Mammals from 'down under': a multi-gene species-level phylogeny of marsupial mammals (Mammalia, Metatheria)

Emx2 underlies the development and evolution of marsupial gliding membranes

Phenotypic variation among species is a product of evolutionary changes to developmental programs1,2. 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.

The Distinctive Biology and Characteristics of the Bare-Nosed Wombat (Vombatus ursinus)

The bare-nosed wombat is an iconic Australian fauna with remarkable biological characteristics and mythology. This solitary, muscular, fossorial, herbivorous marsupial from southeast Australia has continent and continental island subspeciation. Vombatiformes also contains hairy-nosed wombats (Lasiorhinus spp.); koala (Phascolarctos cinereus); and extinct megafauna, Phascolonus gigas (giant wombat), Diprotodon, and Thylacoleo (marsupial lion). Culturally important to Aboriginal people, bare-nosed wombats engineer ecosystems through digging, grazing, and defecation. Olfaction and cubic fecal aggregations appear critical for communication, including identity, courtship, and mating. Though among the largest fossorial herbivores, they have a nutrient-poor diet, a home range up to an order of magnitude smaller than expected, and a metabolism among the lowest extreme for mammals >10 kg. Metabolic depression may confer advantages over resource competitors and fossorial lifestyle protection from predators, fires, and climatic extremes. Bare-nosed wombats are loved and persecuted by European colonists. Recent population increases may reflect softening attitudes toward, and greater protections of, bare-nosed wombats.

Improved mammalian family phylogeny using gap-rare multiple sequence alignment: A timetree of extant placentals and marsupials

The timing of mammalian diversification in relation to the Cretaceous-Paleogene (KPg) mass extinction continues to be a subject of substantial debate. Previous studies have either focused on limited taxonomic samples with available whole-genome data or relied on short sequence alignments coupled with extensive species samples. In the present study, we improved an existing dataset from the landmark study of Meredith et al. (2011) by filling in missing fragments and further generated another dataset containing 120 taxa and 98 exonic markers. Using these two datasets, we then constructed phylogenies for extant mammalian families, providing improved resolution of many conflicting relationships. Moreover, the timetrees generated, which were calibrated using appropriate molecular clock models and multiple fossil records, indicated that the interordinal diversification of placental mammals initiated before the Late Cretaceous period. Additionally, intraordinal diversification of both extant placental and marsupial lineages accelerated after the KPg boundary, supporting the hypothesis that the availability of numerous vacant ecological niches subsequent to the mass extinction event facilitated rapid diversification. Thus, our results support a scenario of placental radiation characterized by both basal cladogenesis and active interordinal divergences spanning from the Late Cretaceous into the Paleogene.

Reunion of Australasian Possums by Shared SINE Insertions

Although first posited to be of a single origin, the two superfamilies of phalangeriform marsupial possums (Phalangeroidea: brushtail possums and cuscuses and Petauroidea: possums and gliders) have long been considered, based on multiple sequencing studies, to have evolved from two separate origins. However, previous data from these sequence analyses suggested a variety of conflicting trees. Therefore, we reinvestigated these relationships by screening $\sim$200,000 orthologous short interspersed element (SINE) loci across the newly available whole-genome sequences of phalangeriform species and their relatives. Compared to sequence data, SINE presence/absence patterns are evolutionarily almost neutral molecular markers of the phylogenetic history of species. Their random and highly complex genomic insertion ensures their virtually homoplasy-free nature and enables one to compare hundreds of shared unique orthologous events to determine the true species tree. Here, we identify 106 highly reliable phylogenetic SINE markers whose presence/absence patterns within multiple Australasian possum genomes unexpectedly provide the first significant evidence for the reunification of Australasian possums into one monophyletic group. Together, our findings indicate that nucleotide homoplasy and ancestral incomplete lineage sorting have most likely driven the conflicting signal distributions seen in previous sequence-based studies. [Ancestral incomplete lineage sorting; possum genomes; possum monophyly; retrophylogenomics; SINE presence/absence.].

