A probable koala from the Oligocene of central Australia provides insights into early diprotodontian evolution.

Diprotodontians are the morphologically and ecologically most diverse order of marsupials. However, an approximately 30-million-year gap in the Australian terrestrial vertebrate fossil record means that the first half of diprotodontian evolution is unknown. Fossil taxa from immediately either side of this gap are therefore critical for reconstructing the early evolution of the order. Here we report the likely oldest-known koala relatives (Phascolarctidae), from the late Oligocene Pwerte Marnte Marnte Local Fauna (central Australia). These include coeval species of Madakoala and Nimiokoala, as well as a new probable koala (?Phascolarctidae). The new taxon, Lumakoala blackae gen. et sp. nov., was comparable in size to the smallest-known phascolarctids, with body-mass estimates of 2.2-2.6 kg. Its bunoselenodont upper molars retain the primitive metatherian condition of a continuous centrocrista, and distinct stylar cusps B and D which lacked occlusion with the hypoconid. This structural arrangement: (1) suggests a morphocline within Phascolarctidae from bunoselenodonty to selenodonty; and (2) better clarifies the evolutionary transitions between molar morphologies within Vombatomorphia. We hypothesize that the molar form of Lumakoala blackae approximates the ancestral condition of the suborder Vombatiformes. Furthermore, it provides a plausible link between diprotodontians and the putative polydolopimorphians Chulpasia jimthorselli and Thylacotinga bartholomaii from the early Eocene Tingamarra Local Fauna (eastern Australia), which we infer as having molar morphologies consistent with stem diprotodontians.

A review of the late Cenozoic genus Bohra (Diprotodontia: Macropodidae) and the evolution of tree-kangaroos.

Tree-kangaroos of the genus Dendrolagus occupy forest habitats of New Guinea and extreme northeastern Australia, but their evolutionary history is poorly known. Descriptions in the 2000s of near-complete Pleistocene skeletons belonging to larger-bodied species in the now-extinct genus Bohra broadened our understanding of morphological variation in the group and have since helped us to identify unassigned fossils in museum collections, as well as to reassign species previously placed in other genera. Here we describe these fossils and analyse tree-kangaroo systematics via comparative osteology. Including B. planei sp. nov., B. bandharr comb. nov. and B. bila comb. nov., we recognise the existence of at least seven late Cenozoic species of Bohra, with a maximum of three in any one assemblage. All tree-kangaroos (Dendrolagina subtribe nov.) exhibit skeletal adaptations reflective of greater joint flexibility and manoeuvrability, particularly in the hindlimb, compared with other macropodids. The Pliocene species of Bohra retained the stepped calcaneocuboid articulation characteristic of ground-dwelling macropodids, but this became smoothed to allow greater hindfoot rotation in the later species of Bohra and in Dendrolagus. Tree-kangaroo diversification may have been tied to the expansion of forest habitats in the early Pliocene. Following the onset of late Pliocene aridity, some tree-kangaroo species took advantage of the consequent spread of more open habitats, becoming among the largest late Cenozoic tree-dwellers on the continent. Arboreal Old World primates and late Quaternary lemurs may be the closest ecological analogues to the species of Bohra.

A giant armoured skink from Australia expands lizard morphospace and the scope of the Pleistocene extinctions.

There are more species of lizards and snakes (squamates) alive today than any other order of land vertebrates, yet their fossil record has been poorly documented compared with other groups. Here, we describe a gigantic Pleistocene skink from Australia based on extensive material that includes much of the skull and postcranial skeleton, and spans ontogenetic stages from neonate to adult. Tiliqua frangens substantially expands the known ecomorphological diversity of squamates. At approximately 2.4 kg, it was more than double the mass of any living skink, with an exceptionally broad, deep skull, squat limbs and heavy, ornamented body armour. It probably filled the armoured herbivore niche that land tortoises (testudinids), absent from Australia, occupy on other continents. Tiliqua frangens and other giant Plio-Pleistocene skinks suggest that small-bodied groups that dominate vertebrate biodiversity might have lost their largest and often most morphologically extreme representatives in the Late Pleistocene, expanding the scope of these extinctions.

