South Australian Museum

The marsupial moles are arguably Australia’s most enigmatic marsupials. Almost indistinguishable from placental(eutherian) moles, they provide a striking example of convergent evolution. Exploring the genome of the south-ern marsupial mole, we provide insights into its unusual biology. We show definitively by retrophylogenomicanalysis that marsupial moles are most closely related to bandicoots and bilbies (order Peramelemorphia). We findevidence of a marked decline in marsupial mole effective population size, most likely preceding the arrival of hu-mans in regions near its range, and potentially corresponding to periods of climatic change. Our analysis of loss ofeye function—an adaptation to subterranean life—reveals a structured order of loss of gene function associatedfirst with the lens, then cone, and finally rod cells. Last, we identify genetic changes suggestive of adaptation to anoxygen-poor environment and of its evolution of partially descended testes.

The life cycle, nesting behaviour and diet breadth of the resin bee Megachile ( Hackeriapis ) tosticauda (Cockerell) are described for the first time. Microscopic imaging of the larval provisions and pollen from the scopa showed that Megachile tosticauda from Adelaide, South Australia, is narrowly oligolectic and specialised on Eucalyptus pollen. Parasites of the nests were identified, and the developmental timeline was outlined. A comparison between behaviour in South Australia (SA) and Western Australia (WA) revealed similarities in nest architecture and parasitism but showed discrepancies in emergence times, nest substrate and potentially diet width. However, the diet analysis from WA was based on visual floral visitations and pollen metabarcoding, neither of which indicate active pollen collection. The difference in diet breadth of this species needs to be ascertained by assessing the larval provisions.

Animal gut microbiomes can be very diverse, and enteric bacteria can profoundly affect the physiology of their host. The gut microbiome can be related to host health and digestion, which ultimately contribute to host body condition. However, we have a limited understanding of the co‐occurrence patterns of gut bacteria in their host, and how co‐occurrence and bacterial diversity change over time. This notion is especially important to animals living in groups as bacteria can transmit through social interactions. We investigated the co‐occurrence patterns of gut bacteria in a lizard host. We repeatedly collected cloacal swabs from 87 sleepy lizards ( Tiliqua rugosa ) from two different study sites over their activity season. We determined the richness and prevalence of 82 enteric bacterial strains and used a probabilistic model to investigate their co‐occurrence. At both study sites, richness and prevalence generally increased over time. We suggest that the lizards acquire strains throughout their activity season by moving through the landscape and inspecting conspecific scats. Lizards continuously tongue‐flick while moving, and thereby ingest bacteria when they move through areas where other animals defaecated. Temperature, rainfall and diet change seasonally, influencing lizard activity, and may influence the observed increase in enterobacterial richness and prevalence. Further, albeit with some exceptions, most strain pairs did not occur significantly more often or less often than expected by chance. This finding shows a lack of structured co‐occurrence, which may imply that most bacterial strains did not facilitate or inhibit each other. The absence of a co‐occurrence pattern could also be driven by random encounters of bacteria shed by other lizards within the habitat. Our results suggest that behaviour (movement patterns, tongue‐flicking), activity patterns and environmental factors collectively drive the temporal pattern of the gut bacterial community in sleepy lizards and potentially other wild reptiles.

Genetic mixing aims to increase the genetic diversity of small or isolated populations, by mitigating genetic drift and inbreeding depression, either by maximally increasing genetic diversity, or minimising the prevalence of recessive, deleterious alleles. However, few studies investigate this beyond a single generation of mixing. Here, we model genetic mixing using captive, low‐diversity recipient population of the threatened Southern brown bandicoot (Isoodon obesulus) over 50 generations and compare wild populations across south‐eastern Australia as candidate source populations. We first assess genetic differentiation between 12 populations, including the first genomic assessment of three mainland Australian and three Tasmanian populations. We assess genetic diversity in the 12 populations using an individualised autosomal heterozygosity pipeline, using these results to identify a candidate recipient population for genetic mixing simulations. We found that populations fell into four major groups of genetic similarity: Adelaide Hills, western Victoria, eastern Victoria, and Tasmania, but populations within these groups were also distinct, and additional substructure was observed in some populations. Our autosomal heterozygosity pipeline indicated significant variability in mean heterozygosity between populations, identifying one extremely genetically degraded population on Inner Sister Island, Tasmania. Genetic mixing simulations of a low heterozygosity captive population in Victoria suggested the greatest increase in heterozygosity would be reached by using highly differentiated populations as mixing sources. However, when removing populations that may represent taxonomically discrete lineages, neither metrics of differentiation nor heterozygosity was strongly correlated with modelled heterozygosity increase, indicating the value of simulation‐based approaches when selecting source populations for population mixing.

