Arthur Rylah Institute for Environmental Research

Abstract Aim Species distribution models have been widely used to tackle ecological, evolutionary and conservation problems. Most species distribution modelling techniques produce continuous suitability predictions, but many real applications (e.g. reserve design, species invasion and climate change impact assessment) and model evaluations require binary outputs, and thresholds are needed for these transformations. Although there are many threshold selection methods for presence/absence data, it is unclear whether these are suitable for presence‐only data. In this paper, we investigate mathematically and empirically which of the existing threshold selection methods can be used confidently with presence‐only data. Location We used real spatially explicit environmental data derived from the western part of the state of V ictoria, south‐eastern A ustralia, and simulated species distributions within this area. Methods Thirteen existing threshold selection methods were investigated mathematically to see whether the same threshold can be produced using either presence/absence data or presence‐only data. We further adopted a simulation approach, created many virtual species with differing prevalences in a real landscape in south‐eastern A ustralia, generated data sets with different proportions of pseudo‐absences, built eight types of models with four modelling techniques, and investigated the behaviours of four threshold selection methods in these situations. Results Three threshold selection methods were not affected by pseudo‐absences, including max SSS (which is based on maximizing the sum of sensitivity and specificity), the prevalence of model training data and the mean predicted value of a set of random points. Max SSS produced higher sensitivity in most cases and higher true skill statistic and kappa in many cases than the other methods. The other methods produced different thresholds from presence‐only data to those determined from presence/absence data. Main conclusions Max SSS is a promising method for threshold selection when only presence data are available.

1 Interpreting the functional diversity of vegetation is important in unravelling the relationship between environmental change, community composition and ecosystem processes. Functional diversity is the range and distribution of functional trait values in a community. It can be described, among other indicators, by community-level weighted means of trait values (CWM) and functional divergence. Standard methods exist for trait measurements but not for assessments of CWM and functional divergence in the field. No research has addressed the effects of different methods of estimating relative abundances, nor the need to estimate traits at individual, population or species level, or whether methods could be used that bypass taxonomy all together. 2 This study reviews and evaluates plot-level assessment methods of functional diversity in herbaceous vegetation. We asked: (i) Should the objective of the study influence the method for estimating relative abundance? (ii) What are the strengths and limitations of intensive vs. ‘rapid’ approaches, and when should either be applied? (iii) Are taxon-free methods robust in comparison to taxon-explicit methods of trait measurement? Under what circumstances might they be applied? 3 Our review of published studies that have measured functional diversity in the field showed that the choice of metric has not generally taken into account the link between the metric and the functions of interest, and that vegetation cover has been most widely used, regardless of study purpose. 4 We compared quantitatively in subalpine grasslands three methods for quantification of species abundances plus one taxon-free method. We found that: (i) data base trait values were robust across years for a diverse set of dominant species; (ii) CWM have little sensitivity to method for estimating relative abundances; this sensitivity also depends on traits, for example, seed mass results were less stable than leaf traits and heights; (iii) robust estimates of CWM were obtained from visual estimates of species ranks and biomass using a dry-weight ranking method (BOTANAL), whereas functional divergence was more sensitive to method; and (iv) the taxon-free method should be treated with more caution and performed particularly poorly for estimates of functional divergence. 5 We conclude that methodology can affect estimates of functional diversity. Although care should be taken in the choice of method and interpretation of results, rapid methods often offer promising avenues for sampling larger areas and/or repeated measures.