Description of the Pliocene marsupial Ambulator keanei gen. nov. (Marsupialia: Diprotodontidae) from inland Australia and its locomotory adaptations.

Diprotodontids were the largest marsupials to exist and an integral part of Australian terrestrial ecosystems until the last members of the group became extinct approximately 40 000 years ago. Despite the frequency with which diprotodontid remains are encountered, key aspects of their morphology, systematics, ecology and evolutionary history remain poorly understood. Here we describe new skeletal remains of the Pliocene taxon Zygomaturus keanei from northern South Australia. This is only the third partial skeleton of a late Cenozoic diprotodontid described in the last century, and the first displaying soft tissue structures associated with footpad impressions. Whereas it is difficult to distinguish Z. keanei and the type species of the genus, Z. trilobus, on dental grounds, the marked cranial and postcranial differences suggest that Z. keanei warrants genus-level distinction. Accordingly, we place it in the monotypic Ambulator gen. nov. We, also recognize the late Miocene Z. gilli as a nomen dubium. Features of the forelimb, manus and pes reveal that Ambulator keanei was more graviportal with greater adaptation to quadrupedal walking than earlier diprotodontids. These adaptations may have been driven by a need to travel longer distances to obtain resources as open habitats expanded in the late Pliocene of inland Australia.

The skeleton of Congruus kitcheneri, a semiarboreal kangaroo from the Pleistocene of southern Australia.

The macropodine kangaroo, Wallabia kitcheneri, was first described in 1989 from a Pleistocene deposit within Mammoth Cave, southwestern Australia, on the basis of a few partial dentaries and maxilla fragments. Here, we recognize W. kitcheneri within the Pleistocene assemblages of the Thylacoleo Caves, south-central Australia, where it is represented by several cranial specimens and two near-complete skeletons, a probable male and female. We reallocate this species to the hitherto monotypic genus Congruus. Congruus kitcheneri differs from all other macropodid species by having a highly unusual pocket within the wall of the nasal cavity. It is distinguished from C. congruus by having a longer, narrower rostrum, a taller occiput and a deeper jugal. Congruus is closest to Protemnodon in overall cranial morphology but is smaller and less robust. In most postcranial attributes, Congruus also resembles Protemnodon, including general limb robustness and the atypical ratio of 14 thoracic to five lumbar vertebrae. It is distinguished by the high mobility of its glenohumeral joints, the development of muscle attachment sites for strong adduction and mobility of the forelimb, and large, robust manual and pedal digits with strongly recurved distal phalanges. These adaptations resemble those of tree-kangaroos more than ground-dwelling macropodines. We interpret this to imply that C. kitcheneri was semiarboreal, with a propensity to climb and move slowly through trees. This is the first evidence for the secondary adoption of a climbing habit within crown macropodines.

Incorporating intraspecific variation into dental microwear texture analysis.

Dental microwear texture analysis (DMTA) quantifies microscopic scar or wear patterns left on teeth by different foods or extraneous ingested items such as grit. It can be a powerful tool for deducing the diets of extinct mammals. Here we investigate how intraspecific variation in the dental microwear of macropodids (kangaroos and their close relatives) can be used to maximize the dietary signal inferable from an inherently limited fossil record. We demonstrate significant intraspecific variation for every factor considered here for both scale-sensitive fractal analysis and International Organization for Standardization surface texture analysis variables. Intraspecific factors were then incorporated into interspecific (dietary) analyses through the use of Linear Mixed Effects modelling, incorporating Akaike's Information Criterion to compare models, and testing models through independent cross-validation. This revealed that for each DMTA variable only a small number of intraspecific factors need to be included to improve differentiation between species. Including specimen as a random factor accounted for stochastic inter-individual variation, and facet, incorporated effects of sampling location. Intraspecific effects of ecoregion, microscope, tooth position and wear were often but not universally important. We conclude that models of microwear data that include intraspecific variation can improve the resolution of dietary reconstructions.