The value of updating GenBank accessions for supermatrix phylogeny: The case of the New Guinean marsupial carnivore genus Myoictis

Erroneous taxonomic attributions in GenBank accessions can mislead phylogenetic inference and appear to be widespread within genera. We investigate the influence of taxonomic misattributions for reconstructing the phylogeny of three-striped dasyures, which include four recognized Myoictis species (Marsupialia: Dasyuridae) that are distributed across New Guinea and nearby islands. Molecular phylogenetic studies that have focused on dasyurids consistently resolve the interrelationships of these small carnivores, grouping M. leucura with M. wavicus, and placing M. wallacei and M. melas as successively deeper divergences from these. Two recent marsupial and mammalian supermatrix phylogenies instead favour an alternative Myoictis topology that is discordant with each of these relationships. We add new nuclear and mitochondrial sequences and employ randomized accession resampling that shows the supermatrix topologies are an artefact of several outdated taxonomic attributions in GenBank. Updating these accessions brings agreement across Myoictis phylogenies with randomly resampled accessions. We encourage authors to update GenBank taxonomic attributions and we argue that an option is needed for flagging accessions that are not demonstrably incorrect, but that provide anomalous results. This would serve both as a caution for future supermatrix construction and to highlight accessions of potentially significant biological interest for further study.

Uterine cellular changes during mammalian pregnancy and the evolution of placentation

There are many different forms of nutrient provision in viviparous (live bearing) species. The formation of a placenta is one method where the placenta functions to transfer nutrients from mother to fetus (placentotrophy), transfer waste from the fetus to the mother and respiratory gas exchange. Despite having the same overarching function, there are different types of placentation within placentotrophic vertebrates, and many morphological changes occur in the uterus during pregnancy to facilitate formation of the placenta. These changes are regulated in complex ways but are controlled by similar hormonal mechanisms across species. This review describes current knowledge of the morphological and molecular changes to the uterine epithelium preceding implantation among mammals. Our aim is to identify the commonalities and constraints of these cellular changes to understand the evolution of placentation in mammals and propose directions for future research. We compare and discuss the complex modifications to the ultrastructure of uterine epithelial cells and show that there are similarities in the changes to the cytoskeleton and gross morphology of the uterine epithelial cells, especially of the apical and lateral plasma membrane of the cells during the formation of a placenta in all eutherians and marsupials studied to date. We conclude that further research is needed to understand the evolution of placentation among viviparous mammals, particularly concerning the level of placental invasiveness, hormonal control and genetic underpinnings of pregnancy in marsupial taxa.

Jaw shape and mechanical advantage are indicative of diet in Mesozoic mammals

Jaw morphology is closely linked to both diet and biomechanical performance, and jaws are one of the most common Mesozoic mammal fossil elements. Knowledge of the dietary and functional diversity of early mammals informs on the ecological structure of palaeocommunities throughout the longest era of mammalian evolution: the Mesozoic. Here, we analyse how jaw shape and mechanical advantage of the masseter (MAM) and temporalis (MAT) muscles relate to diet in 70 extant and 45 extinct mammals spanning the Late Triassic-Late Cretaceous. In extant mammals, jaw shape discriminates well between dietary groups: insectivores have long jaws, carnivores intermediate to short jaws, and herbivores have short jaws. Insectivores have low MAM and MAT, carnivores have low MAM and high MAT, and herbivores have high MAM and MAT. These traits are also informative of diet among Mesozoic mammals (based on previous independent determinations of diet) and set the basis for future ecomorphological studies.