Abstract Abstract Image We report an extensive 1H to 29Si cross-polarization (CP) nuclear magnetic resonance (NMR) investigation of a wide range of opal-AG, opal-AN and opal-CT samples, including both spectra and contact time dependent kinetics. After an extensive study of Hartmann–Hahn optimization, spin rates and power levels we are forced to conclude that the kinetics of the system is only amenable to comparative analysis rather than determination of absolute values. Q3 peaks showed both signal growth (TIS) and decay (T1ρI) while Q4 centers only showed the TIS component for all opals studied, consistent with isolated proton sources in the latter. Q2 centers are only a minor factor in most cases. Initial 1H–29Si 2D-HETCOR spectral evidence suggests that multiple Q3 and Q4 sites, with differing chemical shifts, are involved in the CP process. Active silicate centers and water sites may differ for single pulse (SP) and CP modes. Both SP and CP techniques are best used for comparative studies within each and between opal classes. Differing geometries are implied for all three types of opal. © 2024 American Chemical Society

Ediacaran fossils, obtained in stratigraphic context in 1993, 1995, and 1996, with the assistance of A. Seilacher, IGCP project 320 scientists, and the Geological Survey of Namibia, are described for the first time. Most are from the Kliphoek and Buchholzbrunn members of the Dabis Formation and the Huns and Spitskop members of the Urusis Formation, Witputs subbasin, but a significant number, including Pteridinium , are from the Kliphoek Member, Zaris Formation, and the Neiderhagen Member, Nudaus Formation, north of the Osis arch, which separates the two subbasins. We extend the stratigraphic ranges and geographic distributions of several important taxa, including Archaeichnium , Ernietta , Pteridinium , and Swartpuntia , provide reassessments of the paleobiology of these and other organisms, and describe a new sponge—possibly an unmineralized archaeocyath— Arimasia germsi n. gen. n. sp. We also describe and illustrate various ichnofossils (including the oldest known traces from the Nama Group), narrow down the first appearance of Treptichnus in the Nama succession, and reinforce the idea that there was a prolific infauna of micrometazoans during the latest Ediacaran by naming and describing previously reported microburrows found on the surfaces of gutter casts as Ariichnus vagus n. igen. n. isp. UUID: http://zoobank.org/8c267425-135a-4b0a-98b6-cf726515cbf2

High-resolution computed tomography (HRCT) has become a widely used tool for studying the inner ear morphology of vertebrates. Amphisbaenians are one of the most specialized groups of fossorial reptiles but are poorly understood relative to other squamate reptile. In this paper we survey the anatomy of the inner and middle ear of these fossorial reptiles using HRCT models and we describe qualitatively and quantitatively (using 3D morphometrics) the anatomy of the inner ear. Amphisbaenians are diverse in skull anatomy, especially in the configuration of the snout, which correlates with digging modes. We demonstrate that the ear also exhibits a diversity of configurations, which are independent of phylogenetic relationships. Results from morphological analyses also allow us to describe 11 new potentially informative phylogenetic characters including some that help to diagnose amphisbaenians, such as: 1) the globular vestibule, ii) semicircular canals arranged in a circular trajectory, and iii) an extensive area of interaction between the columella footplate and the lagenar recess. Among extant amphisbaenians, Rhineura floridana has the most unusual inner ear configuration, including a horizontal semicircular canal that is in the same orientation as the inclined snout. The new morphological information helps us to better understand the morphology of headfirst-burrowing fossorial reptiles and contributes new data for resolution of phylogenetic relationships among amphisbaenians.