Rapid Pliocene adaptive radiation of modern kangaroos.

Differentiating between ancient and younger, more rapidly evolved clades is important for determining paleoenvironmental drivers of diversification. Australia possesses many aridity-adapted lineages, the origins of which have been closely linked to late Miocene continental aridification. Using dental macrowear and molar crown height measurements, spanning the past 25 million years, we show that the most iconic Australian terrestrial mammals, "true" kangaroos (Macropodini), adaptively radiated in response to mid-Pliocene grassland expansion rather than Miocene aridity. In contrast, low-crowned, short-faced kangaroos radiated into predominantly browsing niches as the late Cenozoic became more arid, contradicting the view that this was an interval of global browser decline. Our results implicate warm-to-cool climatic oscillations as a trigger for adaptive radiation and refute arguments attributing Pleistocene megafaunal extinction to aridity-forced dietary change.

Taxonomic review of the late Cenozoic megapodes (Galliformes: Megapodiidae) of Australia.

Megapodes are unusual galliform birds that use passive heat sources to incubate their eggs. Evolutionary relationships of extant megapode taxa have become clearer with the advent of molecular analyses, but the systematics of large, extinct forms (Progura gallinacea, Progura naracoortensis) from the late Cenozoic of Australia has been a source of confusion. It was recently suggested that the two species of Progura were synonymous, and that this taxon dwarfed into the extant malleefowl Leipoa ocellata in the Late Pleistocene. Here, we review previously described fossils along with newly discovered material from several localities, and present a substantial taxonomic revision. We show that P. gallinacea and P. naracoortensis are generically distinct, describe two new species of megapode from the Thylacoleo Caves of south-central Australia, and a new genus from Curramulka Quarry in southern Australia. We also show that L. ocellata was contemporaneous with larger species. Our phylogenetic analysis places four extinct taxa in a derived clade with the extant Australo-Papuan brush-turkeys Talegalla fuscirostris, L. ocellata, Alectura lathami and Aepypodius bruijnii. Therefore, diversity of brush-turkeys halved during the Quaternary, matching extinction rates of scrubfowl in the Pacific. Unlike extant brush-turkeys, all the extinct taxa appear to have been burrow-nesters.

Cultural innovation and megafauna interaction in the early settlement of arid Australia.

Elucidating the material culture of early people in arid Australia and the nature of their environmental interactions is essential for understanding the adaptability of populations and the potential causes of megafaunal extinctions 50-40 thousand years ago (ka). Humans colonized the continent by 50 ka, but an apparent lack of cultural innovations compared to people in Europe and Africa has been deemed a barrier to early settlement in the extensive arid zone. Here we present evidence from Warratyi rock shelter in the southern interior that shows that humans occupied arid Australia by around 49 ka, 10 thousand years (kyr) earlier than previously reported. The site preserves the only reliably dated, stratified evidence of extinct Australian megafauna, including the giant marsupial Diprotodon optatum, alongside artefacts more than 46 kyr old. We also report on the earliest-known use of ochre in Australia and Southeast Asia (at or before 49-46 ka), gypsum pigment (40-33 ka), bone tools (40-38 ka), hafted tools (38-35 ka), and backed artefacts (30-24 ka), each up to 10 kyr older than any other known occurrence. Thus, our evidence shows that people not only settled in the arid interior within a few millennia of entering the continent, but also developed key technologies much earlier than previously recorded for Australia and Southeast Asia.

A comprehensive database of quality-rated fossil ages for Sahul's Quaternary vertebrates.

