Reconstructing phylogeny from morphological data remains mired in investigator biases, including subjective inclusion and discretization of phenotypic variation. Geometric morphometrics and multivariate statistical analyses provide an alternative array of tools for studying variation in morphological traits. However, direct analysis of landmark data is often unreliable for phylogeny reconstruction. Morphological variation is typically highly correlated among nearby landmarks and may evolve saltationally between adaptive peaks instead of gradually, thereby violating the assumptions of typical continuous models. To address these concerns, we developed an approach to more objectively discretize morphometric data and applied it to 3D surface scans of mandibles and postcranial elements of Macropodiformes (kangaroos, bettongs, and rat-kangaroos). The scanned elements were partitioned into sets of locally co-varying landmarks, which approximate functional units. These subregions were discretized into "atomized" characters using novel approaches to combine the objectivity of continuous shape variation for delineating discrete states with the model flexibility offered for multistate and binary characters. This allows us to 1) potentially reduce the influence of non-independence among neighboring landmarks, 2) accommodate multimodal variation from saltational evolution, 3) accommodate missing data, such as from fragmentary fossils, and 4) promote tree-search efficiency. We built discrete morphological character matrices using three alternative approaches: commonly used clustering algorithms (UPGMA, k-means, k-medoids, and Gaussian mixture modeling), a minimum evolution branch length criterion, and a tree sampling procedure. Our phylogenetic analyses with these novel matrices generally succeeded in recovering genera and several deep-level macropodiform clades, but failed to accurately reconstruct intergeneric relationships within the rapid diversification of the macropodine subfamily; those relationships were also not recovered with continuous morphological data or traditionally discretized characters and are the most poorly resolved with DNA data. On balance, our atomized characters, which derive from only mandibular and three postcranial elements, show promise for improving objectivity, accuracy, and clocklikeness in morphological phylogenetics and provide pathways for accommodating correlated homoplasy and for more accurately estimating rates of morphological evolution, and thereby better integrating phenotypic and genomic data for phylogenetic inference.

Abstract Habitat fragmentation can increase the chance of population bottlenecks and inbreeding, and may ultimately lead to reduced fitness and local extinction. Notelaea lloydii is a native olive species endemic to Australia and listed as vulnerable due to its restricted distribution. A recent molecular systematics study has revealed there might be some geographic structuring among N. lloydii populations. Therefore, we undertook a genome‐wide single nucleotide polymorphism (SNP) analysis to determine levels and patterns of genetic diversity, inbreeding and gene flow within and among N. lloydii populations in south‐eastern Queensland. Furthermore, as the reproductive phase of a plant's life history has a profound influence on genetic diversity, life history reproductive traits were also studied. Our SNP analysis revealed low genetic diversity, inbreeding and significant genetic structuring even among proximate populations. Results of a flower and fruit bagging experiment in two consecutive seasons revealed that N. lloydii produced many flowers but only a few fruits survived to maturity. There were no differences in bagged and un‐bagged flowering and fruiting rates, and therefore, we conclude that the high fruit abortion rate was probably due to inbreeding depression and/or suboptimal conditions, rather than pollinator availability and insect attack. Overall, results of this study indicate that the populations of N. lloydii are small, inbred and genetically isolated and represent unique management units that require local conservation management due to ongoing threats associated with urbanisation.

This JAMA Insights in the Climate Change and Health series discusses the importance of clinicians having awareness of changes in the geographic range, seasonality, and intensity of transmission of infectious diseases to help them diagnose, treat, and prevent these diseases.

