Australian Museum
  • Sydney, New South Wales, Australia
Recent publications
Upside-down jellyfish (Cassiopea spp.) are predominantly tropical, but there have been recent reports of medusae in temperate environments. In 2017 they were recorded in temperate Lake Macquarie, Australia, where they have a tendency to disappear from this area through late winter (Austral, August). This raises questions about the role of temperature as a controlling factor of their abundance, and future density increases with warming oceans as a result of climate change. Here we test the degree to which temperature may drive winter die-offs of the medusa stage in temperate environments, and how this may change with altered thermal regimes. We assessed the physiological response of Cassiopea (via measurement of bell pulsation rate, bell diameter, and routine metabolic rate) under a regime mirroring Lake Macquarie's seasonal temperature drop (autumn into winter) compared to three other temperature profiles: 1) seasonal profile with predicted climate change (+ 2 °C), 2) stable temperatures equivalent to the end of autumn (20 °C) and, 3) a profile that mimicked the increasing temperatures from winter into summer (20 °C increasing to 24 °C). Overall, the results indicate that, compared to the ambient state, elevated temperatures can have positive effects on performance of Cassiopea medusae as evidenced by greater bell pulsation rate and bell diameter. The rate of bell diameter decline was lower in all elevated temperature treatments relative to the ambient profile. This highlights the capacity for elevated temperatures in the future to slow the rate of bell degradation, contributing to an increased probability of overwinter survival, thus increasing the size and duration of Cassiopea blooms in temperate waterways such as Lake Macquarie.
Many coral reef fishes display remarkable genetic and phenotypic variation across their geographic ranges. Understanding how historical and contemporary processes have shaped these patterns remains a focal question in evolutionary biology, since they reveal how diversity is generated and how it may respond to future environmental change. Here we compare the population genomics and demographic histories of a commercially and ecologically important coral reef fish, the common coral grouper (Plectropomus leopardus [Lacépède 1802]), across two adjoining regions (the Great Barrier Reef; GBR, and the Coral Sea, Australia) spanning approximately 14 degrees of latitude and 9 degrees of longitude. We analysed 4,548 single nucleotide polymorphism (SNP) markers across 11 sites and show that genetic connectivity between regions is low, despite their relative proximity (~ 100 km) and an absence of any obvious geographic barrier. Inferred demographic histories using 10,479 markers suggest that the Coral Sea population was founded by a small number of GBR individuals and that divergence occurred ~ 190 kya under a model of isolation with asymmetric migration. We detected population expansions in both regions, but estimates of contemporary effective population sizes were approximately 50 % smaller in Coral Sea sites, which also had lower genetic diversity. Our results suggest that P. leopardus in the Coral Sea have experienced a long period of isolation that precedes the recent glacial period (~ 10 – 120 kya) and may be vulnerable to localised disturbances due to their relative reliance on local larval replenishment. While it is difficult to determine the underlying events that led to the divergence of Coral Sea and GBR lineages, we show that even geographically proximate populations of a widely dispersed coral reef fish can have vastly different evolutionary histories.
Anthropogenic habitat modification significantly challenges biodiversity. With its intensification, understanding species’ capacity to adapt is critical for conservation planning. However, little is known about whether and how different species are responding, particularly among frogs. We used a continental‐scale citizen science dataset of >226,000 audio recordings of 42 Australian frog species to investigate how calling — a proxy for breeding — phenology varied along an anthropogenic modification gradient. Calling started earlier and breeding seasons lengthened with increasing modification intensity. Breeding seasons averaged 22.9 ± 8.25 days (standard error) longer in the most modified compared to the least modified regions, suggesting that frog breeding activity was sensitive to habitat modification. We also examined whether calls varied along a modification gradient by analysing the temporal and spectral properties of advertisement calls from a subset of 441 audio recordings of three broadly distributed frog species. There was no appreciable effect of anthropogenic habitat modification on any of the measured call variables, although there was high variability. With continued habitat modification, species may shift towards earlier and longer breeding seasons, with largely unknown ecological consequences in terms of proximate and ultimate fitness.
