Extinction of eastern Sahul megafauna coincides with sustained environmental deterioration

Genome of the endangered eastern quoll (Dasyurus viverrinus) reveals signatures of historical decline and pelage color evolution

The eastern quoll (Dasyurus viverrinus) is an endangered marsupial native to Australia. Since the extirpation of its mainland populations in the 20th century, wild eastern quolls have been restricted to two islands at the southern end of their historical range. Eastern quolls are the subject of captive breeding programs and attempts have been made to re-establish a population in mainland Australia. However, few resources currently exist to guide the genetic management of this species. Here, we generated a reference genome for the eastern quoll with gene annotations supported by multi-tissue transcriptomes. Our assembly is among the most complete marsupial genomes currently available. Using this assembly, we infer the species' demographic history, identifying potential evidence of a long-term decline beginning in the late Pleistocene. Finally, we identify a deletion at the ASIP locus that likely underpins pelage color differences between the eastern quoll and the closely related Tasmanian devil (Sarcophilus harrisii).

Physiography, foraging mobility, and the first peopling of Sahul

The route and speed of migration into Sahul by Homo sapiens remain a major research question in archaeology. Here, we introduce an approach which models the impact of the physical environment on human mobility by combining time-evolving landscapes with Lévy walk foraging patterns, this latter accounting for a combination of short-distance steps and occasional longer moves that hunter-gatherers likely utilised for efficient exploration of new environments. Our results suggest a wave of dispersal radiating across Sahul following riverine corridors and coastlines. Estimated migration speeds, based on archaeological sites and predicted travelled distances, fall within previously reported range from Sahul and other regions. From our mechanistic movement simulations, we then analyse the likelihood of archaeological sites and highlight areas in Australia that hold archaeological potential. Our approach complements existing methods and provides interesting perspectives on the Pleistocene archaeology of Sahul that could be applied to other regions around the world.

Reconstructing Pleistocene Australian herbivore megafauna diet using calcium and strontium isotopes

Isotopes in fossil tooth enamel provide robust tools for reconstructing food webs, which have been understudied in Australian megafauna. To delineate the isotopic composition of primary consumers and understand dietary behaviour at the base of the food web, we investigate calcium (Ca) and strontium (Sr) isotope compositions of Pleistocene marsupial herbivores from Wellington Caves and Bingara (New South Wales, Australia). Sr isotopes suggest small home ranges across giant and smaller marsupial herbivores. Ca isotopes in Pleistocene marsupial herbivores cover the same range as those in modern wombats and placental herbivores. Early forming teeth are depleted in heavy Ca isotopes compared to late-forming teeth of a given individual, suggesting a weaning signal. Distinct Ca compositions between taxa can be interpreted as dietary niches. Some niches conform to previous dietary reconstructions of taxa, while others provide new insights into niche differentiation across Australian herbivores. Combined with the small roaming ranges suggested by Sr isotopes, the Ca isotope niche diversity suggests rich ecosystems, supporting a diversity of taxa with various diets in a small area.

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.

Back to the future: The advantage of studying key events in human evolution using a new high resolution radiocarbon method

Radiocarbon dating is the most widely applied dating method in archaeology, especially in human evolution studies, where it is used to determine the chronology of key events, such as the replacement of Neanderthals by modern humans in Europe. However, the method does not always provide precise and accurate enough ages to understand the important processes of human evolution. Here we review the newest method developments in radiocarbon dating ('Radiocarbon 3.0'), which can lead us to much better chronologies and understanding of the major events in recent human evolution. As an example, we apply these new methods to discuss the dating of the important Palaeolithic site of Bacho Kiro (Bulgaria).

