Morphological evolution and niche conservatism across a continental radiation of Australian blindsnakes

Understanding how continental radiations are assembled across space and time is a major question in macroevolutionary biology. Here, we use a phylogenomic-scale phylogeny, a comprehensive morphological dataset, and environmental niche models to evaluate the relationship between trait and environment and assess the role of geography and niche conservatism in the continental radiation of Australian blindsnakes. The Australo-Papuan blindsnake genus, Anilios, comprises 47 described species of which 46 are endemic to and distributed across various biomes on continental Australia. Although we expected blindsnakes to be morphologically conserved, we found considerable interspecific variation in all morphological traits we measured. Absolute body length is negatively correlated with mean annual temperature, and body shape ratios are negatively correlated with soil compactness. We found that morphologically similar species are likely not a result of ecological convergence. Age-overlap correlation tests revealed niche similarity decreased with the relative age of speciation events. We also found low geographical overlap across the phylogeny, suggesting that speciation is largely allopatric with low rates of secondary range overlap. Our study offers insights into the eco-morphological evolution of blindsnakes and the potential for phylogenetic niche conservatism to influence continental scale radiations.

Phenotypic plasticity in tropical butterflies is linked to climatic seasonality on a macroevolutionary scale

Phenotypic plasticity can be adaptive in fluctuating environments by providing rapid environment-phenotype matching and this applies particularly in seasonal environments. African Bicyclus butterflies have repeatedly colonized seasonal savannahs from ancestral forests around the late Miocene, and many species now exhibit seasonal polyphenism. On a macroevolutionary scale, it can be expected that savannah species will exhibit higher plasticity because of experiencing stronger environmental seasonality than forest species. We quantified seasonality using environmental niche modeling and surveyed the degree of plasticity in a key wing pattern element (eyespot size) using museum specimens. We showed that species occurring in highly seasonal environments display strong plasticity, while species in less seasonal or aseasonal environments exhibit surprisingly variable degrees of plasticity, including strong to no plasticity. Furthermore, eyespot size plasticity has a moderate phylogenetic signal and the ancestral Bicyclus likely exhibited some degree of plasticity. We propose hypotheses to explain the range of plasticity patterns seen in less seasonal environments and generate testable predictions for the evolution of plasticity in Bicyclus. Our study provides one of the most compelling cases showing links between seasonality and phenotypic plasticity on a macroevolutionary scale and the potential role of plasticity in facilitating the colonization of novel environments.

Genome-wide phylogenetic and genetic evolutionary analyses of mitochondria in Hypoderma bovis and H. sinense on the Qinghai-Tibetan Plateau

Hypoderma bovis (H. bovis) and Hypoderma sinense (H. sinense) are insects that cause hypodermosis in yaks and Bos taurus. Hypodermosis is a severe skin condition that not only impairs the development of local animal husbandry but also poses threats to human health as a zoonosis. The Qinghai-Tibetan Plateau (QTP) is known as the "Roof of the World." Its unique geographical environment and climate conditions have supported the growth of a wide range of mammals, providing favorable conditions for Hypoderma spp. to complete their life cycles. In this study, the whole mitochondrial genomes of H. bovis and H. sinense collected from the QTP were sequenced and phylogenetically analyzed. We found that the whole genomes of H. bovis and H. sinense are 16,283 bp and 16,300 bp in length, respectively. Both the H. bovis and H. sinense genomes have 37 mitochondrial genes, which include two rRNA genes (16S rRNA and 12S rRNA), 22 tRNA genes, the control region (D-loop region), the light chain replication initiation region, and 13 protein-coding genes (PCGs). The phylogenetic tree generated based on the 13 PCGs revealed close phylogenetic relationships between H. sinense, H. bovis, and Hypoderma lineatum. A similar result was also found in our phylogenetic analysis based on 18S rRNA and 28S rRNA. However, analysis of cytochrome oxidase subunit I (COI) showed cluster of H. bovis, H. sinense, and Cuterebra spp. on the same branch, all belonging to Oestridae. The differentiation time generated based on 13 PCGs indicates that H. bovis and H. sinense differentiated and formed ~4.69 million years ago (Mya) and ~4.06 Mya, respectively. This timing coincides with the differentiation and appearance of yak and Bos taurus in the Pliocene (~4.7 Mya), indicating that the parasites and mammals diverged in close temporal proximity. Of note, this period also witnessed a rapid uplift of the QTP, causing significant climate and environmental changes. Thus, we conjecture that the differentiation of Hypoderma spp. is potentially related to the differentiation of their host species, as well as climate changes caused by the uplift of the QTP. Overall, our study can provide valuable data to support further studies on the phylogeny and differentiation of Hypoderma spp. on the QTP.