Isolating phylogenetic signal from morphological data is crucial for accurately merging fossils into the tree of life and for calibrating molecular dating. However, subjective character definition is a major limitation which can introduce biases that mislead phylogenetic inferences and divergence time estimation. The use of quantitative data, e.g., geometric morphometric (GMM; shape) data can allow for more objective integration of morphological data into phylogenetic inference. This systematic review describes the current state of the field in using continuous morphometric data (e.g., GMM data) for phylogenetic reconstruction and assesses the efficacy of these data compared to discrete characters using the PRISMA-EcoEvo v1.0. reporting guideline, and offers some pathways for approaching this task with GMM data. A comprehensive search string yielded 11,123 phylogenetic studies published in English up to Oct 2023 in the Web of Science database. Title and abstract screening removed 10,975 articles, and full-text screening was performed for 132 articles. Of these, a total of twelve articles met final inclusion criteria and were used for downstream analyses. Phylogenetic performance was compared between approaches that employed continuous morphometric and discrete morphological data. Overall, the reconstructed phylogenies did not show increased resolution or accuracy (i.e., benchmarked against molecular phylogenies) as continuous data alone or combined with discrete morphological datasets. An exhaustive search of the literature for existing empirical continuous data resulted in a total of twelve articles for final inclusion following title/abstract, and full-text screening. Our study was performed under a rigorous framework for systematic reviews, which showed that the lack of available comparisons between discrete and continuous data hinders our understanding of the performance of continuous data. Our study demonstrates the problem surrounding the efficacy of continuous data as remaining relatively intractable despite an exhaustive search, due in part to the difficulty in obtaining relevant comparisons from the literature. Thus, we implore researchers to address this issue with studies that collect discrete and continuous data sets with directly comparable properties (i.e., describing shape, or size).

The pathogenic outcome of enteric virus infections is governed by a complex interplay between the virus, intestinal microbiota, and host immune factors, with metabolites serving as a key mediator. Noroviruses bind bile acid metabolites, which are produced by the host and then modified by commensal bacteria. Paradoxically, bile acids can have both proviral and antiviral roles during norovirus infections. Working in an infant mouse model of norovirus infection, we demonstrate that microbiota and their bile acid metabolites protect from norovirus diarrhea, whereas host bile acids promote disease. We also find that maternal bile acid metabolism determines the susceptibility of newborn mice to norovirus diarrhea during breastfeeding. Finally, targeting maternal and neonatal bile acid metabolism can protect newborn mice from norovirus disease. In summary, neonatal metabolic immaturity and breastmilk bile acids are central determinants of heightened newborn vulnerability to norovirus disease.

Theoretical biologist who ‘tamed’ mathematicians and tested the theory of evolution.

The shared functions of the skull are thought to result in common evolutionary patterns in mammalian cranial shape. Craniofacial evolutionary allometry (CREA) is a particularly prominent pattern where larger species display proportionally elongate facial skeletons and smaller braincases. It was recently proposed that CREA arises from biomechanical effects of cranial scaling when diets are similar. Thus, deviations from CREA should occur with changes in cranial biomechanics, for example due to dietary change. Here, we test this using 3D geometric morphometric analysis in a dataset of Australian murine crania, which are highly allometric. We contrast allometric and non-allometric variation in the cranium by comparing evolutionary mode, allometry, ordinations, as well as allometry, integration, and modularity in functional modules. We found evidence of stabilising selection in allometry-containing and size-free shape, and substantial non-allometric variation aligned with dietary specialisation in parallel with CREA. Integration among cranial modules was higher, and modularity lower, with size included, but integration between rostrum and cranial vault, which are involved in the CREA pattern, dropped dramatically after size removal. Our results thus support the hypothesis that CREA is a composite arising from selection on cranial function, with substantial non-allometric shape variation occurring alongside CREA where dietary specialisation impacts selection on gnawing function. This emphasises the need to research mammalian cranial evolution in the context of allometric and non-allometric selection on biomechanical function.

