Australian Museum

Isotopes in fossil tooth enamel provide robust tools for reconstructing food webs, which have been understudied in Australian megafauna. To delineate the isotopic composition of primary consumers and understand dietary behaviour at the base of the food web, we investigate calcium (Ca) and strontium (Sr) isotope compositions of Pleistocene marsupial herbivores from Wellington Caves and Bingara (New South Wales, Australia). Sr isotopes suggest small home ranges across giant and smaller marsupial herbivores. Ca isotopes in Pleistocene marsupial herbivores cover the same range as those in modern wombats and placental herbivores. Early forming teeth are depleted in heavy Ca isotopes compared to late-forming teeth of a given individual, suggesting a weaning signal. Distinct Ca compositions between taxa can be interpreted as dietary niches. Some niches conform to previous dietary reconstructions of taxa, while others provide new insights into niche differentiation across Australian herbivores. Combined with the small roaming ranges suggested by Sr isotopes, the Ca isotope niche diversity suggests rich ecosystems, supporting a diversity of taxa with various diets in a small area.

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.

Reliable maps of species distributions are fundamental for biodiversity research and conservation. The International Union for Conservation of Nature (IUCN) Red List range maps are widely recognized as authoritative representations of species' geographic limits, yet they might not always align with actual occurrence data. Recent Area of Habitat (AOH) maps remove unsuitable habitat from IUCN ranges to reduce commission errors, but remain untested. We tested concordance between occurrences from camera trap surveys and predicted occurrences from IUCN and AOH maps for 510 medium‐ to large‐bodied mammalian species in 80 camera‐trap sampling areas. Across all areas, cameras detected only 39% of species expected to occur based on IUCN ranges or AOH maps, with 85% of the “IUCN‐only” mismatches occurring within 200 kilometers of range edges. Only 4% of species occurrences were detected by cameras outside of IUCN ranges. The probability of mismatches between cameras and IUCN range was significantly higher for smaller‐bodied mammals and habitat specialists in the Neotropics and Indomalaya, and in areas with shorter canopy forests. Our findings suggest that range and AOH maps rarely underrepresent areas where species occur, but may more often overrepresent ranges by including areas where a species may be absent, particularly at range edges. We suggest that combining range maps with accumulating data from ground‐based biodiversity sensors, such as camera traps, provides a richer knowledge base for conservation mapping and planning. This article is protected by copyright. All rights reserved

Biodiversity loss is a major global challenge and minimizing extinction rates is the goal of several multilateral environmental agreements. Policy decisions require comprehensive, spatially explicit information on species’ distributions and threats. We present an analysis of the conservation status of 14,669 European terrestrial, freshwater and marine species (ca. 10% of the continental fauna and flora), including all vertebrates and selected groups of invertebrates and plants. Our results reveal that 19% of European species are threatened with extinction, with higher extinction risks for plants (27%) and invertebrates (24%) compared to vertebrates (18%). These numbers exceed recent IPBES (Intergovernmental Platform on Biodiversity and Ecosystem Services) assumptions of extinction risk. Changes in agricultural practices and associated habitat loss, overharvesting, pollution and development are major threats to biodiversity. Maintaining and restoring sustainable land and water use practices is crucial to minimize future biodiversity declines.

Injured trilobites present insight into how a completely extinct group of arthropodsresponded to traumatic experiences, such as failed predation and moulting complica-tions. These specimens are therefore important for more thoroughly understandingthe Paleozoic predator-prey systems that involved trilobites. To expand the record ofinjured trilobites, we present new examples of injured Ogygopsis klotzi and Olenoidesserratus from the Campsite Cliff Shale Member of the Burgess Shale Formation (Cam-brian, Miaolingian, Wuliuan), Paradoxides (Paradoxides) paradoxissimus gracilis fromthe Jince Formation (Cambrian, Miaolingian, Drumian), Ogygiocarella angustissimafrom the Llanfawr Mudstones Formation (Middle–Late Ordovician, Darriwilian–Sandbian), and Ogygiocarella debuchii from the Meadowtown Formation, (Middle–Late Ordovician, Darriwilian–Sandbian). We consider the possible origins of thesemalformations and conclude that most injuries reflect failed predation. Within thisframework, possible predators are presented, and we uncover a marked shift in thediversity of animals that targeted trilobites in the Ordovician. We also collate otherrecords of injured Ogygo. klotzi and Ol. serratus, and Ogygi. debuchii, highlighting thatthese species are targets for further understanding patterns and records of trilobite injuries.