Time-calibrated phylogeny and ecological niche models indicate Pliocene aridification drove intraspecific diversification of brushtail possums in Australia

Major aridification events in Australia during the Pliocene may have had significant impact on the distribution and structure of widespread species. To explore the potential impact of Pliocene and Pleistocene climate oscillations, we estimated the timing of population fragmentation and past connectivity of the currently isolated but morphologically similar subspecies of the widespread brushtail possum (Trichosurus vulpecula). We use ecological niche modeling (ENM) with the current fragmented distribution of brushtail possums to estimate the environmental envelope of this marsupial. We projected the ENM on models of past climatic conditions in Australia to infer the potential distribution of brushtail possums over 6 million years. D-loop haplotypes were used to describe population structure. From shotgun sequencing, we assembled whole mitochondrial DNA genomes and estimated the timing of intraspecific divergence. Our projections of ENMs suggest current possum populations were unlikely to have been in contact during the Pleistocene. Although lowered sea level during glacial periods enabled connection with habitat in Tasmania, climate fluctuation during this time would not have facilitated gene flow over much of Australia. The most recent common ancestor of sampled intraspecific diversity dates to the early Pliocene when continental aridification caused significant changes to Australian ecology and Trichosurus vulpecula distribution was likely fragmented. Phylogenetic analysis revealed that the subspecies T. v. hypoleucus (koomal; southwest), T. v. arnhemensis (langkurr; north), and T. v. vulpecula (bilda; southeast) correspond to distinct mitochondrial lineages. Despite little phenotypic differentiation, Trichosurus vulpecula populations probably experienced little gene flow with one another since the Pliocene, supporting the recognition of several subspecies and explaining their adaptations to the regional plant assemblages on which they feed.

Ancient proteins resolve controversy over the identity of Genyornis eggshell

The realization that ancient biomolecules are preserved in "fossil" samples has revolutionized archaeological science. Protein sequences survive longer than DNA, but their phylogenetic resolution is inferior; therefore, careful assessment of the research questions is required. Here, we show the potential of ancient proteins preserved in Pleistocene eggshell in addressing a longstanding controversy in human and animal evolution: the identity of the extinct bird that laid large eggs which were exploited by Australia's indigenous people. The eggs had been originally attributed to the iconic extinct flightless bird Genyornis newtoni (†Dromornithidae, Galloanseres) and were subsequently dated to before 50 ± 5 ka by Miller et al. [Nat. Commun. 7, 10496 (2016)]. This was taken to represent the likely extinction date for this endemic megafaunal species and thus implied a role of humans in its demise. A contrasting hypothesis, according to which the eggs were laid by a large mound-builder megapode (Megapodiidae, Galliformes), would therefore acquit humans of their responsibility in the extinction of Genyornis. Ancient protein sequences were reconstructed and used to assess the evolutionary proximity of the undetermined eggshell to extant birds, rejecting the megapode hypothesis. Authentic ancient DNA could not be confirmed from these highly degraded samples, but morphometric data also support the attribution of the eggshell to Genyornis. When used in triangulation to address well-defined hypotheses, paleoproteomics is a powerful tool for reconstructing the evolutionary history in ancient samples. In addition to the clarification of phylogenetic placement, these data provide a more nuanced understanding of the modes of interactions between humans and their environment.

Miocene fossils from the southeastern Pacific shed light on the last radiation of marine crocodylians

The evolution of crocodylians as sea dwellers remains obscure because living representatives are basically freshwater inhabitants and fossil evidence lacks crucial aspects about crocodylian occupation of marine ecosystems. New fossils from marine deposits of Peru reveal that crocodylians were habitual coastal residents of the southeastern Pacific (SEP) for approximately 14 million years within the Miocene (ca 19 to 5 Ma), an epoch including the highest global peak of marine crocodylian diversity. The assemblage of the SEP comprised two long and slender-snouted (longirostrine) taxa of the Gavialidae: the giant Piscogavialis and a new early diverging species, Sacacosuchus cordovai. Although living gavialids (Gavialis and Tomistoma) are freshwater forms, this remarkable fossil record and a suite of evolutionary morphological analyses reveal that the whole evolution of marine crocodylians pertained to the gavialids and their stem relatives (Gavialoidea). This adaptive radiation produced two longirostrine ecomorphs with dissimilar trophic roles in seawaters and involved multiple transmarine dispersals to South America and most landmasses. Marine gavialoids were shallow sea dwellers, and their Cenozoic diversification was influenced by the availability of coastal habitats. Soon after the richness peak of the Miocene, gavialoid crocodylians disappeared from the sea, probably as part of the marine megafauna extinction of the Pliocene.