The study of palaeo-chronologies using fossil data provides evidence for past ecological and evolutionary processes, and is therefore useful for predicting patterns and impacts of future environmental change. However, the robustness of inferences made from fossil ages relies heavily on both the quantity and quality of available data. We compiled Quaternary non-human vertebrate fossil ages from Sahul published up to 2013. This, the FosSahul database, includes 9,302 fossil records from 363 deposits, for a total of 478 species within 215 genera, of which 27 are from extinct and extant megafaunal species (2,559 records). We also provide a rating of reliability of individual absolute age based on the dating protocols and association between the dated materials and the fossil remains. Our proposed rating system identified 2,422 records with high-quality ages (i.e., a reduction of 74%). There are many applications of the database, including disentangling the confounding influences of hypothetical extinction drivers, better spatial distribution estimates of species relative to palaeo-climates, and potentially identifying new areas for fossil discovery.

Behaviour of the Pleistocene marsupial lion deduced from claw marks in a southwestern Australian cave.

The marsupial lion, Thylacoleo carnifex, was the largest-ever marsupial carnivore, and is one of the most iconic extinct Australian vertebrates. With a highly-specialised dentition, powerful forelimbs and a robust build, its overall morphology is not approached by any other mammal. However, despite >150 years of attention, fundamental aspects of its biology remain unresolved. Here we analyse an assemblage of claw marks preserved on surfaces in a cave and deduce that they were generated by marsupial lions. The distribution and skewed size range of claw marks within the cave elucidate two key aspects of marsupial lion biology: they were excellent climbers and reared young in caves. Scrutiny of >10,000 co-located Pleistocene bones reveals few if any marsupial lion tooth marks, which dovetails with the morphology-based interpretation of the species as a flesh specialist.

The role of inhibitory dynamics in the loss and reemergence of macropodoid tooth traits.

The reversibility of phenotypic evolution is likely to be strongly influenced by the ability of underlying developmental systems to generate ancestral traits. However, few studies have quantitatively linked these developmental dynamics to traits that reevolve. In this study, we assess how changes in the inhibitory cascade, a developmental system that regulates relative tooth size in mammals, influenced the loss and reversals of the posthypocristid, a molar tooth crest, in the kangaroo superfamily Macropodoidea. We find that posthypocristid loss is linked with reduced levels of posterior molar inhibition, potentially driven by selection for lophodont, higher-crowned molar teeth. There is strong support for two posthypocristid reversals, each occurring after more than 15 million years of absence, in large-bodied species of Macropus, and two giant extinct species of short-faced sthenurine kangaroo (Procoptodon). We find that whereas primitive posthypocristid expression is linked to higher levels of posterior molar inhibition, reemergence is tied to a relative increase in third molar size associated with increasing body mass, producing molar phenotypes similar to those in mouse where the ectodysplasin pathway is upregulated. We argue that although shifts in the inhibitory cascade may enable reemergence, dietary ecology may limit the frequency of phylogenetic reversal.

Climate change not to blame for late Quaternary megafauna extinctions in Australia.

Late Quaternary megafauna extinctions impoverished mammalian diversity worldwide. The causes of these extinctions in Australia are most controversial but essential to resolve, because this continent-wide event presaged similar losses that occurred thousands of years later on other continents. Here we apply a rigorous metadata analysis and new ensemble-hindcasting approach to 659 Australian megafauna fossil ages. When coupled with analysis of several high-resolution climate records, we show that megafaunal extinctions were broadly synchronous among genera and independent of climate aridity and variability in Australia over the last 120,000 years. Our results reject climate change as the primary driver of megafauna extinctions in the world's most controversial context, and instead estimate that the megafauna disappeared Australia-wide ∼13,500 years after human arrival, with shorter periods of coexistence in some regions. This is the first comprehensive approach to incorporate uncertainty in fossil ages, extinction timing and climatology, to quantify mechanisms of prehistorical extinctions.