A review of the late Cenozoic genus Bohra (Diprotodontia: Macropodidae) and the evolution of tree-kangaroos

Tree-kangaroos of the genus Dendrolagus occupy forest habitats of New Guinea and extreme northeastern Australia, but their evolutionary history is poorly known. Descriptions in the 2000s of near-complete Pleistocene skeletons belonging to larger-bodied species in the now-extinct genus Bohra broadened our understanding of morphological variation in the group and have since helped us to identify unassigned fossils in museum collections, as well as to reassign species previously placed in other genera. Here we describe these fossils and analyse tree-kangaroo systematics via comparative osteology. Including B. planei sp. nov., B. bandharr comb. nov. and B. bila comb. nov., we recognise the existence of at least seven late Cenozoic species of Bohra, with a maximum of three in any one assemblage. All tree-kangaroos (Dendrolagina subtribe nov.) exhibit skeletal adaptations reflective of greater joint flexibility and manoeuvrability, particularly in the hindlimb, compared with other macropodids. The Pliocene species of Bohra retained the stepped calcaneocuboid articulation characteristic of ground-dwelling macropodids, but this became smoothed to allow greater hindfoot rotation in the later species of Bohra and in Dendrolagus. Tree-kangaroo diversification may have been tied to the expansion of forest habitats in the early Pliocene. Following the onset of late Pliocene aridity, some tree-kangaroo species took advantage of the consequent spread of more open habitats, becoming among the largest late Cenozoic tree-dwellers on the continent. Arboreal Old World primates and late Quaternary lemurs may be the closest ecological analogues to the species of Bohra.

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.

Diving into a dead-end: asymmetric evolution of diving drives diversity and disparity shifts in waterbirds

Diving is a relatively uncommon and highly specialized foraging strategy in birds, mostly observed within the Aequorlitornithes (waterbirds) by groups such as penguins, cormorants and alcids. Three key diving techniques are employed within waterbirds: wing-propelled pursuit diving (e.g. penguins), foot-propelled pursuit diving (e.g. cormorants) and plunge diving (e.g. gannets). How many times diving evolved within waterbirds, whether plunge diving is an intermediate state between aerial foraging and submarine diving, and whether the transition to a diving niche is reversible are not known. Here, we elucidate the evolutionary history of diving in waterbirds. We show that diving has been acquired independently at least 14 times within waterbirds, and this acquisition is apparently irreversible, in a striking example of asymmetric evolution. All three modes of diving have evolved independently, with no evidence for plunge diving as an intermediate evolutionary state. Net diversification rates differ significantly between diving versus non-diving lineages, with some diving clades apparently prone to extinction. We find that body mass is evolving under multiple macroevolutionary regimes, with unique optima for each diving type with varying degrees of constraint. Our findings highlight the vulnerability of highly specialized lineages during the ongoing sixth mass extinction.

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.

Molecules and fossils tell distinct yet complementary stories of mammal diversification

Reconstructing the tempo at which biodiversity arose is a fundamental goal of evolutionary biologists, yet the relative merits of evolutionary-rate estimates are debated based on whether they are derived from the fossil record or time-calibrated phylogenies (timetrees) of living species. Extinct lineages unsampled in timetrees are known to "pull" speciation rates downward, but the temporal scale at which this bias matters is unclear. To investigate this problem, we compare mammalian diversification-rate signatures in a credible set of molecular timetrees (n = 5,911 species, ∼70% from DNA) to those in fossil genus durations (n = 5,320). We use fossil extinction rates to correct or "push" the timetree-based (pulled) speciation-rate estimates, finding a surge of speciation during the Paleocene (∼66-56 million years ago, Ma) between the Cretaceous-Paleogene (K-Pg) boundary and the Paleocene-Eocene Thermal Maximum (PETM). However, about two-thirds of the K-Pg-to-PETM originating taxa did not leave modern descendants, indicating that this rate signature is likely undetectable from extant lineages alone. For groups without substantial fossil records, thankfully all is not lost. Pushed and pulled speciation rates converge starting ∼10 Ma and are equal at the present day when recent evolutionary processes can be estimated without bias using species-specific "tip" rates of speciation. Clade-wide moments of tip rates also enable enriched inference, as the skewness of tip rates is shown to approximate a clade's extent of past diversification-rate shifts. Molecular timetrees need fossil-correction to address deep-time questions, but they are sufficient for shallower time questions where extinctions are fewer.