Abstract Medium to large rainforest mammals are key conservation flagship groups that offer non‐redundant ecosystem functions, but anthropic pressures, such as illegal hunting, may strongly affect their occupancy in Amazonia. We combined camera traps and occupancy models to assess the influence of distance from human settlements, the number of families per settlement and the synergetic effect of the average weight of 27 species on the occupancy probability of mammals. Specifically, we classified mammal species according to the game preferences of hunters (i.e. a group of species depleted for bushmeat, a group of species hunted for retaliation and a group of non‐hunted species). We also accounted for the influence on the detection probability of each group of both the number of days each camera operated and the body weight of mammals. The occupancy probability of the bushmeat group (i.e. deer, peccaries, agoutis, pacas and armadillos) was lower at locations closer to human settlements. Still, the number of families correlated positively with occupancy, with the occupancy probability of the group being slightly higher at sites with more families. This difference was probably due to larger and more abundant crops and fruiting trees attracting wildlife at such sites. Conversely, the occupancy probability of the retaliation group (i.e. carnivores) and the non‐hunted group (i.e. opossums, spiny rats, squirrels and anteaters) were indifferent to anthropogenic stressors. The detection probability of the non‐hunted and particularly the most depleted species correlated negatively with body weight. This may suggest that larger species, especially those from the bushmeat group, are rarer or less abundant in the system, possibly because they are the preferable target of hunters. In the long term, locals will likely need to travel long distances to find harvest meat. Poaching also threatens food security since game bushmeat is an essential source of protein for isolated rural Amazonians.

The manufacturing of thin films with structured surfaces by large‐scale rolling has distinct advantages over other techniques, such as lithography, due to scalability. However, it is not well understood or quantified how processing conditions can affect the microstructure at different physical scales. Hence, the objective of this investigation is to develop a validated computational model of the symmetric forward‐roll coating process to understand, predict, and control the morphology of carbon nanotube (CNT) – polydimethylsiloxane (PDMS) pastes. The effects of the thin‐film rheological properties and the roller gap on the ribbing behavior are investigated and a ribbing instability prediction model is formulated from experimental measurements and computational predictions. The CNT–PDMS thin‐film system is modeled by a nonlinear implicit dynamic finite‐element method that accounts for ribbing instabilities, large displacements, rolling contact, and material viscoelasticity. Dynamic mechanical analysis is used to obtain the viscoelastic properties of the CNT–PDMS paste for various CNT weight distributions. Furthermore, a Morris sensitivity analysis is conducted to obtain insights on the dominant predicted characteristics pertaining to the ribbing microstructure. Based on the sensitivity analysis, a critical ribbing aspect ratio is identified for the CNT–PDMS system corresponding to a critical roller gap.

Conservation decision‐making and prioritization of management actions for taxa at high risk of extinction require a clear understanding of systematic relationships and species boundaries. Taxonomic uncertainty surrounds two threatened species of native olive (genus Notelaea ) endemic to Australia. Notelaea ipsviciensis is known from only one small population and is listed as critically endangered under Australian and Queensland legislation, while Notelaea lloydii is listed as vulnerable due to its restricted distribution in south‐east Queensland, Australia. Notelaea ipsviciensis occurs in sympatry with N. lloydii , at the only site where it is found, and exhibits intermediate morphology between N. lloydii and Notelaea ovata raising speculation that it is a natural hybrid of the two. To address this uncertainty, we have reconstructed the molecular phylogeny of the genus Notelaea using both single‐gene sequencing and single nucleotide polymorphism (SNP) data. While the chloroplast DNA markers were not found to be informative, the genome‐wide SNPs used in this study have unequivocally resolved the long‐standing question of the hybrid origin of N. ipsviciensis . Results of the phylogenetics and hybrid analyses of SNP data show that N. ipsviciensis is a natural hybrid of N. lloydii and N. ovata , and the taxon's circumscription needs to be re‐evaluated. Our results also revealed unclear species boundaries among numerous other Notelaea species, including the threatened N. lloydii , indicating that further investigation and taxonomic revision may be necessary.