Presence-only data present challenges for selecting thresholds to transform species distribution modeling results into binary outputs. In this article, we compare two recently published threshold selection methods (maxSSS and maxF pb) and examine the effectiveness of the threshold-based prevalence estimation approach. Six virtual species with varying prevalence were simulated within a real landscape in southeastern Australia. Presence-only models were built with DOMAIN, generalized linear model, Maxent, and Random Forest. Thresholds were selected with two methods maxSSS and maxF pb with four presence-only datasets with different ratios of the number of known presences to the number of random points (KP-RP ratio). Sensitivity, specificity, true skill statistic, and F measure were used to evaluate the performance of the results. Species prevalence was estimated as the ratio of the number of predicted presences to the total number of points in the evaluation dataset. Thresholds selected with maxF pb varied as the KP-RP ratio of the threshold selection datasets changed. Datasets with the KP-RP ratio around 1 generally produced better results than scores distant from 1. Results produced by We conclude that maxFpb had specificity too low for very common species using Random Forest and Maxent models. In contrast, maxSSS produced consistent results whichever dataset was used. The estimation of prevalence was almost always biased, and the bias was very large for DOMAIN and Random Forest predictions. We conclude that maxF pb is affected by the KP-RP ratio of the threshold selection datasets, but maxSSS is almost unaffected by this ratio. Unbiased estimations of prevalence are difficult to be determined using the threshold-based approach.

Abstract A large array of species distribution model ( SDM ) approaches has been developed for explaining and predicting the occurrences of individual species or species assemblages. Given the wealth of existing models, it is unclear which models perform best for interpolation or extrapolation of existing data sets, particularly when one is concerned with species assemblages. We compared the predictive performance of 33 variants of 15 widely applied and recently emerged SDM s in the context of multispecies data, including both joint SDM s that model multiple species together, and stacked SDM s that model each species individually combining the predictions afterward. We offer a comprehensive evaluation of these SDM approaches by examining their performance in predicting withheld empirical validation data of different sizes representing five different taxonomic groups, and for prediction tasks related to both interpolation and extrapolation. We measure predictive performance by 12 measures of accuracy, discrimination power, calibration, and precision of predictions, for the biological levels of species occurrence, species richness, and community composition. Our results show large variation among the models in their predictive performance, especially for communities comprising many species that are rare. The results do not reveal any major trade‐offs among measures of model performance; the same models performed generally well in terms of accuracy, discrimination, and calibration, and for the biological levels of individual species, species richness, and community composition. In contrast, the models that gave the most precise predictions were not well calibrated, suggesting that poorly performing models can make overconfident predictions. However, none of the models performed well for all prediction tasks. As a general strategy, we therefore propose that researchers fit a small set of models showing complementary performance, and then apply a cross‐validation procedure involving separate data to establish which of these models performs best for the goal of the study.

Migratory animals are threatened by human-induced global change. However, little is known about how stopover habitat, essential for refuelling during migration, affects the population dynamics of migratory species. Using 20 years of continent-wide citizen science data, we assess population trends of ten shorebird taxa that refuel on Yellow Sea tidal mudflats, a threatened ecosystem that has shrunk by >65% in recent decades. Seven of the taxa declined at rates of up to 8% per year. Taxa with the greatest reliance on the Yellow Sea as a stopover site showed the greatest declines, whereas those that stop primarily in other regions had slowly declining or stable populations. Decline rate was unaffected by shared evolutionary history among taxa and was not predicted by migration distance, breeding range size, non-breeding location, generation time or body size. These results suggest that changes in stopover habitat can severely limit migratory populations.

See Letter to the Editor on this article by Adam et al ., 26, 3756–3758 . See also Response to the Letter by Bradstock et al ., 26, e8–e9 .

OBJECTIVE: To investigate the distribution and incidence of chytridiomycosis in eastern Australian frogs and to examine the effects of temperature on this disease. DESIGN: A pathological survey and a transmission experiment were conducted. PROCEDURE: Diagnostic pathology examinations were performed on free-living and captive, ill and dead amphibians collected opportunistically from eastern Australia between October 1993 and December 2000. We conducted a transmission experiment in the laboratory to investigate the effects of temperature: eight great barred frogs (Mixophyes fasciolatus) exposed to zoospores of Batrachochytrium dendrobatidis and six unexposed frogs were housed individually in each of three rooms held at 17 degrees C, 23 degrees C and 27 degrees C. RESULTS: Chytridiomycosis was the cause of death or morbidity for 133 (55.2%) of 241 free-living amphibians and for 66 (58.4%) of 113 captive amphibians. This disease occurred in 34 amphibian species, was widespread around the eastern seaboard of Australia and affected amphibians in a variety of habitats at high and low altitudes on or between the Great Dividing Range and the coast. The incidence of chytridiomycosis was higher in winter, with 53% of wild frogs from Queensland and New South Wales dying in July and August. Other diseases were much less common and were detected mostly in spring and summer. In experimental infections, lower temperatures enhanced the pathogenicity of B. dendrobatidis in M. fasciolatus. All 16 frogs exposed to B. dendrobatidis at 17 degrees C and 23 degrees C died, whereas 4 of 8 frogs exposed at 27 degrees C survived. However, the time until death for the frogs that died at 27 degrees C was shorter than at the lower temperatures. Infections in survivors were eliminated by 98 days. CONCLUSION: Chytridiomycosis is a major cause of mortality in free-living and captive amphibians in Australia and mortality rate increases at lower temperatures.