Surveys of larval fishes require accurate identifications of larvae, which are essential to understand early life history of fish, fish ecology and fisheries. However, the identification of larval fishes requires microscopic examination that is substantially more difficult than that of juvenile and adult fishes, as many larval stages remain undescribed. Furthermore, the traditional, formalin fixation of larval fishes were previously thought to prevent genetic sequencing compared to ethanol preserved larvae. In this study, we used an integrative taxonomic approach based on morphology, imaging and DNA barcoding of the mitochondrial (mtDNA) cytochrome c oxidase subunit (COI) gene. We used this approach in both cultured yellowtail kingfish, Seriola lalandi and wild sourced fish larvae that had been fixed in 5% formalin. Based on controlled and in-field formalin treatments, DNA barcoding and genetic species identification was 100% successful in cultured yellowtail kingfish fixed in formalin for up to 6 months, while barcoding of wild caught fish larvae enabled species identification of 93% of up to 8-weeks formalin fixed specimens. Furthermore, we demonstrated the viability of using either whole larval individuals or a single eyeball (<1 mm diameter, thus retaining the specimen intact) from formalin fixed larval fish for genetic species identification. While COI genetic identifications from the in-field experiments were patchier than the controlled experiments, our study highlights the possibility of recovering suitable DNA from larvae that have been fixed in formalin for up to six months. This was achieved by applying DNA extraction methods that use de-cross-linking steps and species identification based on both full-length reference and mini-barcodes. Our study provides the larval fish research community with a practical framework for undertaking both morphological and genetic identifications of larval fish assemblages, particularly when geographic relevant reference sequence databases (based on vouchered adult fishes) are available for interrogation. It also simplifies field-based collection of samples allowing their preservation in formalin without compromising the genetic identification of species.
The application of high-throughput, short-read sequencing to degraded DNA has greatly increased the feasibility of generating genomic data from historical museum specimens. While many published studies report successful sequencing results from historical specimens; in reality, success and quality of sequence data can be highly variable. To examine predictors of sequencing quality, and methodological approaches to improving data accuracy, we generated and analyzed genomic sequence data from 115 historically collected museum specimens up to 180 years old. Data span both population genomic and phylogenomic scales, including historically collected specimens from 34 specimens of four species of Australian rock-wallabies (genus Petrogale) and 92 samples from 79 specimens of Australo-Papuan murine rodents (subfamily Murinae). For historical rodent specimens, where the focus was sampling for phylogenomics, we found that regardless of specimen age, DNA sequence libraries prepared from toe pad or bone subsamples performed significantly better than those taken from the skin (in terms of proportion of reads on target, number of loci captured, and data accuracy). In total, 93% of DNA libraries from toe pad or bone subsamples resulted in reliable data for phylogenetic inference, compared to 63% of skin subsamples. For skin subsamples, proportion of reads on target weakly correlated with collection year. Then using population genomic data from rock-wallaby skins as a test case, we found substantial improvement in final data quality by mapping to a high-quality “closest sister” de novo assembly from fresh tissues, compared to mapping to a sample-specific historical de novo assembly. Choice of mapping approach also affected final estimates of the number of segregating sites and Watterson's θ, both important parameters for population genomic inference. The incorporation of accurate and reliable sequence data from historical specimens has important outcomes for evolutionary studies at both population and phylogenomic scales. By assessing the outcomes of different approaches to specimen subsampling, library preparation and bioinformatic processing, our results provide a framework for increasing sequencing success for irreplaceable historical specimens.