The external ear morphology and presence of tragi in Australian marsupials

Multiple studies have described the anatomy and function of the external ear (pinna) of bats, and other placental mammals, however, studies of marsupial pinna are largely absent. In bats, the tragus appears to be especially important for locating and capturing insect prey. In this study, we aimed to investigate the pinnae of Australian marsupials, with a focus on the presence/absence of tragi and how they may relate to diet. We investigated 23 Australian marsupial species with varying diets. The pinnae measurements (scapha width, scapha length) and tragi (where present) were measured. The interaural distance and body length were also recorded for each individual. Results indicated that all nectarivorous, carnivorous, and insectivorous species had tragi with the exception of the insectivorous striped possum (Dactylopsila trivirgata), numbat (Myrmecobius fasciatus), and nectarivorous sugar glider (Petaurus breviceps). No herbivorous or omnivorous species had tragi. Based on the findings in this study, and those conducted on placental mammals, we suggest marsupials use tragi in a similar way to placentals to locate and target insectivorous prey. The Tasmanian devil (Sarcophilus harrisii) displayed the largest interaural distance that likely aids in better localization and origin of noise associated with prey detection. In contrast, the smallest interaural distance was exhibited by a macropod. Previous studies have suggested the hearing of macropods is especially adapted to detect warnings of predators made by conspecifics. While the data in this study demonstrate a diversity in pinnae among marsupials, including presence and absence of tragi, it suggests that there is a correlation between pinna structure and diet choice among marsupials. A future study should investigate a larger number of individuals and species and include marsupials from Papua New Guinea, and Central and South America as a comparison.

Evolution of the patella and patelloid in marsupial mammals

The musculoskeletal system of marsupial mammals has numerous unusual features beyond the pouch and epipubic bones. One example is the widespread absence or reduction (to a fibrous “patelloid”) of the patella (“kneecap”) sesamoid bone, but prior studies with coarse sampling indicated complex patterns of evolution of this absence or reduction. Here, we conducted an in-depth investigation into the form of the patella of extant marsupial species and used the assembled dataset to reconstruct the likely pattern of evolution of the marsupial patella. Critical assessment of the available literature was followed by examination and imaging of museum specimens, as well as CT scanning and histological examination of dissected wet specimens. Our results, from sampling about 19% of extant marsupial species-level diversity, include new images and descriptions of the fibrocartilaginous patelloid in Thylacinus cynocephalus (the thylacine or “marsupial wolf”) and other marsupials as well as the ossified patella in Notoryctes ‘marsupial moles’, Caenolestes shrew opossums, bandicoots and bilbies. We found novel evidence of an ossified patella in one specimen of Macropus rufogriseus (Bennett’s wallaby), with hints of similar variation in other species. It remains uncertain whether such ossifications are ontogenetic variation, unusual individual variation, pathological or otherwise, but future studies must continue to be conscious of variation in metatherian patellar sesamoid morphology. Our evolutionary reconstructions using our assembled data vary, too, depending on the reconstruction algorithm used. A maximum likelihood algorithm favours ancestral fibrocartilaginous “patelloid” for crown clade Marsupialia and independent origins of ossified patellae in extinct sparassodonts, peramelids, notoryctids and caenolestids. A maximum parsimony algorithm favours ancestral ossified patella for the clade [Marsupialia + sparassodonts] and subsequent reductions into fibrocartilage in didelphids, dasyuromorphs and diprotodonts; but this result changed to agree more with the maximum likelihood results if the character state reconstructions were ordered. Thus, there is substantial homoplasy in marsupial patellae regardless of the evolutionary algorithm adopted. We contend that the most plausible inference, however, is that metatherians independently ossified their patellae at least three times in their evolution. Furthermore, the variability of the patellar state we observed, even within single species (e.g. M. rufogriseus), is fascinating and warrants further investigation, especially as it hints at developmental plasticity that might have been harnessed in marsupial evolution to drive the complex patterns inferred here.