Divergent locomotor evolution in "giant" kangaroos: Evidence from foot bone bending resistances and microanatomy

The extinct sthenurine (giant, short-faced) kangaroos have been proposed to have a different type of locomotor behavior to extant (macropodine) kangaroos, based both on physical limitations (the size of many exceeds the proposed limit for hopping) and anatomical features (features of the hind limb anatomy suggestive of weight-bearing on one leg at a time). Here, we use micro computerised tomography (micro-CT) scans of the pedal bones of six kangaroos, three sthenurine, and three macropodine, ranging from ~50 to 150 kg, to investigate possible differences in bone resistances to bending and cortical bone distribution that might relate to differences in locomotion. Using second moment of area analysis, we show differences in resistance to bending between the two subfamilies. Distribution of cortical bone shows that sthenurines had less resistant calcaneal tubers, implying a different foot posture during locomotion, and the long foot bones were more resistant to the medial bending stresses. These differences were the most pronounced between Pleistocene monodactyl sthenurines (Sthenurus stirlingi and Procoptodon browneorum) and the two species of Macropus (the extant M. giganteus and the extinct M. cf. M. titan) and support the hypothesis that these derived sthenurines employed bipedal striding. The Miocene sthenurine Hadronomas retains some more macropodine-like features of bone resistance to bending, perhaps reflecting its retention of the fifth pedal digit. The Pleistocene macropodine Protemnodon has a number of unique features, possibly indicative of a type of locomotion unlike the other kangaroos.

Comment on "A global environmental crisis 42,000 years ago"

Cooper et al. (Research Articles, 19 February 2021, p. 811) propose that the Laschamps geomagnetic inversion ~42 ka BP drove global climatic shifts, causing major behavioural changes within prehistoric groups, and events of human and megafaunal extinction. Other scientific studies indicate that this proposition is unproven from the current archaeological, paleoanthropological, and genetic records.

Response to Comment on "A global environmental crisis 42,000 years ago"

[Figure: see text].

Distal Humeral Morphology Indicates Locomotory Divergence in Extinct Giant Kangaroos

Previous studies of the morphology of the humerus in kangaroos showed that the shape of the proximal humerus could distinguish between arboreal and terrestrial taxa among living mammals, and that the extinct “giant” kangaroos (members of the extinct subfamily Sthenurinae and the extinct macropodine genus Protemnodon) had divergent humeral anatomies from extant kangaroos. Here, we use 2D geometric morphometrics to capture the shape of the distal humerus in a range of extant and extinct marsupials and obtain similar results: sthenurines have humeral morphologies more similar to arboreal mammals, while large Protemnodon species (P. brehus and P. anak) have humeral morphologies more similar to terrestrial quadrupedal mammals. Our results provide further evidence for prior hypotheses: that sthenurines did not employ a locomotor mode that involved loading the forelimbs (likely employing bipedal striding as an alternative to quadrupedal or pentapedal locomotion at slow gaits), and that large Protemnodon species were more reliant on quadrupedal locomotion than their extant relatives. This greater diversity of locomotor modes among large Pleistocene kangaroos echoes studies that show a greater diversity in other aspects of ecology, such as diet and habitat occupancy.