Developmental influence on evolutionary rates and the origin of placental mammal tooth complexity

Interactions during development among genes, cells, and tissues can favor the more frequent generation of some trait variants compared with others. This developmental bias has often been considered to constrain adaptation, but its exact influence on evolution is poorly understood. Using computer simulations of development, we provide evidence that molecules promoting the formation of mammalian tooth cusps could help accelerate tooth complexity evolution. Only relatively small developmental changes were needed to derive the more complex, rectangular upper molar typical of early placental mammals from the simpler triangular ancestral pattern. Development may therefore have enabled the relatively fast divergence of the early placental molar dentition.

Development has often been viewed as a constraining force on morphological adaptation, but its precise influence, especially on evolutionary rates, is poorly understood. Placental mammals provide a classic example of adaptive radiation, but the debate around rate and drivers of early placental evolution remains contentious. A hallmark of early dental evolution in many placental lineages was a transition from a triangular upper molar to a more complex upper molar with a rectangular cusp pattern better specialized for crushing. To examine how development influenced this transition, we simulated dental evolution on “landscapes” built from different parameters of a computational model of tooth morphogenesis. Among the parameters examined, we find that increases in the number of enamel knots, the developmental precursors of the tooth cusps, were primarily influenced by increased self-regulation of the molecular activator (activation), whereas the pattern of knots resulted from changes in both activation and biases in tooth bud growth. In simulations, increased activation facilitated accelerated evolutionary increases in knot number, creating a lateral knot arrangement that evolved at least ten times on placental upper molars. Relatively small increases in activation, superimposed on an ancestral tritubercular molar growth pattern, could recreate key changes leading to a rectangular upper molar cusp pattern. Tinkering with tooth bud geometry varied the way cusps initiated along the posterolingual molar margin, suggesting that small spatial variations in ancestral molar growth may have influenced how placental lineages acquired a hypocone cusp. We suggest that development could have enabled relatively fast higher-level divergence of the placental molar dentition.

The skeleton of Congruus kitcheneri, a semiarboreal kangaroo from the Pleistocene of southern Australia

The macropodine kangaroo, Wallabia kitcheneri, was first described in 1989 from a Pleistocene deposit within Mammoth Cave, southwestern Australia, on the basis of a few partial dentaries and maxilla fragments. Here, we recognize W. kitcheneri within the Pleistocene assemblages of the Thylacoleo Caves, south-central Australia, where it is represented by several cranial specimens and two near-complete skeletons, a probable male and female. We reallocate this species to the hitherto monotypic genus Congruus. Congruus kitcheneri differs from all other macropodid species by having a highly unusual pocket within the wall of the nasal cavity. It is distinguished from C. congruus by having a longer, narrower rostrum, a taller occiput and a deeper jugal. Congruus is closest to Protemnodon in overall cranial morphology but is smaller and less robust. In most postcranial attributes, Congruus also resembles Protemnodon, including general limb robustness and the atypical ratio of 14 thoracic to five lumbar vertebrae. It is distinguished by the high mobility of its glenohumeral joints, the development of muscle attachment sites for strong adduction and mobility of the forelimb, and large, robust manual and pedal digits with strongly recurved distal phalanges. These adaptations resemble those of tree-kangaroos more than ground-dwelling macropodines. We interpret this to imply that C. kitcheneri was semiarboreal, with a propensity to climb and move slowly through trees. This is the first evidence for the secondary adoption of a climbing habit within crown macropodines.

Diversification of the mygalomorph spider genus Aname (Araneae: Anamidae) across the Australian arid zone: Tracing the evolution and biogeography of a continent-wide radiation