Understanding patterns of connectivity across remote atoll reefs is important for managing fishery target species, as they often have small population sizes and limited options for replenishment in the event of localised decline. In this study, we used a comprehensive hierarchical sampling design combined with reduced representation genotyping to compare the population genomics of two sympatric species of coral trout (Plectropomus) within and between three isolated offshore atoll reef systems in north-western Australia. The blue spot coral trout, Plectropomus laevis (8979 single nucleotide polymorphisms—SNPs, 223 individuals, 25 sites) and the passionfruit coral trout, P. areolatus (3702 SNPs, 452 individuals, 20 sites) showed high levels of connectivity within reef systems and restricted connectivity between reef systems, indicating that biological stocks primarily occur at the scale of each reef system. Despite being closely related and co-managed species, inter-specific variation in the magnitude of genetic structure was notable. Plectropomus areolatus at the southern-most reef system display modest genetic structure with populations ~ 450 km to the north, whilst P. laevis at the same location show a level of genetic divergence that reflects deep historical isolation. Our results provide the most comprehensive assessment of genetic connectivity across these remote atoll reefs, facilitating management advice that reflect empirically determined population dynamics for these species. We identify contrasting patterns of genetic connectivity among closely related sympatric species, and highlight the role of extrinsic (e.g., geography/environment) and intrinsic (e.g., life history) factors in shaping population dynamics.

Systematic assessments of species extinction risk at regular intervals are necessary for informing conservation action1,2. Ongoing developments in taxonomy, threatening processes and research further underscore the need for reassessment3,4. Here we report the findings of the second Global Amphibian Assessment, evaluating 8,011 species for the International Union for Conservation of Nature Red List of Threatened Species. We find that amphibians are the most threatened vertebrate class (40.7% of species are globally threatened). The updated Red List Index shows that the status of amphibians is deteriorating globally, particularly for salamanders and in the Neotropics. Disease and habitat loss drove 91% of status deteriorations between 1980 and 2004. Ongoing and projected climate change effects are now of increasing concern, driving 39% of status deteriorations since 2004, followed by habitat loss (37%). Although signs of species recoveries incentivize immediate conservation action, scaled-up investment is urgently needed to reverse the current trends.

In tropical marine ecosystems, the coral-based diet of benthic-feeding reef fishes provides a window into the composition and health of coral reefs. In this study, for the first time, we compare multi-assay metabarcoding sequences of environmental DNA (eDNA) isolated from seawater and partially digested gut items from an obligate corallivore butterflyfish (Chaetodon lunulatus) resident to coral reef sites in the South China Sea. We specifically tested the proportional and statistical overlap of the different approaches (seawater vs gut content metabarcoding) in characterizing eukaryotic community composition on coral reefs. Based on 18S and ITS2 sequence data, which differed in their taxonomic sensitivity, we found that gut content detections were only partially representative of the eukaryotic communities detected in the seawater based on low levels of taxonomic overlap (3 to 21%) and significant differences between the sampling approaches. Overall, our results indicate that dietary metabarcoding of specialized feeders can be complimentary to, but is no replacement for, more comprehensive environmental DNA assays of reef environments that might include the processing of different substrates (seawater, sediment, plankton) or traditional observational surveys. These molecular assays, in tandem, might be best suited to highly productive but cryptic oceanic environments (kelp forests, seagrass meadows) that contain an abundance of organisms that are often small, How to cite this article DiBattista JD, Liu SYV, De Brauwer M, Wilkinson SP, West K, Koziol A, Bunce M. 2023. Gut content metabarcoding of specialized feeders is not a replacement for environmental DNA assays of seawater in reef environments. PeerJ 11:e16075

