Potential for host-symbiont communication via neurotransmitters and neuromodulators in an aneural animal, the marine sponge Amphimedon queenslandica

Interkingdom signalling within a holobiont allows host and symbionts to communicate and to regulate each other's physiological and developmental states. Here we show that a suite of signalling molecules that function as neurotransmitters and neuromodulators in most animals with nervous systems, specifically dopamine and trace amines, are produced exclusively by the bacterial symbionts of the demosponge Amphimedon queenslandica. Although sponges do not possess a nervous system, A. queenslandica expresses rhodopsin class G-protein-coupled receptors that are structurally similar to dopamine and trace amine receptors. When sponge larvae, which express these receptors, are exposed to agonists and antagonists of bilaterian dopamine and trace amine receptors, we observe marked changes in larval phototactic swimming behaviour, consistent with the sponge being competent to recognise and respond to symbiont-derived trace amine signals. These results indicate that monoamines synthesised by bacterial symbionts may be able to influence the physiology of the host sponge.

Is Mushy Tuna Syndrome a Growing Problem for the Tuna Industry?

Reducing food loss and waste is crucial for a sustainable global food system and an efficient use of natural resources. Fast-growing tuna provides a key contribution to global nutrition targets; however, reports suggest that an appreciable proportion of the catch is lost from its value chain due to flesh quality issues, one of which is Mushy Tuna Syndrome (MTS). MTS-affected tuna flesh becomes soft and pasty, unfit for canning or human consumption, resulting in high wastage of partially processed material. We investigated the prevalence of MTS globally by surveying the tuna industry using a questionnaire. Of the responses from 32 companies across 14 nations, 97% acknowledged MTS as an issue that predominantly affects skipjack (Katsuwonus pelamis) tuna. The cost of rejects reported by participants from 2017 to 2019 varied greatly, from less than 1000 USD per year to over 1 million USD. The median cost was over 60,000 USD and the average rejection rate was 1.8%. The occurrence of MTS was noted to be seasonal, mainly in the summer months. More than half of the respondents who experience MTS reported an increasing trend of occurrence. Industry perceptions suggest MTS causes are associated with environmental, physiological, and biological factors. The survey results highlight that MTS is prevalent in the industry and demonstrate the need to identify amelioration strategies for the fishers and processors to minimise loss and maximise resource efficiency.

Anthropogenic impacts on threatened species erode functional diversity in chelonians and crocodilians

The Anthropocene is tightly associated with a drastic loss of species worldwide and the disappearance of their key ecosystem functions. The orders Testudines (turtles and tortoises) and Crocodilia (crocodiles, alligators, and gharials) contain numerous threatened, long-lived species for which the functional diversity and potential erosion by anthropogenic impacts remains unknown. Here, we examine 259 (69%) of the existing 375 species of Testudines and Crocodilia, quantifying their life history strategies (i.e., trade-offs in survival, development, and reproduction) from open-access data on demography, ancestry, and threats. We find that the loss of functional diversity in simulated extinction scenarios of threatened species is greater than expected by chance. Moreover, the effects of unsustainable local consumption, diseases, and pollution are associated with life history strategies. In contrast, climate change, habitat disturbance, and global trade affect species independent of their life history strategy. Importantly, the loss of functional diversity for threatened species by habitat degradation is twice that for all other threats. Our findings highlight the importance of conservation programmes focused on preserving the functional diversity of life history strategies jointly with the phylogenetic representativity of these highly threatened groups.

The relative performance of geometric morphometrics and linear‐based methods in the taxonomic resolution of a mammalian species complex