New dicrocoeliid digeneans from mammals in Ecuador including a highly genetically divergent new genus from an ancient marsupial lineage

The Dicrocoeliidae is a highly diverse and broadly distributed family of digeneans typically parasitic in the gall bladder and liver of their tetrapod hosts. So far, no study has reported dicrocoeliids, or any digeneans, from the ancient marsupial family Caenolestidae. Herein, we describe a new genus of dicrocoeliids (Otongatrema n. gen.) from Tate's shrew opossum Caenolestes fuliginosus and a new species of Metadelphis (Metadelphis cesartapiai n. sp.) from a phyllostomid bat Anoura peruana collected in Ecuador. Otongatrema can be readily distinguished from the morphologically closest dicrocoeliid genera Concinnum, Conspicuum and Canaania based on the position of the genital pore, distribution/position of the uterus and extent of vitellarium. Metadelphis cesartapiai can be easily differentiated from other Metadelphis spp. based on a combination of morphological characters including body shape and size, distribution of vitellarium, shape of the gonads as well as size of suckers and cirrus sac. In addition, we used newly generated partial sequences of the nuclear 28S rRNA gene and mitochondrial cox1 genes to examine phylogenetic affinities of the new taxa within the Dicrocoeliidae. Both the 28S and cox1 phylogenies confidently positioned Otongatrema as a sister/basal group to all other dicrocoeliids sequenced so far. The phylogenetic position of Otongatrema may be explained by a close co-evolutionary relationship with Caenolestidae, one of the most basal and most ancient groups of marsupials. In addition, our 28S phylogeny provides evidence that the complete or partial loss of intestinal structures has likely occurred independently at least 3 times in the evolutionary history of the Dicrocoeliidae.

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.

Evolution of Marsupial Genomes

Marsupial genomes, which are packaged into large chromosomes, provide a powerful resource for studying the mechanisms of genome evolution. The extensive and valuable body of work on marsupial cytogenetics, combined more recently with genome sequence data, has enabled prediction of the 2n = 14 karyotype ancestral to all marsupial families. The application of both chromosome biology and genome sequencing, or chromosomics, has been a necessary approach for various aspects of mammalian genome evolution, such as understanding sex chromosome evolution and the origin and evolution of transmissible tumors in Tasmanian devils. The next phase of marsupial genome evolution research will employ chromosomics approaches to begin addressing fundamental questions in marsupial genome evolution and chromosome evolution more generally. The answers to these complex questions will impact our understanding across a broad range of fields, including the genetics of speciation, genome adaptation to environmental stressors, and species management.

Didelphis albiventris: an overview of unprecedented transcriptome sequencing of the white-eared opossum

BACKGROUND

The white-eared opossum (Didelphis albiventris) is widely distributed throughout Brazil and South America. It has been used as an animal model for studying different scientific questions ranging from the restoration of degraded green areas to medical aspects of Chagas disease, leishmaniasis and resistance against snake venom. As a marsupial, D. albiventris can also contribute to the understanding of the molecular mechanisms that govern the different stages of organogenesis. Opossum joeys are born after only 13 days, and the final stages of organogenesis occur when the neonates are inside the pouch, depending on lactation. As neither the genome of this opossum species nor its transcriptome has been completely sequenced, the use of D. albiventris as an animal model is limited. In this work, we sequenced the D. albiventris transcriptome by RNA-seq to obtain the first catalogue of differentially expressed (DE) genes and gene ontology (GO) annotations during the neonatal stages of marsupial development.

RESULTS

The D. albiventris transcriptome was obtained from whole neonates harvested at birth (P0), at 5 days of age (P5) and at 10 days of age (P10). The de novo assembly of these transcripts generated 85,338 transcripts. Approximately 30% of these transcripts could be mapped against the amino acid sequences of M. domestica, the evolutionarily closest relative of D. albiventris to be sequenced thus far. Among the expressed transcripts, 2077 were found to be DE between P0 and P5, 13,780 between P0 and P10, and 1453 between P5 and P10. The enriched GO terms were mainly related to the immune system, blood tissue development and differentiation, vision, hearing, digestion, the CNS and limb development.