Summary Assessments of the ‘quality’, condition or status of stands of native vegetation or habitat are now commonplace and are often an essential component of ecological studies and planning processes. Even when soundly based upon ecological principles, these assessments are usually highly subjective and involve implicit value judgements. The present paper describes a novel approach to vegetation or habitat quality assessment (habitat hectares approach) that can be used in almost all types of terrestrial vegetation. It is based on explicit comparisons between existing vegetation features and those of ‘benchmarks’ representing the average characteristics of mature stands of native vegetation of the same community type in a ‘natural’ or ‘undisturbed’ condition. Components of the index incorporate vegetation physiognomy and critical aspects of viability (e.g. degree of regeneration, impact of weeds) and spatial considerations (e.g. area, distribution and connectivity of remnant vegetation in the broader landscape). The approach has been developed to assist in making more objective and explicit decisions about where scarce conservation resources are allocated. Although the approach does not require an intimate botanical knowledge, it is believed to be ecologically valid and useful in many contexts. Importantly, the index does not provide a definitive statement on conservation status nor habitat suitability for individual species. It purposefully takes a ‘broad‐brush’ approach and is primarily intended for use by people involved with making environmentally sensitive planning and management decisions, but may be useful within environmental research programmes. The ‘habitat hectares’ approach is subject to further research and ongoing refinement and constructive feedback is sought from practitioners.

Abstract Failure to act quickly on evidence of rapid population decline has led to the first mammal extinction in Australia in the last 50 years, the Christmas Island Pipistrelle ( Pipistrellus murrayi ). The fate of another iconic species, the migratory Orange‐bellied Parrot ( Neophema chrysogaster ), monitored intensively for over 20 years, hangs in the balance. To inform future conservation management and decision making, we investigate the decision process that has led to the plight of both species. Our analysis suggests three globally relevant recommendations for minimizing species extinction worldwide: (1) informed, empowered, and responsive governance and leadership is essential; (2) processes that ensure institutional accountability must be in place, and; (3) decisions must be made whilst there is an opportunity to act. The bottom line is that, unless responsive and accountable institutional processes are in place, decisions will be delayed and extinction will occur.

Sinclair, S. J., M. D. White, and G. R. Newell. 2010. How useful are species distribution models for managing biodiversity under future climates? Ecology and Society 15(1): 8. https://doi.org/10.5751/ES-03089-150108

Summary 1. The invasion of carp ( Cyprinus carpio L.) in Australia illustrates how quickly an introduced fish species can spread and dominate fish communities. This species has become the most abundant large freshwater fish in south‐east Australia, now distributed over more than 1 million km 2 . 2. Carp exhibit most of the traits predicted for a successful invasive fish species. In addition, degradation of aquatic environments in south‐east Australia has given them a relative advantage over native species. 3. Derivation of relative measures of 13 species‐specific attributes allowed a quantitative comparison between carp and abundant native fish species across five major Australian drainage divisions. In four of six geographical regions analysed, carp differed clearly from native species in their behaviour, resource use and population dynamics. 4. Climate matching was used to predict future range expansion of carp in Australia. All Australian surface waters appear to be climatically suitable for carp. 5. This assessment strongly reinforces the need for immediate management of carp in Australia to include targeted control of human‐assisted dispersal, such as use of carp as bait by anglers, distribution to new locations by anglers and the use of the ‘Koi’ strain in the aquarium industry. 6. Given their historical spread, dispersal mechanisms and ecological requirements, the expansion of carp across most of the remainder of Australia is to be expected.