Species identification of Australian marsupials using collagen fingerprinting

The study of faunal remains from archaeological sites is often complicated by the presence of large numbers of highly fragmented, morphologically unidentifiable bones. In Australia, this is the combined result of harsh preservation conditions and frequent scavenging by marsupial carnivores. The collagen fingerprinting method known as zooarchaeology by mass spectrometry (ZooMS) offers a means to address these challenges and improve identification rates of fragmented bones. Here, we present novel ZooMS peptide markers for 24 extant marsupial and monotreme species that allow for genus-level distinctions between these species. We demonstrate the utility of these new peptide markers by using them to taxonomically identify bone fragments from a nineteenth-century colonial-era pearlshell fishery at Bandicoot Bay, Barrow Island. The suite of peptide biomarkers presented in this study, which focus on a range of ecologically and culturally important species, have the potential to significantly amplify the zooarchaeological and paleontological record of Australia.

Phylogenetic analysis of a new morphological dataset elucidates the evolutionary history of Crocodylia and resolves the long-standing gharial problem

First appearing in the latest Cretaceous, Crocodylia is a clade of semi-aquatic, predatory reptiles, defined by the last common ancestor of extant alligators, caimans, crocodiles, and gharials. Despite large strides in resolving crocodylian interrelationships over the last three decades, several outstanding problems persist in crocodylian systematics. Most notably, there has been persistent discordance between morphological and molecular datasets surrounding the affinities of the extant gharials, Gavialis gangeticus and Tomistoma schlegelii. Whereas molecular data consistently support a sister taxon relationship, in which they are more closely related to crocodylids than to alligatorids, morphological data indicate that Gavialis is the sister taxon to all other extant crocodylians. Here we present a new morphological dataset for Crocodylia based on a critical reappraisal of published crocodylian character data matrices and extensive firsthand observations of a global sample of crocodylians. This comprises the most taxonomically comprehensive crocodylian dataset to date (144 OTUs scored for 330 characters) and includes a new, illustrated character list with modifications to the construction and scoring of characters, and 46 novel characters. Under a maximum parsimony framework, our analyses robustly recover Gavialis as more closely related to Tomistoma than to other extant crocodylians for the first time based on morphology alone. This result is recovered regardless of the weighting strategy and treatment of quantitative characters. However, analyses using continuous characters and extended implied weighting (with high k-values) produced the most resolved, well-supported, and stratigraphically congruent topologies overall. Resolution of the gharial problem reveals that: (1) several gavialoids lack plesiomorphic features that formerly drew them towards the stem of Crocodylia; and (2) more widespread similarities occur between species traditionally divided into tomistomines and gavialoids, with these interpreted here as homology rather than homoplasy. There remains significant temporal incongruence regarding the inferred divergence timing of the extant gharials, indicating that several putative gavialids ('thoracosaurs') are incorrectly placed and require future re-appraisal. New alligatoroid interrelationships include: (1) support for a North American origin of Caimaninae in the latest Cretaceous; (2) the recovery of the early Paleogene South American taxon Eocaiman as a 'basal' alligatoroid; and (3) the paraphyly of the Cenozoic European taxon Diplocynodon. Among crocodyloids, notable results include modifications to the taxonomic content of Mekosuchinae, including biogeographic affinities of this clade with latest Cretaceous-early Paleogene Asian crocodyloids. In light of our new results, we provide a comprehensive review of the evolutionary and biogeographic history of Crocodylia, which included multiple instances of transoceanic and continental dispersal.

Thinking about the Biodiversity Loss in This Changing World

Extinction of species has been a recurrent phenomenon in the history of our planet, but it was generally outweighed in the course of quite a long geological time by the appearance of new species, except, especially, for the five geologically short times when the so-called “Big Five” mass extinctions occurred. Could the current decline in biodiversity be considered as a signal of an ongoing, human-driven sixth mass extinction? This note briefly examines some issues related to: (i) The hypothesized current extinction rate and the magnitude of contemporary global biodiversity loss; (ii) the challenges of comparing them to the background extinction rate and the magnitude of the past Big Five mass extinction events; (iii) briefly considering the effects of the main anthropogenic stressors on ecosystems, including the risk of the emergence of pandemic diseases. A comparison between the Pleistocene fauna dynamics with the present defaunation process and the cascading effects of recent anthropogenic actions on ecosystem structure and functioning suggests that habitat degradation, ecosystem fragmentation, and alien species introduction are important stressors increasing the negative impact on biodiversity exerted by anthropogenic-driven climate changes and their connected effects. In addition, anthropogenic ecological stressors such as urbanization, landscapes, and wildlife trade, creating new opportunities for virus transmission by augmenting human contact with wild species, are among the main factors triggering pandemic diseases.

