Museum genomics reveals the rapid decline and extinction of Australian rodents since European settlement

Australia has the highest historically recorded rate of mammalian extinction in the world, with 34 terrestrial species declared extinct since European colonization in 1788. Among Australian mammals, rodents have been the most severely affected by these recent extinctions; however, given a sparse historical record, the scale and timing of their decline remain unresolved. Using museum specimens up to 184 y old, we generate genomic-scale data from across the entire assemblage of Australian hydromyine rodents (i.e., eight extinct species and their 42 living relatives). We reconstruct a phylogenomic tree for these species spanning ∼5.2 million years, revealing a cumulative total of 10 million years (>10%) of unique evolutionary history lost to extinction within the past ∼150 y. We find no evidence for reduced genetic diversity in extinct species just prior to or during decline, indicating that their extinction was extremely rapid. This suggests that populations of extinct Australian rodents were large prior to European colonization, and that genetic diversity does not necessarily protect species from catastrophic extinction. In addition, comparative analyses suggest that body size and biome interact to predict extinction and decline, with larger species more likely to go extinct. Finally, we taxonomically resurrect a species from extinction, Gould's mouse (Pseudomys gouldii Waterhouse, 1839), which survives as an island population in Shark Bay, Western Australia (currently classified as Pseudomys fieldi Waite, 1896). With unprecedented sampling across a radiation of extinct and living species, we unlock a previously inaccessible historical perspective on extinction in Australia. Our results highlight the capacity of collections-based research to inform conservation and management of persisting species.

Insights into the pre-European mammalian fauna of the southern Flinders Ranges, South Australia

Many Australian mammal species have suffered significant declines since European colonisation. During the first century of settlement, information on species distribution was rarely recorded. However, fossil accumulations can assist the reconstruction of historical distributions. We examine a fossil vertebrate assemblage from Mair’s Cave, one of few known from the southern Flinders Ranges, South Australia. The Mair’s Cave assemblage was dominated by mammals but also included birds and reptiles. Of the 18 mammals recovered, two have not previously been recorded from the southern Flinders Ranges, at least one is extinct and seven are recognised as threatened nationally. Characteristics of the assemblage suggest that it was accumulated by a Tyto owl species. Remains of Tyto delicatula and a larger unidentified owl were recovered from the assemblage. Most mammals identified from the assemblage presently occupy Australia’s semiarid zone, but a single specimen of the broad-toothed rat (Mastacomys fuscus), which primarily occurs in high-moisture, low-temperature environments was also recovered. This suggests either that the southern Flinders Ranges once experienced higher past precipitation, or that M. fuscus can tolerate a broader climatic range than its current distribution suggests. Our study contributes new knowledge on the biogeography and ecology of several mammal species, data useful for helping to refine restoration targets.

The biology and palaeontology of the Peramelemorphia: a review of current knowledge and future research directions

Bandicoots and bilbies (Marsupialia : Peramelemorphia) represent the dominant omnivorous clade of Australasian marsupials and, as ground-dwelling, small- to medium-sized mammals, have not fared well in the 200 years since European settlement. Unlike large or charismatic marsupial species, the cryptic nature of bandicoots and bilbies tends to keep them out of the public eye, at a time when public interest plays a significant role in conservation efforts. The inconspicuous ‘rat-like’ appearance of many bandicoots and a generalist ecological strategy belie a complex biology of adaptive traits and evolutionary diversity. For a few species these biological traits have enabled them to make use of urban environments. In the main, however, peramelemorphians are facing ongoing pressure from introduced predators and human impacts. Basic biological information for many species, particularly those from New Guinea, is still lacking. In this review, we examine advances in the knowledge of the biology of this group over the past 25 years including anatomical, physiological and ecological studies. We also provide a comprehensive review of the fossil records of bandicoots in order to provide an up-to-date platform for future studies. From this work, it is clear that there is still much to be done regarding the taxonomy and biology of these animals before a more detailed understanding of the evolutionary history of this group can be elucidated.