Morphology-based taxonomic research frequently applies linear morphometrics (LMM) in skulls to quantify species distinctions. The choice of which measurements to collect generally relies on the expertise of the investigators or a set of standard measurements, but this practice may ignore less obvious or common discriminatory characteristics. In addition, taxonomic analyses often ignore the potential for subgroups of an otherwise cohesive population to differ in shape purely due to size differences (or allometry). Geometric morphometrics (GMM) is more complicated as an acquisition technique but can offer a more holistic characterization of shape and provides a rigorous toolkit for accounting for allometry. In this study, we used linear discriminant analysis (LDA) to assess the discriminatory performance of four published LMM protocols and a 3D GMM dataset for three clades of antechinus known to differ subtly in shape. We assessed discrimination of raw data (which are frequently used by taxonomists); data with isometry (i.e., overall size) removed; and data after allometric correction (i.e., with nonuniform effects of size removed). When we visualized the principal component analysis (PCA) plots, we found that group discrimination among raw data was high for LMM. However, LMM datasets may inflate PC variance accounted in the first two PCs, relative to GMM. GMM discriminated groups better after isometry and allometry were removed in both PCA and LDA. Although LMM can be a powerful tool to discriminate taxonomic groups, we show that there is substantial risk that this discrimination comes from variation in size, rather than shape. This suggests that taxonomic measurement protocols might benefit from GMM-based pilot studies, because this offers the option of differentiating allometric and nonallometric shape differences between species, which can then inform on the development of the easier-to-apply LMM protocols.

Using 3D geometric morphometrics to aid taxonomic and ecological understanding of a recent speciation event within a small Australian marsupial (Antechinus: Dasyuridae)

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.

Testing hypotheses of marsupial brain size variation using phylogenetic multiple imputations and a Bayesian comparative framework

Considerable controversy exists about which hypotheses and variables best explain mammalian brain size variation. We use a new, high-coverage dataset of marsupial brain and body sizes, and the first phylogenetically imputed full datasets of 16 predictor variables, to model the prevalent hypotheses explaining brain size evolution using phylogenetically corrected Bayesian generalized linear mixed-effects modelling. Despite this comprehensive analysis, litter size emerges as the only significant predictor. Marsupials differ from the more frequently studied placentals in displaying a much lower diversity of reproductive traits, which are known to interact extensively with many behavioural and ecological predictors of brain size. Our results therefore suggest that studies of relative brain size evolution in placental mammals may require targeted co-analysis or adjustment of reproductive parameters like litter size, weaning age or gestation length. This supports suggestions that significant associations between behavioural or ecological variables with relative brain size may be due to a confounding influence of the extensive reproductive diversity of placental mammals.

Skull shape of a widely distributed, endangered marsupial reveals little evidence of local adaptation between fragmented populations

The biogeographic distribution of diversity among populations of threatened mammalian species is generally investigated using population genetics. However, intraspecific phenotypic diversity is rarely assessed beyond taxonomy-focused linear measurements or qualitative descriptions. Here, we use a technique widely used in the evolutionary sciences-geometric morphometrics-to characterize shape diversity in the skull of an endangered marsupial, the northern quoll, across its 5,000 km distribution range along Northern Australia. Skull shape is a proxy for feeding, behavior, and phenotypic differentiation, allowing us to ask whether populations can be distinguished and whether patterns of variation indicate adaptability to changing environmental conditions. We analyzed skull shape in 101 individuals across four mainland populations and several islands. We assessed the contribution of population, size, sex, rainfall, temperature, and geography to skull shape variation using principal component analysis, Procrustes ANOVA, and variation partitioning analyses. The populations harbor similar amounts of broadly overlapping skull shape variation, with relatively low geographic effects. Size predicted skull shape best, coinciding with braincase size variation and differences in zygomatic arches. Size-adjusted differences in populations explained less variation with far smaller effect sizes, relating to changes in the insertion areas of masticatory muscles, as well as the upper muzzle and incisor region. Climatic and geographic variables contributed little. Strikingly, the vast majority of shape variation-76%-remained unexplained. Our results suggest a uniform intraspecific scope for shape variation, possibly due to allometric constraints or phenotypic plasticity beyond the relatively strong allometric effect. The lack of local adaptation indicates that cross-breeding between populations will not reduce local morphological skull (and probably general musculoskeletal) adaptation because none exists. However, the potential for heritable morphological variation (e.g., specialization to local diets) seems exceedingly limited. We conclude that 3D geometric morphometrics can provide a comprehensive, statistically rigorous phenomic contribution to genetic-based conservation studies.

