Late pleistocene Australian marsupial DNA clarifies the affinities of extinct megafaunal kangaroos and wallabies

Ancient genomes reveal over two thousand years of dingo population structure

Dingoes are culturally and ecologically important free-living canids whose ancestors arrived in Australia over 3,000 B.P., likely transported by seafaring people. However, the early history of dingoes in Australia-including the number of founding populations and their routes of introduction-remains uncertain. This uncertainty arises partly from the complex and poorly understood relationship between modern dingoes and New Guinea singing dogs, and suspicions that post-Colonial hybridization has introduced recent domestic dog ancestry into the genomes of many wild dingo populations. In this study, we analyzed genome-wide data from nine ancient dingo specimens ranging in age from 400 to 2,746 y old, predating the introduction of domestic dogs to Australia by European colonists. We uncovered evidence that the continent-wide population structure observed in modern dingo populations had already emerged several thousand years ago. We also detected excess allele sharing between New Guinea singing dogs and ancient dingoes from coastal New South Wales (NSW) compared to ancient dingoes from southern Australia, irrespective of any post-Colonial hybrid ancestry in the genomes of modern individuals. Our results are consistent with several demographic scenarios, including a scenario where the ancestry of dingoes from the east coast of Australia results from at least two waves of migration from source populations with varying affinities to New Guinea singing dogs. We also contribute to the growing body of evidence that modern dingoes derive little genomic ancestry from post-Colonial hybridization with other domestic dog lineages, instead descending primarily from ancient canids introduced to Sahul thousands of years ago.

Mitogenome of the extinct Desert 'rat-kangaroo' times the adaptation to aridity in macropodoids

The evolution of Australia's distinctive marsupial fauna has long been linked to the onset of continent-wide aridity. However, how this profound climate change event affected the diversification of extant lineages is still hotly debated. Here, we assemble a DNA sequence dataset of Macropodoidea-the clade comprising kangaroos and their relatives-that incorporates a complete mitogenome for the Desert 'rat-kangaroo', Caloprymnus campestris. This enigmatic species went extinct nearly 90 years ago and is known from a handful of museum specimens. Caloprymnus is significant because it was the only macropodoid restricted to extreme desert environments, and therefore calibrates the group's specialisation for increasingly arid conditions. Our robustly supported phylogenies nest Caloprymnus amongst the bettongs Aepyprymnus and Bettongia. Dated ancestral range estimations further reveal that the Caloprymnus-Bettongia lineage originated in nascent xeric settings during the middle to late Miocene, ~ 12 million years ago (Ma), but subsequently radiated into fragmenting mesic habitats after the Pliocene to mid-Pleistocene. This timeframe parallels the ancestral divergences of kangaroos in woodlands and forests, but predates their adaptive dispersal into proliferating dry shrublands and grasslands from the late Miocene to mid-Pleistocene, after ~ 7 Ma. We thus demonstrate that protracted changes in both climate and vegetation likely staged the emergence of modern arid zone macropodoids.

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.

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.

Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes

Marine sedimentary ancient DNA (sedaDNA) is increasingly used to study past ocean ecosystems, however, studies have been severely limited by the very low amounts of DNA preserved in the subseafloor, and the lack of bioinformatic tools to authenticate sedaDNA in metagenomic data. We applied a hybridisation capture 'baits' technique to target marine eukaryote sedaDNA (specifically, phyto- and zooplankton, 'Planktonbaits1'; and harmful algal bloom taxa, 'HABbaits1'), which resulted in up to 4- and 9-fold increases, respectively, in the relative abundance of eukaryotes compared to shotgun sequencing. We further used the bioinformatic tool 'HOPS' to authenticate the sedaDNA component, establishing a new proxy to assess sedaDNA authenticity, "% eukaryote sedaDNA damage", that is positively correlated with subseafloor depth. We used this proxy to report the first-ever DNA damage profiles from a marine phytoplankton species, the ubiquitous coccolithophore Emiliania huxleyi. Our approach opens new avenues for the detailed investigation of long-term change and evolution of marine eukaryotes over geological timescales.