CONCLUSIONS

The elucidation of opossum transcriptomes provides an out-group for better understanding the distinct characteristics associated with the evolution of mammalian species. This study provides the first transcriptome sequences and catalogue of genes for a marsupial species at different neonatal stages, allowing the study of the mechanisms involved in organogenesis.

A tail of evolution: evaluating body length, weight and locomotion as potential drivers of tail length scaling in Australian marsupial mammals

Although mammalian tail length relative to body length is considered indicative of locomotor mode, this association has been difficult to quantify. This could be because the counterweight function of the tail might associate it more with body weight than body length. Alternatively, relative tail length might not be evolutionarily flexible owing to its integration with the remaining skeleton, particularly the spine. Using comparative analyses of morphological means and ranges in Australian marsupials, including the first co-assessment with body weight, our study supports the second hypothesis, i.e. tail length ranges within species, and tail lengths among species are explained better by body length than by body weight. However, all three variables do not differ in phylogenetic signal or rates of evolution. Associations of tail lengths with locomotion are limited, but suggest that scaling slopes, rather than intercepts, are responsible for limited divergence between relative tail lengths at different locomotor modes. This complicates (palaeo-)ecological interpretations of tail length further. We conclude that relative tail length is not a strong predictor of locomotor mode, probably owing to strong integration of tail and body length. The many well-documented bony and soft-tissue adaptations of tails are likely to be better suited to interpretations of locomotor adaptations.

The pre-Pleistocene fossil thylacinids (Dasyuromorphia: Thylacinidae) and the evolutionary context of the modern thylacine

The thylacine is popularly used as a classic example of convergent evolution between placental and marsupial mammals. Despite having a fossil history spanning over 20 million years and known since the 1960s, the thylacine is often presented in both scientific literature and popular culture as an evolutionary singleton unique in its morphological and ecological adaptations within the Australian ecosystem. Here, we synthesise and critically evaluate the current state of published knowledge regarding the known fossil record of Thylacinidae prior to the appearance of the modern species. We also present phylogenetic analyses and body mass estimates of the thylacinids to reveal trends in the evolution of hypercarnivory and ecological shifts within the family. We find support that Mutpuracinus archibaldi occupies an uncertain position outside of Thylacinidae, and consider Nimbacinus richi to likely be synonymous with N. dicksoni. The Thylacinidae were small-bodied (< ~8 kg) unspecialised faunivores until after the ~15-14 Ma middle Miocene climatic transition (MMCT). After the MMCT they dramatically increase in size and develop adaptations to a hypercarnivorous diet, potentially in response to the aridification of the Australian environment and the concomitant radiation of dasyurids. This fossil history of the thylacinids provides a foundation for understanding the ecology of the modern thylacine. It provides a framework for future studies of the evolution of hypercarnivory, cursoriality, morphological and ecological disparity, and convergence within mammalian carnivores.

Endometrial recognition of pregnancy occurs in the grey short-tailed opossum ( Monodelphis domestica)

In human pregnancy, recognition of an embryo within the uterus is essential to support the fetus through gestation. In most marsupials, such as the opossums, pregnancy is shorter than the oestrous cycle and the steroid hormone profile during pregnancy and oestrous cycle are indistinguishable. For these reasons, it was assumed that recognition of pregnancy, as a trait, evolved in the eutherian (placental) stem lineage and independently in wallabies and kangaroos. To investigate whether uterine recognition of pregnancy occurs in species with pregnancy shorter than the oestrous cycle, we examined reproduction in the short-tailed opossum ( Monodelphis domestica), a marsupial with a plesiomorphic mode of pregnancy. We examined the morphological and gene expression changes in the uterus of females in the non-pregnant oestrous cycle and compared these to pregnancy. We found that the presence of an embryo did not alter some aspects of uterine development but increased glandular activity. Transcriptionally, we saw big differences between the uterus of pregnant and cycling animals. These differences included an upregulation of genes involved in transport, inflammation and metabolic-activity in response to the presence of a fetus. Furthermore, transcriptional differences reflected protein level differences in transporter abundance. Our results suggest that while the uterus exhibits programmed changes after ovulation, its transcriptional landscape during pregnancy responds to the presence of a fetus and upregulates genes that may be essential for fetal support. These results are consistent with endometrial recognition of pregnancy occurring in the opossum. While the effects on maternal physiology appear to differ, recognition of pregnancy has now been observed in eutherian mammals, as well as, Australian and American marsupials.

