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We describe three new bandicoot species of the genus Galadi from the Miocene of Riversleigh World Heritage Area in northern Australia. The first species, which is represented by a complete dentary and several isolated upper molars, is restricted to Riversleigh's Faunal Zone B. It is the largest bandicoot as yet known from Riversleigh. The second species is represented by 19 specimens, including a partial skull and several maxillae and dentaries, from Riversleigh's Faunal Zone C. Several features distinguishing this species from the similarly sized type species G. speciosus are of interest, notably the presence of larger maxillopalatine fenestrae and additional maxillary fenestrae, incomplete centrocrista on all upper molars, a more complete posterior cingulum on upper molars, and higher degree of dental wear, which together suggest a more omnivorous diet. The third species is represented by a single maxillary, which exhibits a quite different combination of dental features compared with other Galadi species. All Galadi species appear to be restricted to Riversleigh's Faunal Zones B and C, which are interpreted to be early and middle Miocene in age, respectively, with rainforest habitats persisting throughout.

Phenotypic variation among species is a product of evolutionary changes to developmental programs 1 , 2 . However, how these changes generate novel morphological traits remains largely unclear. Here we studied the genomic and developmental basis of the mammalian gliding membrane, or patagium—an adaptative trait that has repeatedly evolved in different lineages, including in closely related marsupial species. Through comparative genomic analysis of 15 marsupial genomes, both from gliding and non-gliding species, we find that the Emx2 locus experienced lineage-specific patterns of accelerated cis -regulatory evolution in gliding species. By combining epigenomics, transcriptomics and in-pouch marsupial transgenics, we show that Emx2 is a critical upstream regulator of patagium development. Moreover, we identify different cis -regulatory elements that may be responsible for driving increased Emx2 expression levels in gliding species. Lastly, using mouse functional experiments, we find evidence that Emx2 expression patterns in gliders may have been modified from a pre-existing program found in all mammals. Together, our results suggest that patagia repeatedly originated through a process of convergent genomic evolution, whereby regulation of Emx2 was altered by distinct cis -regulatory elements in independently evolved species. Thus, different regulatory elements targeting the same key developmental gene may constitute an effective strategy by which natural selection has harnessed regulatory evolution in marsupial genomes to generate phenotypic novelty. Patagia—the mammalian gliding membrane—repeatedly originated through a process of convergent genomic evolution, whereby the regulation of Emx2 was altered by distinct cis -regulatory elements in independently evolved species.

An early date for mammal divergence Almost all living mammals are placentals. A key event in mammalian evolution was the divergence between the ancestors of today's placentals and those of the marsupials. The discovery of a fossil on the placental side of the split takes that divergence back 35 million years, to around 160 million years ago, deep into the Jurassic period. The fossil, from China, shows that the earliest members of the group that includes ourselves and most familiar mammals was a small creature adapted for climbing and scampering among the trees, presumably keeping well clear of the dinosaurs below. The age of the fossil suggests that there was a higher rate of mammal evolution in the Jurassic than previously believed. Placentals are the most abundant mammals that have diversified into every niche for vertebrates and dominated the world’s terrestrial biotas in the Cenozoic. A critical event in mammalian history is the divergence of eutherians, the clade inclusive of all living placentals, from the metatherian–marsupial clade 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 . Here we report the discovery of a new eutherian of 160 Myr from the Jurassic of China, which extends the first appearance of the eutherian–placental clade by about 35 Myr from the previous record, reducing and resolving a discrepancy between the previous fossil record and the molecular estimate for the placental–marsupial divergence 9 , 10 , 11 , 12 , 13 . This mammal has scansorial forelimb features, and provides the ancestral condition for dental and other anatomical features of eutherians.

Genomic imprinting is widespread in eutherian mammals. Marsupial mammals also have genomic imprinting, but in fewer loci. It has long been thought that genomic imprinting is somehow related to placentation and/or viviparity in mammals, although neither is restricted to mammals. Most imprinted genes are expressed in the placenta. There is no evidence for genomic imprinting in the egg-laying monotreme mammals, despite their short-lived placenta that transfers nutrients from mother to embryo. Post natal genomic imprinting also occurs, especially in the brain. However, little attention has been paid to the primary source of nutrition in the neonate in all mammals, the mammary gland. Differentially methylated regions (DMRs) play an important role as imprinting control centres in each imprinted region which usually comprises both paternally and maternally expressed genes (PEGs and MEGs). The DMR is established in the male or female germline (the gDMR). Comprehensive comparative genome studies demonstrated that two imprinted regions, PEG10 and IGF2-H19, are conserved in both marsupials and eutherians and that PEG10 and H19 DMRs emerged in the therian ancestor at least 160 Ma, indicating the ancestral origin of genomic imprinting during therian mammal evolution. Importantly, these regions are known to be deeply involved in placental and embryonic growth. It appears that most maternal gDMRs are always associated with imprinting in eutherian mammals, but emerged at differing times during mammalian evolution. Thus, genomic imprinting could evolve from a defence mechanism against transposable elements that depended on DNA methylation established in germ cells.