Coadaptation of mitochondrial and nuclear genes is essential for proper cellular function. When populations become isolated, theory predicts that they should maintain mito‐nuclear coadaptation in each population, even as they diverge in genotype. Mito‐nuclear incompatibilities may therefore arise when individuals from populations with divergent co‐evolved mito‐nuclear gene sets are re‐united and hybridise, contributing to selection against inter‐population hybrids and, potentially, to speciation. Here, we explored genetic divergence and gene flow between populations of a stingless bee (Tetragonula hockingsi) that have highly divergent mitogenomes. We identified three distinct populations across the species' 2500 km range on the east coast of Queensland (Australia): ‘Cape York’, ‘Northern’, and ‘Southern’. The mitogenomes of each population showed > 12% pairwise nucleotide divergence from each other, and > 7% pairwise amino acid divergence. Based on nuclear SNPs from reduced representation sequencing, we identified at least two zones of gene flow between populations: a narrow natural zone between Northern and Southern populations (coinciding with a biogeographic barrier, the Burdekin Gap), and an artificial zone at the southern edge of the species' distribution, where Cape York, Northern, and Southern mito‐lineages have been brought together in recent decades due to beekeeping. In the artificial hybrid zone, we also confirmed that males of all three mito‐lineages were attracted to the mating aggregations of Southern queens, consistent with inter‐population hybridisation. Populations of T. hockingsi thus appear to be in the ‘grey zone’ of the speciation continuum, having strong genetic differentiation but incomplete reproductive isolation. Among the nuclear SNPs most differentiated between Northern and Southern populations, several were associated with genes involved in mitochondrial function, consistent with populations having co‐diverged mito‐nuclear gene sets. Our observations suggest that coadapted sets of mitochondrial and nuclear genes unique to each population of T. hockingsi may play a role in maintaining population boundaries, though more study is needed to confirm the fitness costs of mito‐nuclear incompatibilities in hybrid individuals.

Understanding the profound influence of climatic and tectonic histories on adaptation and speciation is a crucial focus in biology research. While voyages like Humboldt’s expedition shaped our understanding of adaptation, the origin of current biodiversity remains unclear – whether it arose in situ or through dispersal from analogous habitats. Situated in the geologically complex Australopacific region, our study focuses on Limbodessus diving beetles (Dytiscidae), a diverse genus distributed from underground aquifers in Western Australia to alpine meadows in New Guinea. Using low-coverage whole-genome sequencing, we established a time-calibrated phylogenetic tree, elucidating Limbodessus’ origin in the mid-late Miocene, most likely in the Sahul continent (i.e., Australia and New Guinea) and western Pacific archipelagos. Our results provide evidence for parallel colonization and speciation at extreme altitudinal ends, driven by aridification in Australia, influencing subterranean colonization, and in situ diversification of alpine taxa by passive-uplifting of local biota in New Guinea. Furthermore, our findings highlight instances of subterranean speciation in isolated underground aquifers, marked by recurrent independent colonizations of this habitat.