The systematics of Madagascar’s extinct elephant birds remains controversial due to large gaps in the fossil record and poor biomolecular preservation of skeletal specimens. Here, a molecular analysis of 1000-year-old fossil eggshells provides the first description of elephant bird phylogeography and offers insight into the ecology and evolution of these flightless giants. Mitochondrial genomes from across Madagascar reveal genetic variation that is correlated with eggshell morphology, stable isotope composition, and geographic distribution. The elephant bird crown is dated to ca. 30 Mya, when Madagascar is estimated to have become less arid as it moved northward. High levels of between-clade genetic variation support reclassifying Mullerornis into a separate family. Low levels of within-clade genetic variation suggest there were only two elephant bird genera existing in southern Madagascar during the Holocene. However, we find an eggshell collection from Madagascar’s far north that represents a unique lineage of Aepyornis . Furthermore, divergence within Aepyornis coincides with the aridification of Madagascar during the early Pleistocene ca. 1.5 Ma, and is consistent with the fragmentation of populations in the highlands driving diversification and the evolution of extreme gigantism over shorts timescales. We advocate for a revision of their taxonomy that integrates palaeogenomic and palaeoecological perspectives.

Noroviruses are the leading cause of severe childhood diarrhea and foodborne disease worldwide. While they are a major cause of disease in all age groups, infections in the very young can be quite severe, with annual estimates of 50,000–200,000 fatalities in children under 5 years old. In spite of the remarkable disease burden associated with norovirus infections, very little is known about the pathogenic mechanisms underlying norovirus diarrhea, principally because of the lack of tractable small animal models. The development of the murine norovirus (MNV) model nearly two decades ago has facilitated progress in understanding host–norovirus interactions and norovirus strain variability. However, MNV strains tested thus far either do not cause intestinal disease or were isolated from extraintestinal tissue, raising concerns about translatability of research findings to human norovirus disease. Consequently, the field lacks a strong model of norovirus gastroenteritis. Here we provide a comprehensive characterization of a new small animal model system for the norovirus field that overcomes prior weaknesses. Specifically, we demonstrate that the WU23 MNV strain isolated from a mouse naturally presenting with diarrhea causes a transient reduction in weight gain and acute self-resolving diarrhea in neonatal mice of several inbred mouse lines. Moreover, our findings reveal that norovirus-induced diarrhea is associated with infection of subepithelial cells in the small intestine and systemic spread. Finally, type I interferons (IFNs) are critical to protect hosts from norovirus-induced intestinal disease whereas type III IFNs exacerbate diarrhea. This latter finding is consistent with other emerging data implicating type III IFNs in the exacerbation of some viral diseases. This new model system should enable a detailed investigation of norovirus disease mechanisms.

Large-scale molecular datasets have generally outperformed morphological data for inferring phylogeny, and sources of error in the latter are poorly understood. The morphologically and ecologically diverse marsupial order Diprotodontia (kangaroos and their relatives, the koala, wombats and possums) is well suited to considering these issues. Recent molecular results provide a phylogenetic benchmark for comparing previous molecular and morphological studies, encompassing all of the major phylogenetic data sources and methods that have been employed over the past 50 years. We show here that most molecular methodologies and ‘informal-comparative’ morphological studies have inferred diprotodontian relationships that closely resemble the recent molecular consensus. However, and perhaps surprisingly, algorithmic morphology, such as maximum parsimony analysis of morphological matrices, has inferred markedly inaccurate phylogenies, and is not improved by re-analysis with more recently developed, model-based (e.g., likelihood and Bayesian) methods. This is particularly concerning because algorithmic morphology is the primary approach for integrating fossils into the tree of life, and hence, for both calibrating molecular timescales and extending phylogenetic inferences of evolutionary processes beyond the snapshot provided by modern species. A novel simulation study presented here suggests that the inaccuracies in the marsupial algorithmic morphology studies partly stem from functional and body-size correlations among taxa that over-ride phylogenetic signals. We use the results to trial a reverse engineered phylogeny approach to correcting for such functional and developmental correlations among morphological data. In addition, we interrogated a newly published, densely taxon-sampled morphological matrix. Deeper level phylogeny reconstruction was improved by including fossils alongside extant taxa and counterintuitively, by increased effort to resolve relationships among shallow taxa.Matthew J. Phillips [m9.phillips@qut.edu.au]; Mélina A. Celik [melina.celik@gmail.com] School of Biology and Environmental Science, Queensland University of Technology, 2 George Street, Brisbane, Qld, 4000, Australia; Robin M.D Beck [r.m.d.beck@salford.ac.uk] Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK.