Environmental DNA (eDNA) metabarcoding is increasingly being used to assess community composition in coastal ecosystems. In this study, we chose to examine temporal and spatial changes in the aquatic community of Manly Lagoon-one of the most heavily developed and polluted estuaries in eastern Australia. Based on met-abarcoding of the 16S mitochondrial gene (for fish) and the 18S nuclear gene (for macroinvertebrates), we identified seasonal differences in fish and macroinvertebrate community composition as well as species richness, which correlated, in some cases, with the environmental parameters of sea surface temperature and freshwater input. Moreover, given the greater taxonomic resolution of fish versus macroinvertebrate assignments, we identified several known migratory fish species of management importance that contributed significantly to the overall patterns observed. Overall, our data support the use of eDNA metabarcoding to track fish assemblages shifting in response to environmental drivers in polluted estuaries with increased sampling and consultation with historical data.
The consumption of fungi by animals is a significant trophic interaction in most terrestrial ecosystems, yet the role mammals play in these associations has been incompletely studied. In this review, we compile 1 154 references published over the last 146 years and provide the first comprehensive global review of mammal species known to eat fungi (508 species in 15 orders). We review experimental studies that found viable fungal inoculum in the scats of at least 40 mammal species, including spores from at least 58 mycorrhizal fungal species that remained viable after ingestion by mammals. We provide a summary of mammal behaviours relating to the consumption of fungi, the nutritional importance of fungi for mammals, and the role of mammals in fungal spore dispersal. We also provide evidence to suggest that the morphological evolution of sequestrate fungal sporocarps (fruiting bodies) has likely been driven in part by the dispersal advantages provided by mammals. Finally, we demonstrate how these interconnected associations are widespread globally and have far-reaching ecological implications for mammals, fungi and associated plants in most terrestrial ecosystems.
We introduce a new method of estimating accepted species diversity by adapting mark-recapture methods to comparisons of taxonomic databases. A taxonomic database should become more complete over time, so the error bar on an estimate of its completeness and the known diversity of the taxon it treats will decrease. Independent databases can be correlated, so we use the time course of estimates comparing them to understand the effect of correlation. If a later estimate is significantly larger than an earlier one, the databases are positively correlated, if it is significantly smaller, they are negatively correlated, and if the estimate remains roughly constant, then the correlations have averaged out. We tested this method by estimating how complete MolluscaBase is for accepted names of terrestrial gastropods. Using random samples of names from an independent database, we determined whether each name led to a name accepted in MolluscaBase. A sample tested in August 2020 found that 16.7% of tested names were missing; one in July 2021 found 5.3% missing. MolluscaBase grew by almost 3,000 accepted species during this period, reaching 27,050 species. The estimates ranged from 28,409 ± 365 in 2021 to 29,063 ± 771 in 2020. All estimates had overlapping 95% confidence intervals, indicating that correlations between the databases did not cause significant problems. Uncertainty beyond sampling error added 475 ± 430 species, so our estimate for accepted terrestrial gastropods species at the end of 2021 is 28,895 ± 630 species. This estimate is more than 4,000 species higher than previous ones. The estimate does not account for ongoing flux of species into and out of synonymy, new discoveries, or changing taxonomic methods and concepts. The species naming curve for terrestrial gastropods is still far from reaching an asymptote, and combined with the additional uncertainties, this means that predicting how many more species might ultimately be recognized is presently not feasible. Our methods can be applied to estimate the total number of names of Recent mollusks (as opposed to names currently accepted), the known diversity of fossil mollusks, and known diversity in other phyla.
Examining why human populations used specific technologies in the Final Pleistocene is critical to understanding our evolutionary path. A key Final Pleistocene techno-tradition is the Howiesons Poort, which is marked by an increase in behavioral complexity and technological innovation. Central to this techno-tradition is the production of backed artifacts—small, sharp blades likely used as insets in composite tools. Although backed artifacts were manufactured for thousands of years before the Howiesons Poort, this period is marked by a phenomenal increase in their production. In this paper we test both social and environmental hypotheses to explain this phenomenon. We correlate environmental data with changing frequencies of backed artifact production at Sibudu and assess morphological similarity across seven sites in southern Africa. We find that these artifacts are made to a similar template across different regions and that their increased production correlates with multiple paleo-environmental proxies. When compared to an Australian outgroup, the backed artifacts from the seven southern African sites cluster within the larger shape space described by the Australian group. This leads us to argue that the observed standardized across southern Africa is related to cultural similarities and marks a strengthening of long-distance social ties during the MIS4.