Puttapaite, Pb2Mn 2+ 2ZnCr 3+ 4O2(AsO4)4(OH)6·12H2O, is a new mineral from the Beltana deposit, Puttapa, Flinders Ranges, South Australia, Australia. It forms rosette-like aggregates to 50 um across composed of diamond-shaped tablets to 45 um in length and 5 um in thickness. Crystals are flattened on {001} and the observed forms are {001} and {110}. The calculated density is 3.562 g/cm-3. Optically, Puttapaite is biaxial (−) with α = 1.700(5), β = 1.720(5), γ = 1.730(5) and 2V (meas.) = 67(1)º. Electron microprobe analyses gave the empirical formula (based on 36 oxygen atoms pfu) Pb1.96(Mn 2+ 1.52Ca0.28Sr0.22)Σ2.02(Zn0.40Mg0.39Cu0.15)Σ0.94(Cr 3+ 2.89Al0.45Fe 3+ 0.40,Mn 3+ 0.26)Σ4.00 O2[(AsO4)3.71(Cr 6+ O4)0.29]Σ4.00(OH)6.13·11.87H2O. Puttapaite is monoclinic, C2/m, with a = 12.405(3), b = 10.565(2), c = 12.311(3) Å, β = 106.06(3)º, V = 1550.4(6) Å 3 and Z = 2. The structure was solved using synchrotron single-crystal x-ray diffraction data and refined to R1 = 0.1189 on the basis of 915 observed reflections with F0 > 4s(F0). Puttapaite has a unique structure that consists of M4O16 clusters that share corners with TO4 tetrahedra, which in turn share corners with M1 octahedra in the [010] direction. https://doi.org/10.1180/mgm.2024.60 Published online by Cambridge University Press 2 Clusters link in the [001] direction via corner sharing M2 octahedra to form sheets parallel to {100}. Pb anions lie between the sheets.

We studied ontogenetic variation in skull morphology in tiger snakes sampled from mainland South Australia (Coffin Bay), mainland Western Australia (Herdsman Lake), Franklin Island, and Hopkins Island. The snakes from the two islands were selected because of their unusually large absolute body and head size, likely attained as a result of dietary constraints and strong selective pressure during thousands of years of isolation on islands. We performed geometric morphometric analysis of the skulls from these snakes to identify and precisely quantify morphological differences. Island snakes are born larger (trunk length) than mainland snakes, and consequently also tend to have larger absolute head size at birth. The heads of island snakes also show a faster relative growth rate (positive allometry) compared to those of mainland snakes, likely to cope with the large prey items found on these islands. However, the snakes from the two islands differ from each other in terms of morphological change associated with ontogeny, especially with regard to a palatal bone (ectopterygoid), which, compared to mainland snakes, is relatively longer in the snakes from Hopkins Island but shorter in the snakes from Franklin Island. Some morphological traits potentially associated with promoting a larger gape were also observed in one of the mainland populations (Herdsman Lake), consistent with standing variability for selection. Our results reveal that discernible changes in morphology and allometry in skull bones have evolved in island populations of tiger snakes in less than 10 000 years, and suggest that the large heads of island tiger snakes might develop via slightly different paths through morphospace on different islands.

The early evolution of sex chromosomes has remained obscure for more than a century. The Vandiemenella viatica species group of morabine grasshoppers is highly suited for studying the early stages of sex chromosome divergence and degeneration of the Y chromosome. This stems from the fact that neo‐XY sex chromosomes have independently evolved multiple times by X‐autosome fusions with different autosomes. Here, we generated new chromosome‐level assemblies for two chromosomal races representing karyotypes with and without neo‐sex chromosomes (P24XY and P24X0), and sequence data of a third chromosomal race with a different neo‐XY chromosome system (P25XY). Interestingly, these two neo‐XY chromosomal races are formed by different X‐autosome fusions (involving chr1 and chrB, respectively), and we found that both neo‐Y chromosomes have partly ceased to recombine with their neo‐X counterpart. We show that the neo‐XY chromosomes have diverged through accumulation of SNPs and structural mutations, and that many neo‐Y‐linked genes have degenerated since recombination ceased. However, the non‐recombining regions of neo‐Y chromosomes host non‐degenerated genes crucial for sex determination, such as sex‐lethal and transformer , alongside genes associated with spermatogenesis, fertility, and reproduction, illustrating their integrative role as a masculinizing supergene. Contrary to expectations, the neo‐Y chromosomes showed (slightly) lower density of transposable elements (TEs) compared to other genomic regions. The study reveals the unique dynamics of young sex chromosomes, with evolution of recombination suppression and pronounced decay of (some) neo‐sex chromosome genes, and provides a compelling case illustrating how chromosomal fusions and post‐fusion mutational processes contribute to the evolution of supergenes.