Platycephalids Ambiserrula jugosa (McCulloch 1914) and Inegocia harrisii (McCulloch 1914) were described as new species based on 10 and 2 specimens, respectively, collected from the coast of Queensland, Australia by the F.I.S. Endeavour in 1910. McCulloch (1914) listed additional specimens at the end of the description, which he did not exclude from the type series. Previous authors considered the specimens, which McCulloch stated the species to have been described from, to be types of the two species, it was revealed that all 43 and 9 specimens included in these species by McCulloch are type specimens, according to the fourth edition of International Code of Zoological Nomenclature, stating “type series of a nominal taxon consists of all the specimens included by the author in the new nominal taxon” in Article 72.4.1. In I. harrisii, it was assumed that a specimen later designated as the lectotype was figured with the original description. Because its plate legend includes the words “sp. nov. Type”, the specimen is regarded to be the holotype of the species and the designation of the lectotype was unnecessary. This study newly recognizes additional 12 paratypes of A. jugosa and 5 paratypes of I. harrisii, and gives taxonomic accounts of the two species to show range extensions of intraspecific variation and distribution newly found. Also comments are given about the type status of other species taken by the Endeavour described by McCulloch in a series of five papers.

Translocation programmes are increasingly being informed by genetic data to monitor and enhance conservation outcomes for both natural and established populations. These data provide a window into contemporary patterns of genetic diversity, structure and relatedness that can guide managers in how to best source animals for their translocation programmes. The inclusion of historical samples, where possible, strengthens monitoring by allowing assessment of changes in genetic diversity over time and by providing a benchmark for future improvements in diversity via management practices. Here, we used reduced representation sequencing (ddRADseq) data to report on the current genetic health of three remnant and seven translocated boodie ( Bettongia lesueur ) populations, now extinct on the Australian mainland. In addition, we used exon capture data from seven historical mainland specimens and a subset of contemporary samples to compare pre‐decline and current diversity. Both data sets showed the significant impact of population founder source (whether multiple or single) on the genetic diversity of translocated populations. Populations founded by animals from multiple sources showed significantly higher genetic diversity than the natural remnant and single‐source translocation populations, and we show that by mixing the most divergent populations, exon capture heterozygosity was restored to levels close to that observed in pre‐decline mainland samples. Relatedness estimates were surprisingly low across all contemporary populations and there was limited evidence of inbreeding. Our results show that a strategy of genetic mixing has led to successful conservation outcomes for the species in terms of increasing genetic diversity and provides strong rationale for mixing as a management strategy.

Modern advances in DNA sequencing hold the promise of facilitating descriptions of new organisms at ever finer precision but have come with challenges as the major Codes of bionomenclature contain poorly defined requirements for species and subspecies diagnoses (henceforth, species diagnoses), which is particularly problematic for DNA-based taxonomy. We, the commissioners of the International Commission on Zoological Nomenclature, advocate a tightening of the definition of "species diagnosis" in future editions of Codes of bionomenclature, for example, through the introduction of requirements for specific information on the character states of differentiating traits in comparison with similar species. Such new provisions would enhance taxonomic standards and ensure that all diagnoses, including DNA-based ones, contain adequate taxonomic context. Our recommendations are intended to spur discussion among biologists, as broad community consensus is critical ahead of the implementation of new editions of the International Code of Zoological Nomenclature and other Codes of bionomenclature.

Global change is causing an unprecedented restructuring of ecosystems, with the spread of invasive species being a key driver. While population declines of native species due to invasives are well documented, much less is known about whether new biotic interactions reshape niches of native species. Here we quantify geographic range and realized-niche contractions in Australian frog species following the introduction of amphibian chytrid fungus Batrachochytrium dendrobatidis, a pathogen responsible for catastrophic amphibian declines worldwide. We show that chytrid-impacted species experienced proportionately greater contractions in niche breadth than geographic distribution following chytrid emergence. Furthermore, niche contractions were directional, with contemporary distributions of chytrid-impacted species characterized by higher temperatures, lower diurnal temperature range, higher precipitation and lower elevations. Areas with these conditions may enable host persistence with chytrid through lower pathogenicity of the fungus and/or greater demographic resilience. Nevertheless, contraction to a narrower subset of environmental conditions could increase host vulnerability to other threatening processes and should be considered in assessments of extinction risk and during conservation planning. More broadly, our results emphasize that biotic interactions can strongly shape species realized niches and that large-scale niche contractions due to new species interactions—particularly emerging pathogens—could be widespread.