The assembly of the Australian arid zone biota has long fascinated biogeographers. Covering over two-thirds of the continent, Australia's vast arid zone biome is home to a distinctive fauna and flora, including numerous lineages which have diversified since the Eocene. Tracing the origins and speciation history of these arid zone taxa has been an ongoing endeavour since the advent of molecular phylogenetics, and an increasing number of studies on invertebrate animals are beginning to complement a rich history of research on vertebrate and plant taxa. In this study, we apply continent-wide genetic sampling and one of the largest phylogenetic data matrices yet assembled for a genus of Australian spiders, to reconstruct the phylogeny and biogeographic history of the open-holed trapdoor spider genus Aname L. Koch, 1873. This highly diverse lineage of Australian mygalomorph spiders has a distribution covering the majority of Australia west of the Great Dividing Range, but apparently excluding the high rainfall zones of eastern Australia and Tasmania. Original and legacy sequences were obtained for three mtDNA and four nuDNA markers from 174 taxa in seven genera, including 150 Aname specimen terminals belonging to 102 species-level operational taxonomic units, sampled from 32 bioregions across Australia. Reconstruction of the phylogeny and biogeographic history of Aname revealed three radiations (Tropical, Temperate-Eastern and Continental), which could be further broken into eight major inclusive clades. Ancestral area reconstruction revealed the Pilbara, Monsoon Tropics and Mid-West to be important ancestral areas for the genus Aname and its closest relatives, with the origin of Aname itself inferred in the Pilbara bioregion. From these origins in the arid north-west of Australia, our study found evidence for a series of subsequent biome transitions in separate lineages, with at least eight tertiary incursions back into the arid zone from more mesic tropical, temperate or eastern biomes, and only two major clades which experienced widespread (primary) in situ diversification within the arid zone. Based on our phylogenetic results, and results from independent legacy divergence dating studies, we further reveal the importance of climate-driven biotic change in the Miocene and Pliocene in shaping the distribution and composition of the Australian arid zone biota, and the value of continent-wide studies in revealing potentially complex patterns of arid zone diversification in dispersal-limited invertebrate taxa.

Seasonal environments drive convergent evolution of a faster pace-of-life in tropical butterflies

New ecological niches that may arise due to climate change can trigger diversification, but their colonisation often requires adaptations in a suite of life-history traits. We test this hypothesis in species-rich Mycalesina butterflies that have undergone parallel radiations in Africa, Asia, and Madagascar. First, our ancestral state reconstruction of habitat preference, using c. 85% of extant species, revealed that early forest-linked lineages began to invade seasonal savannahs during the late Miocene-Pliocene. Second, rearing replicate pairs of forest and savannah species from the African and Malagasy radiation in a common garden experiment, and utilising published data from the Asian radiation, demonstrated that savannah species consistently develop faster, have smaller bodies, higher fecundity with an earlier investment in reproduction, and reduced longevity, compared to forest species across all three radiations. We argue that time-constraints for reproduction favoured the evolution of a faster pace-of-life in savannah species that facilitated their persistence in seasonal habitats.

Increased diversification rates are coupled with higher rates of climate space exploration in Australian Acacia (Caesalpinioideae)

Australia is an excellent setting to explore relationships between climate change and diversification dynamics. Aridification since the Eocene has resulted in spectacular radiations within one or more Australian biomes. Acacia is the largest plant genus on the Australian continent, with around 1000 species, and is present in all biomes. We investigated the macroevolutionary dynamics of Acacia within climate space. We analysed phylogenetic and climatic data for 503 Acacia species to estimate a time-calibrated phylogeny and central climatic tendencies for BioClim layers from 132 000 herbarium specimens. Diversification rate heterogeneity and rates of climate space exploration were tested. We inferred two diversification rate increases, both associated with significantly higher rates of climate space exploration. Observed spikes in climate disparity within the Pleistocene correspond with onset of Pleistocene glacial-interglacial cycling. Positive time dependency in environmental disparity applies in the basal grade of Acacia, though climate space exploration rates were lower. Incongruence between rates of climate space exploration and disparity suggests different Acacia lineages have experienced different macroevolutionary processes. The second diversification rate increase is associated with a south-east Australian mesic lineage, suggesting adaptations to progressively aridifying environments and ability to transition into mesic environments contributed to Acacia's dominance across Australia.

The evolutionary diversity of locomotor innovation in rodents is not linked to proximal limb morphology

Rodents are the most species-rich order within Mammalia and have evolved disparate morphologies to accommodate numerous locomotor niches, providing an excellent opportunity to understand how locomotor innovation can drive speciation. To evaluate the connection between the evolutionary success of rodents and the diversity of rodent locomotor ecologies, we used a large dataset of proximal limb CT scans from across Myomorpha and Geomyoidea to examine internal and external limb shape. Only fossorial rodents displayed a major reworking of their proximal limbs in either internal or external morphology, with other locomotor modes plotting within a generalist morphospace. Fossorial rodents were also the only locomotor mode to consistently show increased rates of humerus/femur morphological evolution. We propose that these rodent clades were successful at spreading into ecological niches due to high behavioral plasticity and small body sizes, allowing them to modify their locomotor mode without requiring major changes to their proximal limb morphology.

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.

Marsupial responses to global aridification

Tooth evolution in Australian kangaroos was a late response to climate change in the Neogene