A new giant sauropod, Australotitan cooperensis gen. et sp. nov., from the mid-Cretaceous of Australia

A new giant sauropod, Australotitan cooperensis gen. et sp. nov., represents the first record of dinosaurs from the southern-central Winton Formation of the Eromanga Basin, Australia. We estimate the type locality to be 270–300 m from the base of the Winton Formation and compare this to the semi-contemporaneous sauropod taxa, Diamantinasaurus matildaeHocknull et al., 2009, Wintonotitan wattsiHocknull et al., 2009 and Savannasaurus elliottorumPoropat et al., 2016. The new titanosaurian is the largest dinosaur from Australia as represented by osteological remains and based on limb-size comparisons it reached a size similar to that of the giant titanosaurians from South America. Using 3-D surface scan models we compare features of the appendicular skeleton that differentiate Australotitan cooperensis gen. et sp. nov. as a new taxon. A key limitation to the study of sauropods is the inability to easily and directly compare specimens. Therefore, 3-D cybertypes have become a more standard way to undertake direct comparative assessments. Uncoloured, low resolution, and uncharacterized 3-D surface models can lead to misinterpretations, in particular identification of pre-, syn- and post-depositional distortion. We propose a method for identifying, documenting and illustrating these distortions directly onto the 3-D geometric surface of the models using a colour reference scheme. This new method is repeatable for researchers when observing and documenting specimens including taphonomic alterations and geometric differences. A detailed comparative and preliminary computational phylogenetic assessment supports a shared ancestry for all four Winton Formation taxa, albeit with limited statistical support. Palaeobiogeographical interpretations from these resultant phylogenetic hypotheses remain equivocal due to contrary Asian and South American relationships with the Australian taxa. Temporal and palaeoenvironmental differences between the northern and southern-central sauropod locations are considered to explain the taxonomic and morphological diversity of sauropods from the Winton Formation. Interpretations for this diversity are explored, including an eco-morphocline and/or chronocline across newly developed terrestrial environments as the basin fills.

Low elbow mobility indicates unique forelimb posture and function in a giant extinct marsupial

Joint mobility is a key factor in determining the functional capacity of tetrapod limbs, and is important in palaeobiological reconstructions of extinct animals. Recent advances have been made in quantifying osteological joint mobility using virtual computational methods; however, these approaches generally focus on the proximal limb joints and have seldom been applied to fossil mammals. Palorchestes azael is an enigmatic, extinct ~1000 kg marsupial with no close living relatives, whose functional ecology within Australian Pleistocene environments is poorly understood. Most intriguing is its flattened elbow morphology, which has long been assumed to indicate very low mobility at this important joint. Here, we tested elbow mobility via virtual range of motion (ROM) mapping and helical axis analysis, to quantitatively explore the limits of Palorchestes' elbow movement and compare this with their living and extinct relatives, as well as extant mammals that may represent functional analogues. We find that Palorchestes had the lowest elbow mobility among mammals sampled, even when afforded joint translations in addition to rotational degrees of freedom. This indicates that Palorchestes was limited to crouched forelimb postures, something highly unusual for mammals of this size. Coupled flexion and abduction created a skewed primary axis of movement at the elbow, suggesting an abducted forelimb posture and humeral rotation gait that is not found among marsupials and unlike that seen in any large mammals alive today. This work introduces new quantitative methods and demonstrates the utility of comparative ROM mapping approaches, highlighting that Palorchestes' forelimb function was unlike its contemporaneous relatives and appears to lack clear functional analogues among living mammals.

