats, and other placental mammals, however, studies of marsupial pinna are largely absent. In bats, the tragus appears to be especially important for locating and capturing insect prey. In this study, we aimed to investigate the pinnae of Australian marsupials, with a focus on the presence/absence of tragi and how they may relate to diet. We investigated 23 Australian marsupial species with varying diets. The pinnae measurements (scapha width, scapha length) and tragi (where present) were measured. The interaural distance and body length were also recorded for each individual. Results indicated that all nectarivorous, carnivorous, and insectivorous species had tragi with the exception of the insectivorous striped possum (Dactylopsila trivirgata), numbat (Myrmecobius fasciatus), and nectarivorous sugar glider (Petaurus breviceps). No herbivorous or omnivorous species had tragi. Based on the findings in this study, and those conducted on placental mammals, we suggest marsupials use tragi in a similar way to placentals to locate and target insectivorous prey. The Tasmanian devil (Sarcophilus harrisii) displayed the largest interaural distance that likely aids in better localization and origin of noise associated with prey detection. In contrast, the smallest interaural distance was exhibited by a macropod. Previous studies have suggested the hearing of macropods is especially adapted to detect warnings of predators made by conspecifics. While the data in this study demonstrate a diversity in pinnae among marsupials, including presence and absence of tragi, it suggests that there is a correlation between pinna structure and diet choice among marsupials. A future study should investigate a larger number of individuals and species and include marsupials from Papua New Guinea, and Central and South America as a comparison.

A conceptual framework for habitat use and research priorities for the greater bilby (Macrotis lagotis) in the north of Western Australia

Little is known of the area of occupancy, extent of occurrence, abundance, density or habitat use of the greater bilby (Macrotis lagotis) in the north of Western Australia. To seek broad collaborative agreement on a research agenda, the Western Australian Department of Parks and Wildlife hosted a workshop where research priorities were identified through a facilitated process. Five key areas for future research effort were identified: (1) refine survey methods, (2) improve understanding of habitat use, (3) improve understanding of the genetic structure of (meta)populations, (4) improve understanding of the threat posed by introduced predators and herbivores, and (5) improve understanding of how fire regimes affect bilby conservation. A conceptual model describing the main landscape components thought to be influencing distribution is used to reconcile existing knowledge, link research priorities for the bilby in the north of Western Australia, and guide the development of an integrated program of research. The broad nature of the priorities reflects the limited knowledge of bilbies in the north of the state; however, this research program provides an opportunity to increase knowledge to enact both species- and ecosystem-focused approaches to conservation, and potentially contributes towards the implementation of more dynamic conservation approaches for mobile species.

Adaptations for digging in the forelimb muscle anatomy of the southern brown bandicoot (Isoodon obesulus) and bilby (Macrotis lagotis)

Bandicoots and bilbies (Peramelemorphia) represent a distinct lineage within the marsupial adaptive radiation, which despite several curious anatomical traits has received little morphological attention. Many bandicoot species (family Peramelidae) dig for subterranean food, while bilbies (family Thylacomyidae) employ their forelimbs to dig extensive burrow systems for shelter. In the current study, dissections of the southern brown bandicoot (Isoodon obesulus) (n = 7) and greater bilby (Macrotis lagotis) (n = 4) provide the first anatomical descriptions of forelimb musculature in these species. The anatomical arrangement of forelimb muscles in I. obesulus and M. lagotis differs from that of other marsupials and corresponds to the aclaviculate pectoral girdle and modified arrangement of digits in the study species. Comparative and functional interpretations indicate that the forelimb of I. obesulus is well equipped for scratch digging and demonstrates muscular modifications in order to generate large out-forces. The bones of the forelimb, and in particular the antebrachium, are relatively short, stout bones, improving both their resistance to mechanical forces and providing a mechanical advantage via a reduced out-lever length. There has been an increase in the absolute volume of muscles employed during digging, thereby increasing the magnitude of the in-force. Increased in-lever lengths have been achieved via the migration of muscle insertions, including the elongate olecranon for the insertion of the m. triceps brachii, and the distal migration of the humeral attachments of the teres major, latissimus dorsi and superficial pectoral muscles.

The genetic mating system, male reproductive success and lack of selection on male traits in the greater bilby

The greater bilby (Macrotis lagotis) is the sole remaining species of desert bandicoot on the Australian mainland. The mating system of this species remains poorly understood, due to the bilby’s cryptic nature. We investigated the genetic mating system of the greater bilby in a five-year study of a semi-free-ranging captive population that simulated their wild environment. Morphological traits were examined to determine whether these influenced patterns of male reproductive success and whether selection was acting on them. In any given year more than half the males (59.2 ± 9.3%) failed to sire any offspring. Approximately 70% of sires fathered one offspring, and 30% two or three offspring. Since paternity was not dominated by few males, and given the species’ solitary nature, lack of territoriality and large home ranges, it is likely that males adopt a roving strategy to find receptive females. These results are consistent with an overlap promiscuous mating system. Sires and non-sires could not be distinguished by their morphological traits, and there was no evidence for strong linear or non-linear selection on male traits. These data increase our understanding of bandicoot life-history traits and will assist conservation and management efforts.