Skin hydrophobicity as an adaptation for self-cleaning in geckos

Hydrophobicity is common in plants and animals, typically caused by high relief microtexture functioning to keep the surface clean. Although the occurrence and physical causes of hydrophobicity are well understood, ecological factors promoting its evolution are unclear. Geckos have highly hydrophobic integuments. We predicted that, because the ground is dirty and filled with pathogens, high hydrophobicity should coevolve with terrestrial microhabitat use. Advancing contact-angle (ACA) measurements of water droplets were used to quantify hydrophobicity in 24 species of Australian gecko. We reconstructed the evolution of ACA values, in relation to microhabitat use of geckos. To determine the best set of structural characteristics associated with the evolution of hydrophobicity, we used linear models fitted using phylogenetic generalized least squares (PGLS), and then model averaging based on AICc values. All species were highly hydrophobic (ACA > 132.72°), but terrestrial species had significantly higher ACA values than arboreal ones. The evolution of longer spinules and smaller scales was correlated with high hydrophobicity. These results suggest that hydrophobicity has coevolved with terrestrial microhabitat use in Australian geckos via selection for long spinules and small scales, likely to keep their skin clean and prevent fouling and disease.

Global gene flow releases invasive plants from environmental constraints on genetic diversity

When plants establish outside their native range, their ability to adapt to the new environment is influenced by both demography and dispersal. However, the relative importance of these two factors is poorly understood. To quantify the influence of demography and dispersal on patterns of genetic diversity underlying adaptation, we used data from a globally distributed demographic research network comprising 35 native and 18 nonnative populations of Plantago lanceolata Species-specific simulation experiments showed that dispersal would dilute demographic influences on genetic diversity at local scales. Populations in the native European range had strong spatial genetic structure associated with geographic distance and precipitation seasonality. In contrast, nonnative populations had weaker spatial genetic structure that was not associated with environmental gradients but with higher within-population genetic diversity. Our findings show that dispersal caused by repeated, long-distance, human-mediated introductions has allowed invasive plant populations to overcome environmental constraints on genetic diversity, even without strong demographic changes. The impact of invasive plants may, therefore, increase with repeated introductions, highlighting the need to constrain future introductions of species even if they already exist in an area.

Beyond Brownian Motion and the Ornstein-Uhlenbeck Process: Stochastic Diffusion Models for the Evolution of Quantitative Characters

Gaussian processes, such as Brownian motion and the Ornstein-Uhlenbeck process, have been popular models for the evolution of quantitative traits and are widely used in phylogenetic comparative methods. However, they have drawbacks that limit their utility. Here we describe new, non-Gaussian stochastic differential equation (diffusion) models of quantitative trait evolution. We present general methods for deriving new diffusion models and develop new software for fitting non-Gaussian evolutionary models to trait data. The theory of stochastic processes provides a mathematical framework for understanding the properties of current and future phylogenetic comparative methods. Attention to the mathematical details of models of trait evolution and diversification may help avoid some pitfalls when using stochastic processes to model macroevolution.

Ecological associations among epidermal microstructure and scale characteristics of Australian geckos (Squamata: Carphodactylidae and Diplodactylidae)

A first step in examining factors influencing trait evolution is demonstrating associations between traits and environmental factors. Scale microstructure is a well-studied feature of squamate reptiles (Squamata), including geckos, but few studies examine ecology the of microstructures, and those focus mainly on toe pads. In this study, the ecomorphology of cutaneous microstructures on the dorsum was described for eight Australian species of carphodactylid (Squamata: Carphodactylidae) and 19 diplodactylid (Squamata: Diplodactylidae) geckos. We examined scale dimensions, spinule and cutaneous sensilla (CS) morphology, using scanning electron microscopy, and described associations of these traits with microhabitat selection (arboreal, saxicoline or terrestrial) and relative humidity of each species' habitat (xeric, mesic or humid). We used a phylogenetic flexible discriminant analysis (pFDA) to describe relationships among all traits and then a modeling approach to examine each trait individually. Our analysis showed that terrestrial species tended to have long spinules and CS with more bristles, saxicoline species larger diameter CS and arboreal species tended to have large granule scales and small intergranule scales. There was high overlap in cutaneous microstructural morphology among species from xeric and mesic environments, whereas species from humid environments had large diameter CS and few bristles. Significant associations between epidermal morphology and environmental humidity and habitat suggest that epidermal microstructures have evolved in response to environmental variables. In summary, long spinules, which aid self-cleaning in terrestrial geckos, are consistent with greater exposure to dirt and debris in this habitat. Long spinules were not clearly correlated to environmental humidity. Finally, more complex CS (larger diameter with more bristles) may facilitate better perception of environmental variation in geckos living in drier habitats.