A Comprehensive Approach to Detect Hybridization Sheds Light on the Evolution of Earth's Largest Lizards

Hybridization between species occurs more frequently in vertebrates than traditionally thought but distinguishing ancient hybridization from other phenomena that generate similar evolutionary patterns remains challenging. Here, we used a comprehensive workflow to discover evidence of ancient hybridization between the Komodo dragon (Varanus komodoensis) from Indonesia and a common ancestor of an Australian group of monitor lizards known colloquially as sand monitors. Our data comprises >300 nuclear loci, mitochondrial genomes, phenotypic data, fossil and contemporary records, and past/present climatic data. We show that the four sand monitor species share more nuclear alleles with V. komodoensis than expected given a bifurcating phylogeny, likely as a result of hybridization between the latter species and a common ancestor of sand monitors. Sand monitors display phenotypes that are intermediate between their closest relatives and V. komodoensis. Biogeographic analyses suggest that V. komodoensis and ancestral sand monitors co-occurred in northern Australia. In agreement with the fossil record, this provides further evidence that the Komodo dragon once inhabited the Australian continent. Our study shows how different sources of evidence can be used to thoroughly characterize evolutionary histories that deviate from a treelike pattern, that hybridization can have long-lasting effects on phenotypes and that detecting hybridization can improve our understanding of evolutionary and biogeographic patterns.

Australia's prehistoric 'swamp king': revision of the Plio-Pleistocene crocodylian genus Pallimnarchus de Vis, 1886

The crocodylian fossil record from the Cenozoic of Australasia is notable for its rich taxonomic diversity, and is primarily represented by members of the clade Mekosuchinae. Reports of crocodylian fossils from Australia date back to the late nineteenth century. In 1886, Charles Walter de Vis proposed the name Pallimnarchus pollens for crocodylian fossils from southeast Queensland-the first binomen given to an extinct crocodylian taxon from Australia. Pallimnarchus has come to be regarded as a large, broad-snouted crocodylian from Australia's Plio-Pleistocene, and numerous specimens, few of which are sufficiently complete, have been assigned to it by several authors throughout the twentieth century. In the late 1990s, the genus was expanded to include a second species, Pallimnarchus gracilis. Unfortunately, the original syntype series described as Pallimnarchus pollens is very fragmentary and derives from more than one taxon, while a large part of the subsequently selected lectotype specimen is missing. Because descriptions and illustrations of the complete lectotype do not reveal any autapomorphic features, we propose that Pallimnarchus pollens should be regarded as a nomen dubium. Following this decision, the fossil material previously referred to Pallimnarchus is of uncertain taxonomic placement. A partial skull, formerly assigned to Pallimnarchus pollens and known as 'Geoff Vincent's specimen', possesses many features of diagnostic value and is therefore used as basis to erect a new genus and species-Paludirex vincenti gen. et sp. nov. A comprehensive description is given for the osteology of 'Geoff Vincent's specimen' as well as aspects of its palaeoneurology, the latter being a first for an extinct Australian crocodyliform. The newly named genus is characterized by a unique combination of premaxillary features such as a distinctive arching of the anterior alveolar processes of the premaxillae, a peculiar arrangement of the first two premaxillary alveoli and a large size disparity between the 3rd and 4th premaxillary alveoli. These features presently allow formal recognition of two species within the genus, Paludirex vincenti and Paludirex gracilis comb. nov., with the former having comparatively more robust rostral proportions than the latter. The Paludirex vincenti holotype comes from the Pliocene Chinchilla Sand of the Darling Downs, south-eastern Queensland, whereas the material assigned to Paludirex gracilis is from the Pleistocene of Terrace Site Local Fauna, Riversleigh, northwest Queensland. Phylogenetic analyses recover Paludirex vincenti as a mekosuchine, although further cladistic assessments are needed to better understand the relationships within the clade.