Land-cover change and ecosystem degradation may lead to biotic homogenization, yet our understanding of this phenomenon over large spatial scales and different biotic groups remains weak. We used a multi-taxa dataset from 335 sites and 36 heterogeneous landscapes in the Brazilian Amazon to examine the potential for landscape-scale processes to modulate the cumulative effects of local disturbances. Biotic homogenization was high in production areas but much less in disturbed and regenerating forests, where high levels of among-site and among-landscape β-diversity appeared to attenuate species loss at larger scales. We found consistently high levels of β-diversity among landscapes for all land cover classes, providing support for landscape-scale divergence in species composition. Our findings support concerns that β-diversity has been underestimated as a driver of biodiversity change and underscore the importance of maintaining a distributed network of reserves, including remaining areas of undisturbed primary forest, but also disturbed and regenerating forests, to conserve regional biota.

Abstract Extreme fire seasons characterised by very large ‘mega-fires’ have demonstrably increased area burnt across forested regions globally. However, the effect of extreme fire seasons on fire severity, a measure of fire impacts on ecosystems, remains unclear. Very large wildfires burnt an unprecedented area of temperate forest, woodland and shrubland across south-eastern Australia in 2019/2020, providing an opportunity to examine the impact of extreme fires on fire severity patterns. We developed an atlas of wildfire severity across south-eastern Australia between 1988 and 2020 to test (a) whether the 2019/2020 fire season was more severe than previous fire seasons, and (b) if the proportion of high-severity fire within the burn extent (HSp) increases with wildfire size and annual area burnt. We demonstrate that the 2019/2020 wildfires in south-eastern Australia were generally greater in extent but not proportionally more severe than previous fires, owing to constant scaling between HSp and annual fire extent across the dominant dry-forest communities. However, HSp did increase with increasing annual fire extent across wet-forests and the less-common rainforest and woodland communities. The absolute area of high-severity fire in 2019/2020 (∼1.8 M ha) was larger than previously seen, accounting for ∼44% of the area burnt by high-severity fire over the past 33 years. Our results demonstrate that extreme fire seasons are a rare but defining feature of fire regimes across forested regions, owing to the disproportionate influence of mega-fires on area burnt.

Abstract: The World Conservation Union (IUCN) defined a set of categories for conservation status supported by decision rules based on thresholds of parameters such as distributional range, population size, population history, and risk of extinction. These rules have received international acceptance and have become one of the most important decision tools in conservation biology because of their wide applicability, objectivity, and simplicity of use. The input data for these rules are often estimated with considerable uncertainty due to measurement error, natural variation, and vagueness in definitions of parameters used in the rules. Currently, no specific guidelines exist for dealing with uncertainty. Interpretation of uncertain data by different assessors may lead to inconsistent classifications because attitudes toward uncertainty and risk may have an important influence on the classification of threatened species. We propose a method of dealing with uncertainty that can be applied to the current IUCN criteria without altering the rules, thresholds, or intent of these criteria. Our method propagates the uncertainty in the input parameters and assigns the evaluated species either to a single category (as the current criteria do) or to a range of plausible categories, depending on the nature and extent of uncertainties.