Conspicuous visual signals do not coevolve with increased body size in marine sea slugs

Many taxa use conspicuous colouration to attract mates, signal chemical defences (aposematism) or for thermoregulation. Conspicuousness is a key feature of aposematic signals, and experimental evidence suggests that predators avoid conspicuous prey more readily when they exhibit larger body size and/or pattern elements. Aposematic prey species may therefore evolve a larger body size due to predatory selection pressures, or alternatively, larger prey species may be more likely to evolve aposematic colouration. Therefore, a positive correlation between conspicuousness and body size should exist. Here, we investigated whether there was a phylogenetic correlation between the conspicuousness of animal patterns and body size using an intriguing, understudied model system to examine questions on the evolution of animal signals, namely nudibranchs (opisthobranch molluscs). We also used new ways to compare animal patterns quantitatively with their background habitat in terms of intensity variance and spatial frequency power spectra. In studies of aposematism, conspicuousness is usually quantified using the spectral contrast of animal colour patches against its background; however, other components of visual signals, such as pattern, luminance and spectral sensitivities of potential observers, are largely ignored. Contrary to our prediction, we found that the conspicuousness of body patterns in over 70 nudibranch species decreased as body size increased, indicating that crypsis was not limited to a smaller body size. Therefore, alternative selective pressures on body size and development of colour patterns, other than those inflicted by visual hunting predators, may act more strongly on the evolution of aposematism in nudibranch molluscs.

Convergent maternal care strategies in ungulates and macropods

Mammals show extensive interspecific variation in the form of maternal care. Among ungulates, there is a dichotomy between species in which offspring follow the mother ("following" strategy) versus species in which offspring remain concealed ("hiding" strategy). Here we reveal that the same dichotomy exists among macropods (kangaroos, wallabies and allies). We test three traditional adaptive explanations and one new life history hypothesis, and find very similar patterns among both ungulates and macropods. The three traditional explanations that we tested were that a "following" strategy is associated with (1) open habitat, (2) large mothers, and (3) gregariousness. Our new life-history hypothesis is that a "following strategy" is associated with delayed weaning, and thus with the "slow" end of the slow-fast mammalian life-history continuum, because offspring devote resources to locomotion rather than rapid growth. Our comparative test strongly supports the habitat structure hypothesis and provides some support for this new delayed weaning hypothesis for both ungulates and macropods. We propose that sedentary young in closed habitats benefit energetically by having milk brought to them. In open habitats, predation pressure will select against hiding. Followers will suffer slower growth to independence. Taken together, therefore, our results provide the first quantitative evidence that macropods and ungulates are convergent with respect to interspecific variation in maternal care strategy. In both clades, differences between species in the form of parental care are due to a similar interaction between habitat, social behavior, and life history.

Natural selection and quantitative genetics of life-history traits in Western women: a twin study

Whether contemporary human populations are still evolving as a result of natural selection has been hotly debated. For natural selection to cause evolutionary change in a trait, variation in the trait must be correlated with fitness and be genetically heritable and there must be no genetic constraints to evolution. These conditions have rarely been tested in human populations. In this study, data from a large twin cohort were used to assess whether selection will cause a change among women in a contemporary Western population for three life-history traits: age at menarche, age at first reproduction, and age at menopause. We control for temporal variation in fecundity (the "baby boom" phenomenon) and differences between women in educational background and religious affiliation. University-educated women have 35% lower fitness than those with less than seven years education, and Roman Catholic women have about 20% higher fitness than those of other religions. Although these differences were significant, education and religion only accounted for 2% and 1% of variance in fitness, respectively. Using structural equation modeling, we reveal significant genetic influences for all three life-history traits, with heritability estimates of 0.50, 0.23, and 0.45, respectively. However, strong genetic covariation with reproductive fitness could only be demonstrated for age at first reproduction, with much weaker covariation for age at menopause and no significant covariation for age at menarche. Selection may, therefore, lead to the evolution of earlier age at first reproduction in this population. We also estimate substantial heritable variation in fitness itself, with approximately 39% of the variance attributable to additive genetic effects, the remainder consisting of unique environmental effects and small effects from education and religion. We discuss mechanisms that could be maintaining such a high heritability for fitness. Most likely is that selection is now acting on different traits from which it did in pre-industrial human populations.