Trait databases have become important resources for large-scale comparative studies in ecology and evolution. Here we introduce the AnimalTraits database, a curated database of body mass, metabolic rate and brain size, in standardised units, for terrestrial animals. The database has broad taxonomic breadth, including tetrapods, arthropods, molluscs and annelids from almost 2000 species and 1000 genera. All data recorded in the database are sourced from their original empirical publication, and the original metrics and measurements are included with each record. This allows for subsequent data transformations as required. We have included rich metadata to allow users to filter the dataset. The additional R scripts we provide will assist researchers with aggregating standardised observations into species-level trait values. Our goals are to provide this resource without restrictions, to keep the AnimalTraits database current, and to grow the number of relevant traits in the future.
Global warming experienced during the late Pleistocene transition to the Holocene resulted in an altered paleo-costal landscape. This included the demise of megafauna species, such as mammoth, mastodon and black rhinoceros. Simultaneously the landscape experienced a transition from tundra to that of taiga and coniferous forests that influenced both plant and animal diversity. Rising sea levels inundated the coastal plain and formed enriched ingression bays that supported the propagation of aquatic species, such as shellfish, fish, sea mammals and migratory waterfowl. Some seasonally migratory species, such as salmon, began to penetrate the freshwater streams further inland. The study of maritime adaptations among the prehistoric cultures of the Russian Far East has focused on several problems, including environmental change, the identification of early coastal populations, the transition from land-based hunter-gatherer subsistence practices to the exploitation of river and littoral resources, and accompanying changes in social organization and technology. The late Pleistocene Ustinovka Complex dates to between 22,469 and 10,746 cal BP. This compares to the related Early Neolithic age of the Rudnaya Culture dating between from 8345–6835 ka BP. The presence of bifacial tools, ceramic cooking vessels, fish bones, a stone fish effigy, a carved narwhal effigy, bone harpoon points, marine shell ornaments and buttons, carved bone pendants, light ground structures and lithic caches suggests the function of seasonal base camps engaged in a hunting-gathering-fishing lifestyle that increasingly focused upon aquatic resources.
This study aimed to improve our understanding of the immediate response of 26 priority species of land snail that may have been severely impacted by the 2019/2020 megafire event in north-eastern New South Wales. Our study covered a range of ecosystem types over an area of approximately 20,400 km2. We searched 70 survey sites that differed in burn severity for all species of land snail visually on-site and by sifting leaf litter samples under a microscope in the laboratory. These survey sites were selected for representing pre-existing occurrence records of priority species at sites that differed in mapped fire severity classes as based on Fire Extent and Severity data available from public sources. We also surveyed unburnt sites for comparative purposes. We found that nearly all survey sites encompassed a patchwork of areas with different burn extent and severity and that more humid forest types were overall affected by lower fire extent and severity than surrounding more xeric forest types. Only one site with extreme fire extent and severity was surveyed. The survey covered 165 historical occurrence records, 96 of which (58%) were re-confirmed. We also found 55 new occurrence records, 11 of which were in burnt and 44 in unburnt sites. Burnt and unburnt sites showed slight, yet insignificant differences in the redetection rate of species, which was generally low (on average 50–65%). Our data does not reveal an association between the number of specimens found at sites and burn severity and extent (from unburnt to extreme burnt). While we infer that populations have declined in areas affected by more severe fires, we found proportions of the survey area to be affected by fires of lower severity, which likely did not substantially affect the size of local land snail populations. Based on this, we conclude that initial concerns that the bushfires had led to a substantial deterioration of the conservation status of land snails are not generally corroborated. Instead, we have assessed just 3 species (10% of all studied species) as of conservation concern and 7 species (23%) as near threatened due to direct impacts of the 2019/2020 megafires. However, the paucity of occurrence records for many species and our limited knowledge of their ecology hampers a more detailed assessment of the potential fire impacts on many species, including possible on-going threats. Long-term monitoring and research are critical to ensure effective management especially of narrow range endemics.