Ongoing unraveling of a continental fauna: decline and extinction of Australian mammals since European settlement

The highly distinctive and mostly endemic Australian land mammal fauna has suffered an extraordinary rate of extinction (>10% of the 273 endemic terrestrial species) over the last ∼200 y: in comparison, only one native land mammal from continental North America became extinct since European settlement. A further 21% of Australian endemic land mammal species are now assessed to be threatened, indicating that the rate of loss (of one to two extinctions per decade) is likely to continue. Australia's marine mammals have fared better overall, but status assessment for them is seriously impeded by lack of information. Much of the loss of Australian land mammal fauna (particularly in the vast deserts and tropical savannas) has been in areas that are remote from human population centers and recognized as relatively unmodified at global scale. In contrast to general patterns of extinction on other continents where the main cause is habitat loss, hunting, and impacts of human development, particularly in areas of high and increasing human population pressures, the loss of Australian land mammals is most likely due primarily to predation by introduced species, particularly the feral cat, Felis catus, and European red fox, Vulpes vulpes, and changed fire regimes.

Habitat use and ecological observations of the Ooldea dunnart (Sminthopsis ooldea) at Uluru–Kata Tjuta National Park, Northern Territory

The Ooldea dunnart (Sminthopsis ooldea) is a small (10–11 g) and poorly known dasyurid marsupial that is endemic to the central and western arid regions of Australia. Surveys carried out at Uluru–Kata Tjuta National Park, Northern Territory, from 1994 to 2010 yielded 37 captures of this elusive species, providing novel insights into its biology. Most captures were made in pitfall traps, with spring breeding confirmed by the presence of pregnant or lactating females during October and November. Animals were captured in mallee and mulga woodland and spinifex (Triodia spp.) dominated dune fields and sand plains. Capture rates were variable in most habitat types, but were relatively consistent in one site dominated by mulga (Acacia aneura). Although we found no consistent association between captures of S. ooldea and prior rainfall, fewest animals were captured in the two wettest years of the study. Ooldea dunnarts showed no clear response to fire. We suggest that mulga is a key habitat for S. ooldea, but also that the demography of this species may be shaped by biotic and/or abiotic factors that remain to be fully elucidated.

Temporal analysis of the diet of the central rock-rat

The central rock-rat (Zyzomys pedunculatus) is an endangered endemic rodent that has undergone a dramatic range contraction over the past century. It is currently known from only a small area of the West MacDonnell Ranges near Alice Springs. A previous investigation into the species’ diet that analysed a small number of faecal samples concluded tentatively that it was a granivore. The present study aimed to establish the dietary patterns of Z. pedunculatus across a two-year period in central Australia during which rainfall fluctuated markedly. Diet was determined through the microscopic analysis of material in faecal pellets of Z. pedunculatus trapped at approximately three-month intervals at five sites at Ormiston Gorge. Seed was found to be the most important dietary item, comprising on average 57.0% of the diet across sample periods. Under dry conditions, the amount of seed material in the diet declined and the amount of stem material increased. Plant material from 15 genera was recorded in the diet, most notably Sida spp., Solanum spp. and Triodia brizoides. All of the plant genera identified in the diet to date are widespread and common in the range country of central Australia and most are considered fire tolerant. On the basis that the diet contains more than 50% seeds, Z. pedunculatus can be described as a granivore. However, the diet is broad and includes both seeds and vegetative material from a range of plant species.

Past and present distribution of Dasycercus: toward a better understanding of the identity of specimens in cave deposits and the conservation status of the currently recognised species D. blythi and D. cristicauda (Marsupialia : Dasyuridae)

Maps of the distribution of the two currently recognised species of Dasycercus, D. blythi and D. cristicauda have been prepared following correct identification based on tail morphology of specimens in the modern collections of all Australian museums. Localities in which the remains of Dasycercus have been found in cave deposits have also been mapped and an attempt made to determine the specific identity of some of these specimens. Following examination of larger samples of each species, differences in the premolar dentition were found to no longer be diagnostic. Most cave specimens could not be assigned to species on the basis of some dental measurements. DNA sequences could provide a means for establishing the identity of the cave specimens. Correct identification of specimens, together with knowledge of the search effort underlying the known distribution and persistence of the species in localities over their ranges, is essential for assessment of their conservation status.