Empirical tests of harvest-induced body-size evolution along a geographic gradient in Australian macropods.

Life-history theory predicts the progressive dwarfing of animal populations that are subjected to chronic mortality stress, but the evolutionary impact of harvesting terrestrial herbivores has seldom been tested. In Australia, marsupials of the genus Macropus (kangaroos and wallabies) are subjected to size-selective commercial harvesting. Mathematical modelling suggests that harvest quotas (c. 10-20% of population estimates annually) could be driving body-size evolution in these species. We tested this hypothesis for three harvested macropod species with continental-scale distributions. To do so, we measured more than 2000 macropod skulls sourced from wildlife collections spanning the last 130 years. We analysed these data using spatial Bayesian models that controlled for the age and sex of specimens as well as environmental drivers and island effects. We found no evidence for the hypothesized decline in body size for any species; rather, models that fit trend terms supported minor body size increases over time. This apparently counterintuitive result is consistent with reduced mortality due to a depauperate predator guild and increased primary productivity of grassland vegetation following European settlement in Australia. Spatial patterns in macropod body size supported the heat dissipation limit and productivity hypotheses proposed to explain geographic body-size variation (i.e. skull size increased with decreasing summer maximum temperature and increasing rainfall, respectively). There is no empirical evidence that size-selective harvesting has driven the evolution of smaller body size in Australian macropods. Bayesian models are appropriate for investigating the long-term impact of human harvesting because they can impute missing data, fit nonlinear growth models and account for non-random spatial sampling inherent in wildlife collections.

Scrapheap challenge: a novel bulk-bone metabarcoding method to investigate ancient DNA in faunal assemblages.

Highly fragmented and morphologically indistinct fossil bone is common in archaeological and paleontological deposits but unfortunately it is of little use in compiling faunal assemblages. The development of a cost-effective methodology to taxonomically identify bulk bone is therefore a key challenge. Here, an ancient DNA methodology using high-throughput sequencing is developed to survey and analyse thousands of archaeological bones from southwest Australia. Fossils were collectively ground together depending on which of fifteen stratigraphical layers they were excavated from. By generating fifteen synthetic blends of bulk bone powder, each corresponding to a chronologically distinct layer, samples could be collectively analysed in an efficient manner. A diverse range of taxa, including endemic, extirpated and hitherto unrecorded taxa, dating back to c.46,000 years BP was characterized. The method is a novel, cost-effective use for unidentifiable bone fragments and a powerful molecular tool for surveying fossils that otherwise end up on the taxonomic "scrapheap".

Functional morphology of the forelimb of living and extinct tree-kangaroos (Marsupialia: Macropodidae).

Tree-kangaroos are a unique group of arboreal marsupials that evolved from terrestrial ancestors. The recent discovery of well-preserved specimens of extinct tree-kangaroo species (genus Bohra) within Pleistocene cave deposits of south-central Australia provides a unique opportunity to examine adaptive evolution of tree-kangaroos. Here, we provide the first detailed description of the functional anatomy of the forelimb, a central component of the locomotor complex, in the extant Dendrolagus lumholtzi, and compare its structure and function with representatives of other extant marsupial families. Several features were interpreted as adaptations for coping with a discontinuous, uneven and three-dimensional arboreal substrate through enhanced muscular strength and dexterity for propulsion, grasping, and gripping with the forelimbs. The forelimb musculoskeletal anatomy of Dendrolagus differed from terrestrial kangaroos in the following principal ways: a stronger emphasis on the development of muscles groups responsible for adduction, grasping, and gripping; the enlargement of muscles that retract the humerus; and modified shape of the scapula and bony articulations of the forelimb bones to allow improved mobility. Many of these attributes are convergent with other arboreal marsupials. Tree-kangaroos, however, still retain the characteristic bauplan of their terrestrial ancestors, particularly with regard to skeletal morphology, and the muscular anatomy of the forelimb highlights a basic conservatism within the group. In many instances, the skeletal remains of Bohra have similar features to Dendrolagus that suggest adaptations to an arboreal habit. Despite the irony of their retrieval from deposits of the Nullarbor "Treeless" Plain, forelimb morphology clearly shows that the species of Bohra were well adapted to an arboreal habitat.