Comprehensive assessments of species’ extinction risks have documented the extinction crisis and underpinned strategies for reducing those risks. Global assessments reveal that, among tetrapods, 40.7% of amphibians, 25.4% of mammals and 13.6% of birds are threatened with extinction. Because global assessments have been lacking, reptiles have been omitted from conservation-prioritization analyses that encompass other tetrapods. Reptiles are unusually diverse in arid regions, suggesting that they may have different conservation needs. Here we provide a comprehensive extinction-risk assessment of reptiles and show that at least 1,829 out of 10,196 species (21.1%) are threatened—confirming a previous extrapolation and representing 15.6 billion years of phylogenetic diversity. Reptiles are threatened by the same major factors that threaten other tetrapods—agriculture, logging, urban development and invasive species—although the threat posed by climate change remains uncertain. Reptiles inhabiting forests, where these threats are strongest, are more threatened than those in arid habitats, contrary to our prediction. Birds, mammals and amphibians are unexpectedly good surrogates for the conservation of reptiles, although threatened reptiles with the smallest ranges tend to be isolated from other threatened tetrapods. Although some reptiles—including most species of crocodiles and turtles—require urgent, targeted action to prevent extinctions, efforts to protect other tetrapods, such as habitat preservation and control of trade and invasive species, will probably also benefit many reptiles.
Global warming is modifying the phenology, life‐history traits and biogeography of species around the world. Evidence of these effects have increased over recent decades; however, we still have a poor understanding of the possible outcomes of their interplay across global climatic gradients, hindering our ability to accurately predict the consequences of climate change in populations and ecosystems. We examined the effect that changes in biogeography can have on the life‐history traits of two of the most successful range‐extending fish species in the world: the tropical rabbitfishes Siganus fuscescens and Siganus rivulatus. Both species have established abundant populations at higher latitudes (poleward) in the northern and southern hemispheres and have been identified as important ecological engineers with the potential to alter the community structure of seaweed forests (Laminariales and Fucales) in temperate regions. Life‐history trait information from across their global distribution was compiled from the published literature and meta‐analyses were conducted to assess changes in (i) the onset and duration of reproductive periods, (ii) size at maturity, (iii) fecundity, (iv) growth rates, (v) maximum body sizes and (vi) longevity in populations at the leading edge of range expansion in relation to sea surface temperature and primary productivity (a common proxy for nutritional resource levels). Populations at highest latitudes had shortened their reproductive periods and reduced growth rates, taking longer to reach sexual maturity and maximum sizes, but compensated this with higher fecundity per length class and longer lifespans than populations in warmer environments. Low primary productivity and temperature in the Mediterranean Sea resulted in lower growth rates and body sizes for S. rivulatus, but also lower length at maturity, increasing life‐time reproductive output. The results suggest that plasticity in the phenology and life‐history traits of range‐expanding species would be important to enhance their fitness in high latitude environments, facilitating their persistence and possible further poleward expansions. Quantifying the magnitude and direction of these responses can improve our understanding and ability to forecast species redistributions and its repercussions in the functioning of temperate ecosystems.
Koala rescue from the bushfires over the extended 2019–2020 fire season in NSW was a high-profile media topic over many months. We sought to determine how many fire-affected koalas were rescued and admitted to rehabilitation in NSW, what was the fate of these koalas, what parts of the state were involved, and how many other koalas entered rehabilitation at the same time? These matters are not only of broad public interest, it is important information for the conservation and management of koalas. The fire season ended in March 2020. In June 2020 we wrote to and received replies from, the licensed rehabilitation groups in NSW that rescued koalas, seeking to quantify the impact of the 2019–2020 bushfires. The answers were: 209 koalas came into care due to the bushfires, and of these, 106 were either euthanised or died, 74 were released, and the remainder were still in care, but due for release soon. The number of koalas that came into care for reasons not related to the fires over the same time period was 307. From the point of view of each surviving individual koala, the rehabilitation was a success. What the rescue and rehabilitation has done is highlight the difficulties that koalas face in dealing with fire. This information will contribute to koala management at a local, State and Commonwealth level, particularly in relation to koala rehabilitation policies, and it will be increasingly important given the likelihood of more frequent fires.