The superfamily Orthalicoidea comprises approximately 2,000 species of terrestrial gastropods, mostly concentrated in the Neotropics but also present in southern Africa and Oceania. We provide a multi-marker molecular phylogeny of this superfamily, reassessing its family- and genus-level classification. We exclude two families from the group, Odontostomidae and Vidaliellidae, transferring them to Rhytidoidea based on their phylogenetic relationships as recovered herein. Two new families are recognized herein as members of Orthalicoidea, Tomogeridae and Cyclodontinidae fam. nov. The family Megaspiridae and the subfamily Prestonellinae are paraphyletic but are retained herein for taxonomic stability. The subfamily Placostylinae is synonymized with Bothriembryontinae. The new genera Alterorhinus gen. nov. and Sanniostracus gen. nov. containing some Brazilian species are described here to better reflect the phylogeny. The fossil record and paleobiogeographic history of the group is explored under the new phylogenetic framework.

Sri Lanka’s biota is derived largely from Southeast Asian lineages which immigrated via India following its early-Eocene contact with Laurasia. The island is now separated from southeastern India by the 30 km wide Palk Strait which, during sea-level low-stands, was bridged by the 140 km-wide Palk Isthmus. Consequently, biotic ingress and egress were mediated largely by the climate of the isthmus. Because of their dependence on perennial aquatic habitats, freshwater fish are useful models for biogeographic studies. Here we investigate the timing and dynamics of the colonization of—and diversification on—Sri Lanka by a group of four closely-related genera of cyprinid fishes ( Puntius sensu lato). We construct a molecular phylogeny based on two mitochondrial and two nuclear gene markers, conduct divergence timing analyses and ancestral-range estimations to infer historical biogeography, and use haplotype networks to infer phylogeographic patterns. The origin of Puntius s.l. is dated to ~20 Ma. The source of diversification of Puntius s.l. is Sri Lanka-Peninsular India. Species confined to perhumid rainforests show strong phylogeographic structure, while habitat generalists show little or no such structure. Ancestral range estimations for Plesiopuntius bimaculatus and Puntius dorsalis support an ‘Out of Sri Lanka’ scenario. Sri Lankan Puntius s.l. derive from multiple migrations across the Palk Isthmus between the early Miocene and the late Pleistocene. Species dependent on an aseasonal climate survived aridification in rainforest refugia in the island’s perhumid southwest and went on to recolonize the island and even southern India when pluvial conditions resumed. Our results support an historical extinction of Sri Lanka’s montane aquatic fauna, followed by a recent partial recolonization of the highlands, showing also that headwater stream capture facilitated dispersal across basin boundaries.

Assortative or disassortative aggression – when individuals display more aggression towards conspecifics with similar or different phenotypic characteristics – can either maintain polymorphisms or facilitate gene flow between populations depending on which direction the aggression is aimed. Deciphering which factors elicit or prevent aggression is crucial to improving our knowledge of the origin and maintenance of reproductive barriers and subsequent speciation. The Peruvian mimic poison frog, Ranitomeya imitator , is a monogamous and territorial species that has evolved into four distinct color-pattern morphs in a mimetic radiation. Here we use historical landscape genetic data and competition trials between male individuals sourced from different populations and color-pattern morphs to show that the level of aggression between individuals is not associated with color morph or body size but rather with source population. Individuals spent more time in combat with individuals from their own deme (genetically homogeneous population), irrespective of color morph or size. These findings indicate that genotypic similarity is correlated with increased aggression in R. imitator , though the mechanism by which R. imitator males identify conspecifics as territorial threats remains unclear. As body size and color morph were not significantly associated with aggression levels, this study emphasizes the necessity of further research to identify whether other phenotypic traits are influencing territorial behavior between male frogs, and if these factors play a role in increasing gene flow, or conversely, the formation of reproductive barriers between populations.