Background The ShK toxin from Stichodactyla helianthus has established the therapeutic potential of sea anemone venom peptides, but many lineage-specific toxin families in Actiniarians remain uncharacterised. One such peptide family, sea anemone 8 (SA8), is present in all five sea anemone superfamilies. We explored the genomic arrangement and evolution of the SA8 gene family in Actinia tenebrosa and Telmatactis stephensoni , characterised the expression patterns of SA8 sequences, and examined the structure and function of SA8 from the venom of T . stephensoni . Results We identified ten SA8-family genes in two clusters and six SA8-family genes in five clusters for T. stephensoni and A. tenebrosa , respectively. Nine SA8 T. stephensoni genes were found in a single cluster, and an SA8 peptide encoded by an inverted SA8 gene from this cluster was recruited to venom. We show that SA8 genes in both species are expressed in a tissue-specific manner and the inverted SA8 gene has a unique tissue distribution. While the functional activity of the SA8 putative toxin encoded by the inverted gene was inconclusive, its tissue localisation is similar to toxins used for predator deterrence. We demonstrate that, although mature SA8 putative toxins have similar cysteine spacing to ShK, SA8 peptides are distinct from ShK peptides based on structure and disulfide connectivity. Conclusions Our results provide the first demonstration that SA8 is a unique gene family in Actiniarians, evolving through a variety of structural changes including tandem and proximal gene duplication and an inversion event that together allowed SA8 to be recruited into the venom of T . stephensoni .

Incorporating morphological data into modern phylogenies allows integration of fossil evidence, facilitating divergence dating and macroevolutionary inferences. Improvements in the phylogenetic utility of morphological data have been sought via Procrustes-based geometric morphometrics (GMM), but with mixed success and little clarity over what anatomical areas are most suitable. Here, we assess GMM-based phylogenetic reconstructions in a heavily sampled source of discrete characters for mammalian phylogenetics-the basicranium-in 57 species of marsupial mammals, compared with the remainder of the cranium. We show less phylogenetic signal in the basicranium compared with a 'Rest of Cranium' partition, using diverse metrics of phylogenetic signal (K-mult, phylogenetically aligned principal components analysis, comparisons of UPGMA/neighbour-joining/parsimony trees and cophenetic distances to a reference phylogeny) for scaled, Procrustes-aligned landmarks and allometry-corrected residuals. Surprisingly, a similar pattern emerged from parsimony-based analyses of discrete cranial characters. The consistent results across methods suggest that easily computed metrics such as K-mult can provide good guidance on phylogenetic information in a landmarking configuration. In addition, GMM data may be less informative for intricate but conservative anatomical regions such as the basicranium, while better-but not necessarily novel-phylogenetic information can be expected for broadly characterized shapes such as entire bones.This article is part of the theme issue 'The mammalian skull: development, structure and function'.

The use of correct taxonomy to describe and name the earth’s biodiversity is fundamental to conservation and management. However, there are issues that need to be overcome to ensure that the described taxa and their scientific names are both appropriate and widely adopted. Obstacles to this include the use of different species definitions, taxonomic instability due to accumulation of additional specimens in analyses and the progression of science that allows better resolution of species boundaries, and the inappropriate description and naming of new taxa without adequate scientific basis in self-published journals (known as ‘taxonomic vandalism’). In an effort to manage taxonomic instability, the Australasian Mammal Taxonomy Consortium (AMTC), an affiliated body of the Australian Mammal Society, has developed several tools that include: (1) a standardised list of Australian mammal common and scientific names; (2) recommendations for information that should be included in published species descriptions; and (3) support for the publication of aspidonyms (i.e. a scientifically acceptable name proposed to overwrite a pre-existing unscientific name). This review discusses these issues, reaffirms the foundations for appropriate taxonomic research, and provides guidelines for those publishing taxonomic research on Australian mammals.