Prey productivity and predictability drive different axes of life-history variation in carnivorous marsupials

Variation in life-history strategies has usually been characterized as a single fast-slow continuum of life-history variation, in which mean lifespan increases with age at maturity as reproductive output at each breeding event declines. Analyses of plants and animals suggest that strategies of reproductive timing can vary on an independent axis, with iteroparous species at one extreme and semelparous species at the other. Insectivorous marsupials in the Family Dasyuridae have an unusually wide range of life-history strategies on both purported axes. We test and confirm that reproductive output and degree of iteroparity are independent in females across species. Variation in reproductive output per episode is associated with mean annual rainfall, which predicts food availability. Position on the iteroparity-semelparity axis is not associated with annual rainfall, but species in regions of unpredictable rainfall have longer maximum lifespans, more potential reproductive events per year, and longer breeding seasons. We suggest that these two axes of life-history variation arise because reproductive output is limited by overall food availability, and selection for high offspring survival favours concentrated breeding in seasonal environments. Longer lifespans are favoured when reproductive opportunities are dispersed over longer periods in environments with less predictable food schedules.

Craniomandibular Variation in Phalangeriform Marsupials: Functional Comparisons with Primates

Phalangeriform marsupials have often been compared with primates because of similarity in the range of external morphology, ecological niches, and body size between the two radiations. We explore morphological convergence in the masticatory anatomy of strepsirrhine primates and phalangeriforms, through osteological measurements of the mandible and facial skeleton, and through dissection of the masticatory musculature, presenting new data on the arrangement and proportions of jaw adductors in phalangeriforms. Phalangeriforms and primates have a large number of shape differences in mandibular morphology. Despite these differences in shape on phylogenetic lines, dietary groups used to pool species of phalangeriforms and strepsirrhines also differed from each other in a range of shape variables. Notably, the striped possum (Dactylopsila), previously described as convergent with the aye-aye (Daubentonia), shares a number of features of mandibular shape with Daubentonia, and the exudate-feeding sugar-glider, Petaurus, shares shape features with gummivorous strepsirrhines. Petaurus also has long-fibered jaw adductors for its body mass, as would be expected for a species with a requirement for large gape. Phalangeriform species on the frugivore-folivore continuum were less clearly comparable to strepsirrhine species with similar diets. There are a number of significant dietary contrasts in osteological measurements, but in the masticatory muscles phalangeriforms did not meet all expectations based on available dietary data, highlighting the possible complexity of dietary adaptation in phalangeriform folivores. Anat Rec, 301:227-255, 2018. © 2018 Wiley Periodicals, Inc.

Adaptation and conservation insights from the koala genome

The koala, the only extant species of the marsupial family Phascolarctidae, is classified as 'vulnerable' due to habitat loss and widespread disease. We sequenced the koala genome, producing a complete and contiguous marsupial reference genome, including centromeres. We reveal that the koala's ability to detoxify eucalypt foliage may be due to expansions within a cytochrome P450 gene family, and its ability to smell, taste and moderate ingestion of plant secondary metabolites may be due to expansions in the vomeronasal and taste receptors. We characterized novel lactation proteins that protect young in the pouch and annotated immune genes important for response to chlamydial disease. Historical demography showed a substantial population crash coincident with the decline of Australian megafauna, while contemporary populations had biogeographic boundaries and increased inbreeding in populations affected by historic translocations. We identified genetically diverse populations that require habitat corridors and instituting of translocation programs to aid the koala's survival in the wild.