Forest fire size, frequency and severity are increasing worldwide, with corresponding reductions in long-unburnt habitat and greater modification of forest structure over wider areas. Understanding the implications for animals is imperative in optimizing management for species persistence and overall biodiversity. We investigated how avian responses to historical high-severity fire differ in forests at short (five years) and mid-range (16 years) time since fire, including whether increased time since fire mitigates any negative responses to high-severity fire. Sites were established in fire-prone dry forests of the Greater Blue Mountains World Heritage Area, Australia. A Bayesian latent variable analysis of bird data obtained from acoustic recordings was used to estimate the occurrence of 74 species in relation to time since fire (short, mid-range), the spatial extent of historical high-severity fire (limited, extensive), and their interaction. Time since fire influenced the number of species present, but only where high-severity fire had been extensive. Here, the lowest and highest number of species in the study occurred where time since fire was short and mid-range, respectively. At least ten species responded either positively or negatively to high-severity fire, but for nine of these species the response did not change with time since fire, potentially implicating persistent effects of such fires on habitat. Six other species were unlikely to occur at short time since fire, requiring habitat at mid-range time since fire. This finding suggests that these species would benefit from strategic retention of forest with longer fire-ages under increased fire activity associated with climate change.
We conducted a quantitative literature review of genetic diversity (GD) within and among populations in relation to categorical population size and isolation (together referred to as “insularity”). Using populations from within the same studies, we were able to control for between‐study variation in methodology, as well as demographic and life histories of focal species. Contrary to typical expectations, insularity had relatively minor effects on GD within and among populations, which points to the more important role of other factors in shaping evolutionary processes. Such effects of insularity were sometimes seen—particularly in study systems where GD was already high overall. That is, insularity influenced GD in a study system when GD was high even in non‐insular populations of the same study system—suggesting an important role for the “scope” of influences on GD. These conclusions were more robust for within population GD versus among population GD, although several biases might underlie this difference. Overall, our findings indicate that population‐level genetic assumptions need to be tested rather than assumed in nature, particularly for topics underlying current conservation management practices. We conducted a quantitative literature review of genetic diversity (GD) within and among populations in relation to categorical population size and isolation (together referred to as “insularity”). Contradictory to typical expectations, we found that insularity had relatively minor effects on GD within and among populations, which points to the more important roles of other factors in shaping evolutionary processes. Our findings indicate that population‐level genetic assumptions need to be tested rather than assumed in nature, particularly for topics underlying current conservation management practices.
A new species of the roughy fish genus Hoplostethus is described from 11 types and a non‐type specimen collected from Taiwanese waters. It can be distinguished from its congeners by a combination of characters: pectoral‐fin rays 14–17 (modally 15–16); pyloric caeca 65–84; total gill rakers 19–20; predorsal scales 18–22; oral cavity, branchial chamber, top and underside of tongue, and peritoneum uniformly black; distal margin of membrane between dorsal‐fin spines black; caudal fin without a black margin; caudal‐fin base brownish. Comparisons of the new species with similar species are provided. DNA barcoding supports the monophyly of the new species, which appears to be closely related to H. japonicus (average COI K2P distance of 4.1%). This article is protected by copyright. All rights reserved.
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104 members
Andrew Mitchell
  • Department of Entomology
Jodi J L Rowley
  • Herpetology
Jan Y Poulsen
  • Fish Section
Frank Köhler
  • Australian Museum Research Institute
Kristofer M. Helgen
  • Australian Museum Research Institute
1 William Street, 2010, Sydney, New South Wales, Australia