Ancient Viral Integrations in Marsupials: A Potential Antiviral Defence

Marsupial viruses are understudied compared to their eutherian mammal counterparts, although they may pose severe threats to vulnerable marsupial populations. Genomic viral integrations, termed endogenous viral elements (EVEs) could protect the host from infection. It is widely known past viral infections and EVEs play an active role in antiviral defence in invertebrates and plants. This study aimed to characterise actively transcribed EVEs in Australian marsupial species, because they may play an integral role in cellular defence against viruses. This study screened publicly available RNA sequencing datasets (n=35) and characterised 200 viral transcripts from thirteen Australian marsupial species. Of the 200 transcripts, 188 originated from either Bornaviridae, Filoviridae or Parvoviridae EVEs. The other 12 transcripts were from putative active infections from members of the Herpesviridae and Anelloviridae, and Hepadnaviridae. EVE transcripts (n=188) were mapped to marsupial genomes (where available, n=5/13) to identify the genomic insertion sites. Of the 188 transcripts, 117 mapped to 39 EVEs within the koala, bare-nosed wombat, tammar wallaby, brushtail possum and Tasmanian devil genomes. The remaining eight animals had no available genome (transcripts n=71). Every marsupial have Bornaviridae, Filoviridae and Parvoviridae EVEs, a trend widely observed in eutherian mammals. Whilst eutherian bornavirus EVEs are predominantly nucleoprotein-derived, marsupial bornavirus EVEs demonstrate a surprising replicase gene bias. We predicted these widely distributed EVEs were conserved within marsupials from ancient germline integrations, as many were over 65 million years old. One bornavirus replicase EVE, present in six marsupial genomes, was estimated to be 160 million years old, predating the American-Australian marsupial split. We considered transcription of these EVEs through small non-coding RNA as an ancient viral defence. Consistent with this, in koala small RNA sequence datasets we detected Bornaviridae replicase and Filoviridae nucleoprotein produced piRNA. These were enriched in testis tissue, suggesting they could protect marsupials from vertically transmitted viral integrations.

Using 3D geometric morphometrics to aid taxonomic and ecological understanding of a recent speciation event within a small Australian marsupial (genus Antechinus)

Taxonomic distinction of species forms the foundation of biodiversity assessments and conservation priorities. However, traditional morphological and/or genetics-based taxonomic assessments frequently miss the opportunity of elaborating on the ecological and functional context of species diversification. Here, we used 3D geometric morphometrics of the cranium to improve taxonomic differentiation and add eco-morphological characterisation of a young cryptic divergence within the marsupial carnivorous genus Antechinus. Specifically, we used 168 museum specimens to characterise the recently proposed clades A. stuartii “south”, A. stuartii “north” and A. subtropicus. Beyond slight differences attributable to overall size (and therefore not necessarily diagnostic), we also found clear allometry-independent shape variation. This allowed us to define new, easily measured diagnostic traits in the palate, which differentiate the three clades. Contrary to previous suggestions, we found no support for a latitudinal gradient as causing the differentiation between the clades. However, skull shape co-varied with temperature and precipitation seasonality, suggesting that the clades may be adapted to environmental variables that are likely to be impacted by climate change. Our study demonstrates the use of 3D geometric morphometrics to improve taxonomic diagnosis of cryptic mammalian species, while providing perspectives on the adaptive origins and potential future threats of mammalian diversity.

Viral fossils in marsupial genomes: secret cellular guardians

Genomic viral integrations, termed endogenous viral elements (EVEs), are fragments of viruses in host chromosomes that provide information about viral evolution and could even help protect the host from infection. In the present study we examined EVEs in thirteen different Australian marsupial species to identify trends in their integration, commonality and to investigate their possible cellular function. We found that marsupial EVEs are commonly derived from viruses of the Bornaviridae, Filoviridae and Parvoviridae families, and circulated up to 160 million years ago. We also show the EVEs are actively transcribed into both long and short RNA molecules in marsupials, and propose they are involved in a cellular defence mechanism to protect the germline from viral genomic invasion.

Intestines of non-uniform stiffness mold the corners of wombat feces

The bare-nosed wombat (Vombatus ursinus) is a fossorial, herbivorous, Australian marsupial, renowned for its cubic feces.

Did the thylacine violate the costs of carnivory? Body mass and sexual dimorphism of an iconic Australian marsupial

The relative body masses of predators and their prey strongly affect the predators' ecology. An accurate estimate of the mass of an extinct predator is therefore key to revealing its biology and the structure of the ecosystem it inhabited. Until its extinction, the thylacine was the largest extant carnivorous marsupial, but little data exist regarding its body mass, with an average of 29.5 kg the most commonly used estimate. According to the costs of carnivory model, this estimate predicts that thylacines would have focused on prey subequal to or larger than themselves; however, many studies of their functional morphology suggest a diet of smaller animals. Here, we present new body mass estimates for 93 adult thylacines, including two taxidermy specimens and four complete mounted skeletons, representing 40 known-sex specimens, using three-dimensional volumetric model-informed regressions. We demonstrate that prior estimates substantially overestimated average adult thylacine body mass. We show mixed-sex population mean (16.7 kg), mean male (19.7 kg), and mean female (13.7 kg) body masses well below prior estimates, and below the 21 kg costs of carnivory threshold. Our data show that the thylacine did not violate the costs of carnivory. The thylacine instead occupied the 14.5–21 kg predator/prey range characterized by small-prey predators capable of occasionally switching to relatively large-bodied prey if necessary.

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.