A new family of diprotodontian marsupials from the latest Oligocene of Australia and the evolution of wombats, koalas, and their relatives (Vombatiformes)

We describe the partial cranium and skeleton of a new diprotodontian marsupial from the late Oligocene (~26–25 Ma) Namba Formation of South Australia. This is one of the oldest Australian marsupial fossils known from an associated skeleton and it reveals previously unsuspected morphological diversity within Vombatiformes, the clade that includes wombats (Vombatidae), koalas (Phascolarctidae) and several extinct families. Several aspects of the skull and teeth of the new taxon, which we refer to a new family, are intermediate between members of the fossil family Wynyardiidae and wombats. Its postcranial skeleton exhibits features associated with scratch-digging, but it is unlikely to have been a true burrower. Body mass estimates based on postcranial dimensions range between 143 and 171 kg, suggesting that it was ~5 times larger than living wombats. Phylogenetic analysis based on 79 craniodental and 20 postcranial characters places the new taxon as sister to vombatids, with which it forms the superfamily Vombatoidea as defined here. It suggests that the highly derived vombatids evolved from wynyardiid-like ancestors, and that scratch-digging adaptations evolved in vombatoids prior to the appearance of the ever-growing (hypselodont) molars that are a characteristic feature of all post-Miocene vombatids. Ancestral state reconstructions on our preferred phylogeny suggest that bunolophodont molars are plesiomorphic for vombatiforms, with full lophodonty (characteristic of diprotodontoids) evolving from a selenodont morphology that was retained by phascolarctids and ilariids, and wynyardiids and vombatoids retaining an intermediate selenolophodont condition. There appear to have been at least six independent acquisitions of very large (>100 kg) body size within Vombatiformes, several having already occurred by the late Oligocene.

Proximal Humerus Morphology Indicates Divergent Patterns of Locomotion in Extinct Giant Kangaroos

Sthenurine kangaroos, extinct “giant kangaroos” known predominantly from the Plio-Pleistocene, have been proposed to have used bipedal striding as a mode of locomotion, based on the morphology of their hind limbs. However, sthenurine forelimb morphology has not been considered in this context, and has important bearing as to whether these kangaroos employed quadrupedal or pentapedal locomotion as a slow gait, as in extant kangaroos. Study of the correlation of morphology of the proximal humerus in a broad range of therian mammals shows that humeral morphology is indicative of the degree of weight-bearing on the forelimbs during locomotion, with terrestrial species being distinctly different from arboreal ones. Extant kangaroos have a proximal humeral morphology similar to extant scansorial (semi-arboreal) mammals, but sthenurine humeri resemble those of suspensory arboreal taxa, which rarely bear weight on their forelimbs, supporting the hypothesis that they used bipedal striding rather than quadrupedal locomotion at slow gaits. The humeral morphology of the enigmatic extinct “giant wallaby,” Protemnodon, may be indicative of a greater extent of quadrupedal locomotion than in extant kangaroos.

The anatomy of a crushing bite: The specialised cranial mechanics of a giant extinct kangaroo