Total evidence phylogeny and evolutionary timescale for Australian faunivorous marsupials (Dasyuromorphia)

BACKGROUND

The order Dasyuromorphia is a diverse radiation of faunivorous marsupials, comprising >80 modern species in Australia and New Guinea. It includes dasyurids, the numbat (the myrmecobiid Myrmecobius fasciatus) and the recently extinct thylacine (the thylacinid Thylacinus cyncocephalus). There is also a diverse fossil record of dasyuromorphians and "dasyuromorphian-like" taxa known from Australia. We present the first total evidence phylogenetic analyses of the order, based on combined morphological and molecular data (including a novel set of 115 postcranial characters), to resolve relationships and calculate divergence dates. We use this information to analyse the diversification dynamics of modern dasyuromorphians.

RESULTS

Our morphology-only analyses are poorly resolved, but our molecular and total evidence analyses confidently resolve most relationships within the order, and are strongly congruent with recent molecular studies. Thylacinidae is the first family to diverge within the order, and there is strong support for four tribes within Dasyuridae (Dasyurini, Phascogalini, Planigalini and Sminthopsini). Among fossil taxa, Ankotarinja and Keeuna do not appear to be members of Dasyuromorphia, whilst Barinya and Mutpuracinus are of uncertain relationships within the order. Divergence dates calculated using total evidence tip-and-node dating are younger than both molecular node-dating and total evidence tip-dating, but appear more congruent with the fossil record and are relatively insensitive to calibration strategy. The tip-and-node divergence dates indicate that Dasyurini, Phascogalini and Sminthopsini began to radiate almost simultaneously during the middle-to-late Miocene (11.5-13.1 MYA; composite 95% HPD: 9.5-15.9 MYA); the median estimates for these divergences are shortly after a drop in global temperatures (the middle Miocene Climatic Transition), and coincide with a faunal turnover event in the mammalian fossil record of Australia. Planigalini radiated much later, during the latest Miocene to earliest Pliocene (6.5 MYA; composite 95% HPD: 4.4-8.9 MYA); the median estimates for these divergences coincide with an increase in grass pollen in the Australian palynological record that suggests the development of more open habitats, which are preferred by modern planigale species.

CONCLUSIONS

Our results provide a phylogenetic and temporal framework for interpreting the evolution of modern and fossil dasyuromorphians, but future progress will require a much improved fossil record.

RUNX2 repeat variation does not drive craniofacial diversity in marsupials

BACKGROUND

Runt-related transcription factor 2 (RUNX2) is a transcription factor essential for skeletal development. Variation within the RUNX2 polyglutamine / polyalanine (QA) repeat is correlated with facial length within orders of placental mammals and is suggested to be a major driver of craniofacial diversity. However, it is not known if this correlation exists outside of the placental mammals.

RESULTS

Here we examined the correlation between the RUNX2 QA repeat ratio and facial length in the naturally evolving sister group to the placental mammals, the marsupials. Marsupials have a diverse range of facial lengths similar to that seen in placental mammals. Despite their diversity there was almost no variation seen in the RUNX2 QA repeat across individuals spanning the entire marsupial infraclass. The extreme conservation of the marsupial RUNX2 QA repeat indicates it is under strong purifying selection. Despite this, we observed an unexpectedly high level of repeat purity.

CONCLUSIONS

Unlike within orders of placental mammals, RUNX2 repeat variation cannot drive craniofacial diversity in marsupials. We propose conservation of the marsupial RUNX2 QA repeat is driven by the constraint of accelerated ossification of the anterior skeleton to facilitate life in the pouch. Thus, marsupials must utilize alternate pathways to placental mammals to drive craniofacial evolution.