Taxonomic distinction of species forms the foundation of biodiversity assessments and conservation priorities. However, traditional morphological and/or genetics-based taxonomic assessments frequently miss the opportunity of elaborating on the ecological and functional context of species diversification. Here, we used 3D geometric morphometrics of the cranium to improve taxonomic differentiation and add ecomorphological characterization of a young cryptic divergence within the carnivorous marsupial genus Antechinus. Specifically, we used 168 museum specimens to characterize the recently proposed clades A. stuartii 'south', A. stuartii 'north' and A. subtropicus. Beyond slight differences attributable to overall size (and, therefore, not necessarily diagnostic), we also found clear allometry-independent shape variation. This allowed us to define new, easily measured diagnostic traits in the palate, which differentiate the three clades. Contrary to previous suggestions, we found no support for a latitudinal gradient as causing the differentiation between the clades. However, skull shape co-varied with temperature and precipitation seasonality, suggesting that the clades may be adapted to environmental variables that are likely to be impacted by climate change. Our study demonstrates the use of 3D geometric morphometrics to improve taxonomic diagnosis of cryptic mammalian species, while providing perspectives on the adaptive origins and potential future threats of mammalian diversity.

Dengue is an arboviral disease caused by dengue virus (DENV), leading to approximately 25,000 deaths/year and with over 40% of the world’s population at risk. Increased international travel and trade, poorly regulated urban expansion, and warming global temperatures have expanded the geographic range and incidence of the virus in recent decades. This study used phylogenetic and selection pressure analyses to investigate trends in DENV evolution, using whole genome coding sequences from publicly available databases alongside newly sequenced isolates collected between 1963–1997 from Southeast Asia and the Pacific. Results revealed very similar phylogenetic relationships when using the envelope gene and the whole genome coding sequences. Although DENV evolution is predominantly driven by negative selection, a number of amino acid sites undergoing positive selection were found across the genome, with the majority located in the envelope and NS5 genes. Some genotypes appear to be diversifying faster than others within each serotype. The results from this research improve our understanding of DENV evolution, with implications for disease control efforts such as Wolbachia-based biocontrol and vaccine design.

Abstract Intestinal commensal bacteria contribute to maintaining gut homeostasis. Disruptions to the commensal flora are linked to the development and persistence of disease. The importance of these organisms is further demonstrated by the widespread ability of enteric viruses to exploit commensal bacteria to enhance viral infection. These viruses interact directly with commensal bacteria, and while the impact of this interaction on viral infection is well described for several viruses, the impact on the commensal bacteria has yet to be explored. In this article, we demonstrate, for the first time, that enteric viruses alter the gene expression and phenotype of individual commensal bacteria. Human and murine norovirus interaction with bacteria resulted in genome‐wide differential gene expression and marked changes in the surface architecture of the bacterial cells. Furthermore, the interaction of the virus with bacteria led to increased production of smaller outer membrane vesicles (OMVs). Enhanced production of smaller vesicles was also observed when noroviruses were incubated with other commensal bacteria, indicating a potentially broad impact of norovirus interaction. The vesicle production observed in the in vivo model followed a similar trend where an increased quantity of smaller bacterial vesicles was observed in stool collected from virus‐infected mice compared to mock‐infected mice. Furthermore, changes in vesicle size were linked to changes in protein content and abundance, indicating that viral binding induced a shift in the mechanism of the OMV biogenesis. Collectively, these data demonstrate that enteric viruses induce specific changes in bacterial gene expression, leading to changes in bacterial extracellular vesicle production that can potentially impact host responses to infection.