The Sthenurinae were a diverse subfamily of short-faced kangaroos that arose in the Miocene and diversified during the Pliocene and Pleistocene. Many species possessed skull morphologies that were relatively structurally reinforced with bone, suggesting that they were adapted to incorporate particularly resistant foods into their diets. However, the functional roles of many unique, robust features of the sthenurine cranium are not yet clearly defined. Here, the finite element method is applied to conduct a comprehensive analysis of unilateral biting along the cheek tooth battery of a well-represented sthenurine, Simosthenurus occidentalis. The results are compared with those of an extant species considered to be of most similar ecology and cranial proportions to this species, the koala (Phascolarctos cinereus). The simulations reveal that the cranium of S. occidentalis could produce and withstand comparatively high forces during unilateral biting. Its greatly expanded zygomatic arches potentially housed enlarged zygomaticomandibularis muscles, shown here to reduce the risk of dislocation of the temporomandibular joint during biting with the rear of a broad, extensive cheek tooth row. This may also be a function of the zygomaticomandibularis in the giant panda (Ailuropoda melanoleuca), another species known to exhibit an enlarged zygomatic arch and hypertrophy of this muscle. Furthermore, the expanded frontal plates of the S. occidentalis cranium form broad arches of bone with the braincase and deepened maxillae that each extend from the anterior tooth rows to their opposing jaw joints. These arches are demonstrated here to be a key feature in resisting high torsional forces during unilateral premolar biting on large, resistant food items. This supports the notion that S. occidentalis fed thick, lignified vegetation directly to the cheek teeth in a similar manner to that described for the giant panda when crushing mature bamboo culms.

What caused extinction of the Pleistocene megafauna of Sahul?

During the Pleistocene, Australia and New Guinea supported a rich assemblage of large vertebrates. Why these animals disappeared has been debated for more than a century and remains controversial. Previous synthetic reviews of this problem have typically focused heavily on particular types of evidence, such as the dating of extinction and human arrival, and have frequently ignored uncertainties and biases that can lead to misinterpretation of this evidence. Here, we review diverse evidence bearing on this issue and conclude that, although many knowledge gaps remain, multiple independent lines of evidence point to direct human impact as the most likely cause of extinction.

Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms

The recent expansion of next-generation sequencing has significantly improved biological research. Nevertheless, deep exploration of genomes or metagenomic samples remains difficult because of the sequencing depth and the associated costs required. Therefore, different partitioning strategies have been developed to sequence informative subsets of studied genomes. Among these strategies, hybridization capture has proven to be an innovative and efficient tool for targeting and enriching specific biomarkers in complex DNA mixtures. It has been successfully applied in numerous areas of biology, such as exome resequencing for the identification of mutations underlying Mendelian or complex diseases and cancers, and its usefulness has been demonstrated in the agronomic field through the linking of genetic variants to agricultural phenotypic traits of interest. Moreover, hybridization capture has provided access to underexplored, but relevant fractions of genomes through its ability to enrich defined targets and their flanking regions. Finally, on the basis of restricted genomic information, this method has also allowed the expansion of knowledge of nonreference species and ancient genomes and provided a better understanding of metagenomic samples. In this review, we present the major advances and discoveries permitted by hybridization capture and highlight the potency of this approach in all areas of biology.

Genomic Data from Extinct North American Camelops Revise Camel Evolutionary History

Recent advances in paleogenomic technologies have enabled an increasingly detailed understanding of the evolutionary relationships of now-extinct mammalian taxa. However, a number of enigmatic Quaternary species have never been characterized with molecular data, often because available fossils are rare or are found in environments that are not optimal for DNA preservation. Here, we analyze paleogenomic data extracted from bones attributed to the late Pleistocene western camel, Camelops cf. hesternus, a species that was distributed across central and western North America until its extinction approximately 13,000 years ago. Despite a modal sequence length of only around 35 base pairs, we reconstructed high-coverage complete mitochondrial genomes and low-coverage partial nuclear genomes for each specimen. We find that Camelops is sister to African and Asian bactrian and dromedary camels, to the exclusion of South American camelids (llamas, guanacos, alpacas, and vicuñas). These results contradict previous morphology-based phylogenetic models for Camelops, which suggest instead a closer relationship between Camelops and the South American camelids. The molecular data imply a Late Miocene divergence of the Camelops clade from lineages that separately gave rise to the extant camels of Eurasia. Our results demonstrate the increasing capacity of modern paleogenomic methods to resolve evolutionary relationships among distantly related lineages.