The evolution of limb reduction in squamates is a classic example of convergence, but the skeletal morphological patterns associated with it are underexplored. To provide insights on the biomechanical and developmental consequences of transitions to limb reduction, we use geometric morphometrics to examine the morphology of pectoral and pelvic girdles in 90 species of limb-reduced skinks and their fully limbed relatives. Clavicle shapes converge towards an acute anterior bend when forelimbs are lost but hindlimbs are retained—a morphology typical of sand-swimmers. This may either indicate functional adaptations to locomotion in fine substrates, or a developmental consequence of complete limb loss. The shape of limb-bearing elements of both girdles (coracoid and pelvis) instead closely mirrors limb reduction, becoming more simplified as undulation replaces limbed locomotion. Integration between girdles decreases in taxa lacking elements of the forelimbs but not hindlimbs, indicating differential selection on each girdle in response to distinct locomotory strategies. However, this pattern becomes less clear when considering phylogenetic history, perhaps because it is limited to one specific clade (Lerista). We show how the functional demands of locomotion can induce changes at different levels of organismal organization, including both external and internal structures.

Insects have a complex coevolutionary history with bacterial symbionts, among which Wolbachia pipientis stands out for its prevalence and role in reproductive manipulation. Wolbachia can induce cytoplasmic incompatibility, feminisation, male killing, and parthenogenesis, greatly influence the population genetics of their hosts and are potential drivers of invertebrate speciation. We might then assume that Wolbachia could act synergistically with other factors, such as niche conservation and isolation by distance, to drive speciation in hyper-diverse invertebrate taxa. The Fijian archipelago hosts a remarkable and recently diverged clade of Lasioglossum (Homalictus) bees. Some of these Lasioglossum have highly unusual species-level sex ratios and mitochondrial diversities, which can be hallmarks of infection by a bacterial reproductive manipulator. To examine the role of Wolbachia in Fijian Lasioglossum speciation, we screened the endemic Fijian bees for Wolbachia using the Wolbachia surface protein gene (wsp). We compare the distribution of Wolbachia infection across species with host mitochondrial haplotype diversity and conducted phylogenetic analyses to determine the relationship of host relatedness and symbiont infection status. We found that Wolbachia haplotypes probably span across supergroups A and B. In addition, we found multiple haplotypes were highly similar, with the most abundant group of wsp haplotypes being closely related with the drosophila Wolbachia strain wHa. We found evidence of mostly horizontal and limited vertical transmission, and little evidence for Wolbachia-host cospeciation. We show that, contrary to general patterns, Wolbachia-infected Lasioglossum species have higher mitochondrial diversity. Finally, we present evidence for the potential of multiple modes of host manipulation in this clade.

Snake venoms are complex mixtures of toxic proteins that hold significant medical, pharmacological and evolutionary interest. To better understand the genetic diversity underlying snake venoms, we developed VenomCap, a novel exon‐capture probe set targeting toxin‐coding genes from a wide range of elapid snakes, with a particular focus on the ecologically diverse and medically important subfamily Hydrophiinae. We tested the capture success of VenomCap across 24 species, representing all major elapid lineages. We included snake phylogenomic probes in the VenomCap capture set, allowing us to compare capture performance between venom and phylogenomic loci and to infer elapid phylogenetic relationships. We demonstrated VenomCap's ability to recover exons from ~1500 target markers, representing a total of 24 known venom gene families, which includes the dominant gene families found in elapid venoms. We find that VenomCap's capture results are robust across all elapids sampled, and especially among hydrophiines, with respect to measures of target capture success (target loci matched, sensitivity, specificity and missing data). As a cost‐effective and efficient alternative to full genome sequencing, VenomCap can dramatically accelerate the sequencing and analysis of venom gene families. Overall, our tool offers a model for genomic studies on snake venom gene diversity and evolution that can be expanded for comprehensive comparisons across the other families of venomous snakes.