Timing and dynamics of Late Pleistocene mammal extinctions in southwestern Australia.

Explaining the Late Pleistocene demise of many of the world's larger terrestrial vertebrates is arguably the most enduring and debated topic in Quaternary science. Australia lost >90% of its larger species by around 40 thousand years (ka) ago, but the relative importance of human impacts and increased aridity remains unclear. Resolving the debate has been hampered by a lack of sites spanning the last glacial cycle. Here we report on an exceptional faunal succession from Tight Entrance Cave, southwestern Australia, which shows persistence of a diverse mammal community for at least 100 ka leading up to the earliest regional evidence of humans at 49 ka. Within 10 millennia, all larger mammals except the gray kangaroo and thylacine are lost from the regional record. Stable-isotope, charcoal, and small-mammal records reveal evidence of environmental change from 70 ka, but the extinctions occurred well in advance of the most extreme climatic phase. We conclude that the arrival of humans was probably decisive in the southwestern Australian extinctions, but that changes in climate and fire activity may have played facilitating roles. One-factor explanations for the Pleistocene extinctions in Australia are likely oversimplistic.

Extinction implications of a chenopod browse diet for a giant Pleistocene kangaroo.

Kangaroos are the world's most diverse group of herbivorous marsupials. Following late-Miocene intensification of aridity and seasonality, they radiated across Australia, becoming the continent's ecological equivalents of the artiodactyl ungulates elsewhere. Their diversity peaked during the Pleistocene, but by approximately 45,000 years ago, 90% of larger kangaroos were extinct, along with a range of other giant species. Resolving whether climate change or human arrival was the principal extinction cause remains highly contentious. Here we combine craniodental morphology, stable-isotopic, and dental microwear data to reveal that the largest-ever kangaroo, Procoptodon goliah, was a chenopod browse specialist, which may have had a preference for Atriplex (saltbushes), one of a few dicots using the C(4) photosynthetic pathway. Furthermore, oxygen isotope signatures of P. goliah tooth enamel show that it drank more in low-rainfall areas than its grazing contemporaries, similar to modern saltbush feeders. Saltbushes and chenopod shrublands in general are poorly flammable, so landscape burning by humans is unlikely to have caused a reduction in fodder driving the species to extinction. Aridity is discounted as a primary cause because P. goliah evolved in response to increased aridity and disappeared during an interval wetter than many it survived earlier. Hunting by humans, who were also bound to water, may have been a more decisive factor in the extinction of this giant marsupial.

An arid-adapted middle Pleistocene vertebrate fauna from south-central Australia.

How well the ecology, zoogeography and evolution of modern biotas is understood depends substantially on knowledge of the Pleistocene. Australia has one of the most distinctive, but least understood, Pleistocene faunas. Records from the western half of the continent are especially rare. Here we report on a diverse and exceptionally well preserved middle Pleistocene vertebrate assemblage from caves beneath the arid, treeless Nullarbor plain of south-central Australia. Many taxa are represented by whole skeletons, which together serve as a template for identifying fragmentary, hitherto indeterminate, remains collected previously from Pleistocene sites across southern Australia. A remarkable eight of the 23 Nullarbor kangaroos are new, including two tree-kangaroos. The diverse herbivore assemblage implies substantially greater floristic diversity than that of the modern shrub steppe, but all other faunal and stable-isotope data indicate that the climate was very similar to today. Because the 21 Nullarbor species that did not survive the Pleistocene were well adapted to dry conditions, climate change (specifically, increased aridity) is unlikely to have been significant in their extinction.