Marsupials exhibit great diversity in ecology and morphology. However, compared with their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species. This tree allows us to analyze the evolution of habitat preference and geographic distributions of marsupial species through time. We found a pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change. However, contrary to the general trend, several lineages subsequently appear to have reverted from drier to more mesic habitats. Biogeographic reconstructions suggest that current views on the connectivity between Australia and New Guinea/Wallacea during the Miocene and Pliocene need to be revised. The antiquity of several endemic New Guinean clades strongly suggests a substantially older period of connection stretching back to the Middle Miocene and implies that New Guinea was colonized by multiple clades almost immediately after its principal formation.

The Palorchestidae are a family of marsupial megafauna occurring across the eastern Australian continent from the late Oligocene through to their extinction in the Late Pleistocene. The group is known for their odd 'tapir-like' crania and distinctive clawed forelimbs, but their appendicular anatomy has never been formally described. We provide the first descriptions of the appendicular skeleton and body mass estimates for three palorchestid species, presenting newly-identified, and in some cases associated, material of mid-Miocene Propalorchestes, Plio-Pleistocene Palorchestes parvus and Pleistocene Palorchestes azael alongside detailed comparisons with extant and fossil vombatiform marsupials. We propose postcranial diagnostic characters at the family, genus and species level. Specialisation in the palorchestid appendicular skeleton evidently occurred much later than in the cranium and instead correlates with increasing body size within the lineage. We conclude that palorchestid forelimbs were highly specialised for the manipulation of their environment in the acquisition of browse, and that they may have adopted bipedal postures to feed. Our results indicate palorchestids were bigger than previously thought, with the largest species likely weighing over 1000 kg. Additionally, we show that P. azael exhibits some of the most unusual forelimb morphology of any mammal, with a uniquely fixed humeroulnar joint unlike any of their marsupial kin, living or extinct.

Although cancer rarely acts as an infectious disease, a recently emerged transmissible cancer in Tasmanian devils ( Sarcophilus harrisii ) is virtually 100% fatal. Devil facial tumour disease (DFTD) has swept across nearly the entire species’ range, resulting in localized declines exceeding 90% and an overall species decline of more than 80% in less than 20 years. Despite epidemiological models that predict extinction, populations in long-diseased sites persist. Here we report rare genomic evidence of a rapid, parallel evolutionary response to strong selection imposed by a wildlife disease. We identify two genomic regions that contain genes related to immune function or cancer risk in humans that exhibit concordant signatures of selection across three populations. DFTD spreads between hosts by suppressing and evading the immune system, and our results suggest that hosts are evolving immune-modulated resistance that could aid in species persistence in the face of this devastating disease. A recently emerged infectious cancer has caused the near extinction of the Tasmanian devil, but some populations persist. Here, Epstein et al . provide evidence for possible resistance via rapid evolution in two genomic regions that contain cancer-related immune response genes.

Derived features of a new boreosphenidan mammal from the Lower Cretaceous Yixian Formation of China suggest that it has a closer relationship to metatherians (including extant marsupials) than to eutherians (including extant placentals). This fossil dates to 125 million years ago and extends the record of marsupial relatives with skeletal remains by 50 million years. It also has many foot structures known only from climbing and tree-living extant mammals, suggesting that early crown therians exploited diverse niches. New data from this fossil support the view that Asia was likely the center for the diversification of the earliest metatherians and eutherians during the Early Cretaceous.