Distribution and status of the red-tailed phascogale (Phascogale calura)

The red-tailed phascogale once extended widely across semiarid and arid Australia, but is now entirely confined to the southern wheatbelt of Western Australia, occupying less than 1% of its former range. Here it occurs in a portion of the Avon Wheatbelt, Jarrah Forest, Mallee, and Esperance Plains biogeographical regions. The species persists only in areas that have been extensively cleared for agriculture and where the remaining bushland is highly fragmented. It does not appear to extend into unfragmented habitat in either the Jarrah Forest to the west or Mallee region to the east. It occurs primarily in woodland habitat with old-growth hollow-producing eucalypts, primarily wandoo (Eucalyptus wandoo) or York Gum (E. loxophleba), but records from the periphery of its current range appear to come from a broader range of habitats, including shrublands and various mosaics of woodland, shrubland, and scrub-heath. Key factors limiting persistence are likely to be fragmentation of habitat that is likely to greatly increase the risks associated with dispersal, a shortage of suitable nesting hollows in many vegetation associations, and predation by feral and domestic cats and by foxes. These factors, particularly fragmentation and lack of suitable nesting hollows, suggest that the species’ long-term persistence in areas beyond the wandoo belt is far from assured.

The status of non-volant mammals along a rainfall gradient in the south-west Kimberley, Western Australia

To assess the current status of mammals in relation to mean annual rainfall and to improve knowledge of the original mammalian assemblages in tropical Western Australia, extant terrestrial mammals and subfossil mammalian remains were sought along a rainfall gradient in two parallel ranges in the Kimberley, Western Australia. As expected, extant mammal species richness decreased with decreasing rainfall. Data from other studies in higher-rainfall areas complemented this conclusion and a parallel decline in trap success implied an overall decline in abundance, although numbers of two rodents (Rattus tunneyi and Zyzomys argurus) were highly variable. Small rodents were rare. Subfossil deposits were biased by accumulation processes, with most attributable to tytonid owls. They largely consisted of rodent and, to a lesser extent, small dasyurid bones and there was a high level of consistency in the proportional composition of many common species across the rainfall gradient. Most deposits appear to predate the introduction of stock in the 1880s and some may be much older. All species persist in the study area except two Notomys spp. and three Pseudomys spp. Both the Notomys and one Pseudomys are apparently undescribed, extinct species. However, there were marked ratio differences between subfossil and modern assemblages. Although specimens of species larger than those taken by tytonid owls were scarce, their occurrences were broadly consistent with the modern understanding of distributions.

Natural Resource Management implications of the pre-European non-volant mammal fauna of the southern tip of Eyre Peninsula, South Australia

Sinkholes and coastal caves located in, around and between the Coffin Bay and Lincoln National Parks were surveyed for pre-European fossils, which were collected from or just below the sediment surface. Twenty-four pre-European fossil samples, including eight already in the collections of the South Australian Museum, were analysed and 25 native and five introduced species of non-volant mammal were identified. Native and introduced species were often found together, indicating that the sites have accumulated mammal remains in both pre- and post-European times. Only four of the non-volant native mammals recovered are known to be extant in the study area today: Lasiorhinus latifrons, Macropus fuliginosus, Cercartetus concinnus and Rattus fuscipes. In contrast, 20 native species recorded have been extirpated and one (Potorous platyops) is now extinct. C. concinnus was recorded from only one of the fossil assemblages but is known to be widespread in the study area today. This may indicate recent vegetation change related to European land management practices and have implications for natural resource management in the area.