Almost nothing is known about the diets of bathypelagic fishes, but functional morphology can provide useful tools to infer ecology. Here we quantify variation in jaw and tooth morphologies across anglerfishes (Lophiiformes), a clade spanning shallow and deep-sea habitats. Deep-sea ceratioid anglerfishes are considered dietary generalists due to the necessity of opportunistic feeding in the food-limited bathypelagic zone. We found unexpected diversity in the trophic morphologies of ceratioid anglerfishes. Ceratioid jaws span a functional continuum ranging from species with numerous stout teeth, a relatively slow but forceful bite, and high jaw protrusibility at one end (characteristics shared with benthic anglerfishes) to species with long fang-like teeth, a fast but weak bite and low jaw protrusibility at the other end (including a unique ‘wolftrap’ phenotype). Our finding of high morphological diversity seems to be at odds with ecological generality, reminiscent of Liem's paradox (morphological specialization allowing organisms to have broader niches). Another possible explanation is that diverse ceratioid functional morphologies may yield similar trophic success (many-to-one mapping of morphology to diet), allowing diversity to arise through neutral evolutionary processes. Our results highlight that there are many ways to be a successful predator in the deep sea.

As a case study of the responses of natural history museums to changing scientific and funding environments, we analysed research publications of Australia's Natural History Museums (ANHMs) 1981-2020. Using Scopus, 9,923 relevant documents 1981-2020 were identified, mainly research papers but with a growing proportion of reviews. The number of documents published increased over tenfold from 39 (1981) to 553 (2020), likely driven by collaborations (rising from 28.5% of documents 1981-1985 to 87.2% of documents 2016-2020), contributions from retired staff, and volunteer support. The mean length of documents (pages) ranged from a low of 15.3 in 2001-2005 to a high of 17.4 in 1991-1995, but this statistically significant result was trivial in practical terms. The sources (i.e., journals, book titles, conference proceedings) in which ANHM authors published changed over time, with growing proportions of publications in journals covering molecular ecology/phylogenetics and biological conservation. We identified the major areas of study canvassed within the corpus of publications by developing structural topic models based on patterns of word use in document titles, abstracts and keyword lists. The topics discovered included study subjects traditional for natural history museums (new taxa, phylogeny, systematics, animal morphology, palaeontology, minerals), new directions (molecular genetics, ecology, biological conservation) and marine biology (probably reflecting Australia's large coastline). Most citations came from Australia, USA and UK, although in 2016-2020 only 27.9% of citing documents included an Australian author. Growth in numbers of documents and collaborations, as well as use of documents internationally over a period of great change in scientific and funding environments, indicate an enduring legacy of ANHM research, grounded on the intrinsic value of the collections.

This study documents Middle to Late Ordovician conodont faunas primarily from the Billabong Creek Formation exposed in the Gunningbland area located west of Parkes and northwest of Forbes in central New South Wales. Forty-four identifiable conodont species recovered from 105 limestone samples in this area form the basis of the most complete biostratigraphic succession in shallow-water facies known through this interval from Australia. Four conodont biozones are recognised, extending from the middle Darriwilian Histiodella holodentata–Eoplacognathus pseudoplanus and Eoplacognathus suecicus biozones, through the upper Darriwilian Pygodus serra Biozone, to the Pygodus anserinus Biozone spanning the uppermost Darriwilian to basal Sandbian interval. A lower to middle Sandbian carbonate gap coincides with an unzoned interval, followed by the successively younger Belodina compressa, Phragmodus undatus and Taoqupognathus blandus conodont biozones in the upper Sandbian to lower Katian. The T. blandus Biozone directly correlates with the detailed conodont biozonation established in Katian limestones of the Molong Volcanic Belt further east. These age determinations provide much improved precision for correlation within Phases 2 and 3 in the mineral-rich Macquarie Volcanic Province. Analysis of conodont biofacies data supports an enhanced understanding of the geological evolution of the Macquarie Volcanic Province by interpreting the interplay between volcanic activity and carbonate deposition.