Marsupials and placental mammals exhibit significant differences in reproductive and life history strategies. Marsupials are born highly underdeveloped after an extremely short period of gestation, leading to prioritized development of structures critical for post-birth survival in the pouch. Critically, they must undergo accelerated development of the orofacial region compared to placentals. Previously, we described the accelerated development of the orofacial region in the carnivorous Australian marsupial, the fat-tailed dunnart Sminthopsis crassicaudata , that has one of the shortest gestations of any mammal. By combining genome comparisons of the mouse and dunnart with functional data for the enhancer-associated chromatin modifications, H3K4me3 and H3K27ac, we investigated divergence of craniofacial regulatory landscapes between these species. This is the first description of genome-wide face regulatory elements in a marsupial, with 60,626 putative enhancers and 12,295 putative promoters described. We also generated craniofacial RNA-seq data for the dunnart to investigate expression dynamics of genes near predicted active regulatory elements. While genes involved in regulating facial development were largely conserved in mouse and dunnart, the regulatory landscape varied significantly. Additionally, a subset of dunnart-specific enhancers was associated with genes highly expressed only in dunnart relating to cranial neural crest proliferation, embryonic myogenesis, and epidermis development. Comparative RNA-seq analyses of facial tissue revealed dunnart-specific expression of genes involved in the development of the mechanosensory system. Accelerated development of the dunnart sensory system likely relates to the sensory cues received by the nasal–oral region during the postnatal journey to the pouch. Together, these data suggest that accelerated face development in the dunnart may be driven by dunnart-specific enhancer activity. Our study highlights the power of marsupial–placental comparative genomics for understanding the role of enhancers in driving temporal shifts in development. Marsupials are a distinctive group of mammals best known for their defining trait: a pouch. Unlike monotremes, which lay eggs, and placental mammals, in which young develop fully in the womb, marsupials give birth to highly premature offspring. These young complete most of their development within the mother’s pouch. Because of this strategy, marsupial newborns possess traits critical for immediate survival outside the womb. These include well-developed forelimbs for climbing into the pouch and a mature oral region for attaching to the teat and suckling. Evolution has shaped the development of the head to match the diverse environments vertebrates inhabit. Marsupials diverged from placental mammals over 160 million years ago, and their requirement for early limb and oral development makes them a powerful system for investigating the genetic mechanisms underlying development. The fat-tailed dunnart (Sminthopsis crassicaudata), often called a marsupial mouse, is emerging as an important model organism. With its short gestation period and extremely undeveloped state at birth, the dunnart provides an excellent comparison to the laboratory mouse – a well-established placental model – for studying evolutionary and developmental differences. Cook et al. investigated the genes and regulatory elements driving early orofacial development in the dunnart, comparing their findings with existing craniofacial expression and epigenomic data in mice. Their results showed that although the genes involved in craniofacial development are highly conserved between the two species, the regulatory elements controlling those genes differ markedly. In dunnarts, regulatory elements linked to skin, nervous system, and muscle development were highly active, whereas in mice they were inactive or only weakly expressed. An important feature of marsupial development is the postnatal retention of the periderm (a transient outer cell layer in embryonic skin). This may support gas exchange in prematurely born young. In addition, elevated activity of genes regulating sensory and muscle development suggests early maturation of mechanosensory and olfactory systems, which are essential for the newborn’s journey to the pouch. Notably, pharyngeal and facial muscles develop before the skeletal system, contrasting with the developmental sequence in placental mammals. In summary, marsupials exhibit a unique reproductive strategy, in which young are born in an extremely underdeveloped state and survival depends on accelerated development of specific traits after birth. By comparing gene regulation in marsupials and placentals, researchers gain insights into how evolution shaped developmental pathways. Expanding genomic resources for the dunnart, such as genome editing tools and transgenic models, will further enhance its role as a powerful comparative system for evolutionary developmental biology.

The use of fossil evidence to calibrate divergence time estimation has a long history. More recently, Bayesian Markov chain Monte Carlo has become the dominant method of divergence time estimation, and fossil evidence has been reinterpreted as the specification of prior distributions on the divergence times of calibration nodes. These so-called \"soft calibrations\" have become widely used but the statistical properties of calibrated tree priors in a Bayesian setting hashave not been carefully investigated. Here, we clarify that calibration densities, such as those defined in BEAST 1.5, do not represent the marginal prior distribution of the calibration node. We illustrate this with a number of analytical results on small trees. We also describe an alternative construction for a calibrated Yule prior on trees that allows direct specification of the marginal prior distribution of the calibrated divergence time, with or without the restriction of monophyly. This method requires the computation of the Yule prior conditional on the height of the divergence being calibrated. Unfortunately, a practical solution for multiple calibrations remains elusive. Our results suggest that direct estimation of the prior induced by specifying multiple calibration densities should be a prerequisite of any divergence time dating analysis.