Evolution of the patellar sesamoid bone in mammals

The patella is a sesamoid bone located in the major extensor tendon of the knee joint, in the hindlimb of many tetrapods. Although numerous aspects of knee morphology are ancient and conserved among most tetrapods, the evolutionary occurrence of an ossified patella is highly variable. Among extant (crown clade) groups it is found in most birds, most lizards, the monotreme mammals and almost all placental mammals, but it is absent in most marsupial mammals as well as many reptiles. Here, we integrate data from the literature and first-hand studies of fossil and recent skeletal remains to reconstruct the evolution of the mammalian patella. We infer that bony patellae most likely evolved between four and six times in crown group Mammalia: in monotremes, in the extinct multituberculates, in one or more stem-mammal genera outside of therian or eutherian mammals and up to three times in therian mammals. Furthermore, an ossified patella was lost several times in mammals, not including those with absent hindlimbs: once or more in marsupials (with some re-acquisition) and at least once in bats. Our inferences about patellar evolution in mammals are reciprocally informed by the existence of several human genetic conditions in which the patella is either absent or severely reduced. Clearly, development of the patella is under close genomic control, although its responsiveness to its mechanical environment is also important (and perhaps variable among taxa). Where a bony patella is present it plays an important role in hindlimb function, especially in resisting gravity by providing an enhanced lever system for the knee joint. Yet the evolutionary origins, persistence and modifications of a patella in diverse groups with widely varying habits and habitats-from digging to running to aquatic, small or large body sizes, bipeds or quadrupeds-remain complex and perplexing, impeding a conclusive synthesis of form, function, development and genetics across mammalian evolution. This meta-analysis takes an initial step toward such a synthesis by collating available data and elucidating areas of promising future inquiry.

Cellular Scaling Rules for the Brains of Marsupials: Not as "Primitive" as Expected

In the effort to understand the evolution of mammalian brains, we have found that common relationships between brain structure mass and numbers of nonneuronal (glial and vascular) cells apply across eutherian mammals, but brain structure mass scales differently with numbers of neurons across structures and across primate and nonprimate clades. This suggests that the ancestral scaling rules for mammalian brains are those shared by extant nonprimate eutherians - but do these scaling relationships apply to marsupials, a sister group to eutherians that diverged early in mammalian evolution? Here we examine the cellular composition of the brains of 10 species of marsupials. We show that brain structure mass scales with numbers of nonneuronal cells, and numbers of cerebellar neurons scale with numbers of cerebral cortical neurons, comparable to what we have found in eutherians. These shared scaling relationships are therefore indicative of mechanisms that have been conserved since the first therians. In contrast, while marsupials share with nonprimate eutherians the scaling of cerebral cortex mass with number of neurons, their cerebella have more neurons than nonprimate eutherian cerebella of a similar mass, and their rest of brain has fewer neurons than eutherian structures of a similar mass. Moreover, Australasian marsupials exhibit ratios of neurons in the cerebral cortex and cerebellum over the rest of the brain, comparable to artiodactyls and primates. Our results suggest that Australasian marsupials have diverged from the ancestral Theria neuronal scaling rules, and support the suggestion that the scaling of average neuronal cell size with increasing numbers of neurons varies in evolution independently of the allocation of neurons across structures.

A large carnivorous mammal from the Late Cretaceous and the North American origin of marsupials

Marsupial mammal relatives (stem metatherians) from the Mesozoic Era (252-66 million years ago) are mostly known from isolated teeth and fragmentary jaws. Here we report on the first near-complete skull remains of a North American Late Cretaceous metatherian, the stagodontid Didelphodon vorax. Our phylogenetic analysis indicates that marsupials or their closest relatives evolved in North America, as part of a Late Cretaceous diversification of metatherians, and later dispersed to South America. In addition to being the largest known Mesozoic therian mammal (node-based clade of eutherians and metatherians), Didelphodon vorax has a high estimated bite force and other craniomandibular and dental features that suggest it is the earliest known therian to invade a durophagous predator-scavenger niche. Our results broaden the scope of the ecomorphological diversification of Mesozoic mammals to include therian lineages that, in this case, were linked to the origin and evolution of marsupials.