The study of avian moult has been inhibited not only by its complexity but by convoluted and often conflicting terminologies that have combined to cloud the subject. Over time, two nomenclatures have emerged with differing bases of definition. The ‘life-cycle' system is used widely in the European literature (Cramp 1988, Jenni and Winkler 2020) and defines moult terms based on timing relative to current-day life-history events, primarily breeding. Conversely, the Humphrey–Parkes or ‘H–P' system (Humphrey and Parkes 1959, as modified by Howell et al. 2003), is used more widely in the New World and Australia (Higgins and Davies 1996, Johnson and Wolfe 2018, Pyle 2008, 2022a, Howell 2010), and defines terms based on the principle of how moults have evolved along avian lineages (Howell and Pyle 2015, Pyle 2022b). Recently, Kiat (2023) proposed that moult terminology be simplified, and advocated use of the life-cycle approach as a more understandable system to those not familiar with moult terminology. We appreciate Kiat's (2023) plea for a simpler moult terminology, and we empathize with the frustration that comes from learning an unfamiliar system, but we disagree with his primary conclusion. We argue that if one intends moult to be a subject for study, then a standardized and globally applicable terminology based on the best scientific evidence is preferable to a system that, while perhaps more widely understood among ornithologists and the general public for most passerines in boreal regions, is often imprecise or ambiguous and is difficult to apply to the majority of avian taxa on a global basis (Higgins and Davies 1996, Howell et al. 2004, Johnson and Wolfe 2018, Kiat 2023, Pyle 2022b). The debate over the best moult and plumage terminology to use has persisted since the H–P system was proposed by Humphrey and Parkes (1959) over 60 years ago (c.f. Howell et al. 2003, 2004, Jenni and Winkler 2004, 2004, Kiat 2023, Pyle 2022b). At this point, certain opinions on which system should be favoured are calcified, and we do not wish to belabour the details yet again. In our experience, however, newer students grasp the H–P system quickly, whereas older ornithologists – including ourselves – who first learned life-cycle moult terminology, often have initial difficulty envisioning the H–P system's evolutionary approach. Our goal with this perspective is to propose and illustrate how moults may have evolved from basal to current lineages in birds, with the hope that it will assist future ornithologists to envision and appreciate the H–P system. Adhering to the evolutionary (H–P) approach, we propose considering the prebasic moult (often regarded as similar to the post-breeding moult in life-cycle terminology), and perhaps the preformative moult (often regarded as similar to the post-juvenile moult in life-cycle terminology), as ancestral to all modern bird lineages, having evolved from reptiles (Howell and Pyle 2015, Kiat et al. 2020, 2021, Pyle 2022b, Fig. 1, Box 1). The complete or near-complete prebasic moult occurs in all current-day avian taxa and, rather than being simply a replacement of feathers, appears to be part of an endogenous restoration of body tissues (Voitkevich 1966, Murphy 1996, Kuenzel 2003) that may be ancestral to all vertebrates (King 1972). Considering the prebasic moult as homologous among modern birds is thus a parsimonious hypothesis, providing a robust nomenclatural framework that can be applied to all bird moults and plumages. The preformative moult also appears to be present in most if not all modern bird lineages, and here we further hypothesise that it may have evolved in reptiles as body size developed quickly in the first year of life; if not, it may have evolved early in avian evolution as it is found in most or all basal lineages (Fig. 1, Box 1). Assuming these hypotheses and homology among all modern bird taxa, the prebasic and preformative moults can provide the framework for defining all subsequently evolved moults within the H–P system. Additional inserted moults, including prealternate and presupplemental moults (not adequately defined under life-cycle terminology; c.f. Pyle 2022b), can evolve (both appearing and disappearing) along bird lineages such that, unlike prebasic and preformative moults, they should not be considered homologous across all birds. Instead, they may be regarded as homologous once they have evolved within a lineage (Howell et al. 2003, Johnson and Wolfe 2018, Pyle 2022a,b2022a). Once an evolutionary basis is appreciated, moult strategies become substantially easier to compare across all species and geographic latitudes. For example, the four underlying strategies identified by Howell et al. (2003), which are defined by the number of moults that occur within the first and later moult cycles, can be provisionally placed in an evolutionary context (see Fig. 1 and Box 1 for details). Although it is likely that inserted moults may have disappeared without trace along some bird lineages, envisioning how these four strategies may have evolved for modern-day taxa has the potential to help inform a greater appreciation for the adaptive causes of inserted moults (Fig. 1). We contend that an evolutionary (H–P) system is more applicable on a global basis for studying avian moult than is the life-cycle system, and we thus encourage those who use the life-cycle system to also attempt visualizing an evolutionary approach to moult terminology, rather than trying to simply synonymize H–P terms with life-cycle terms. We suggest first determining the prebasic moult cycle, then whether or not inserted moults occur in the first and/or later cycles, and lastly using an evolutionary approach to infer the correct designation of each inserted moult. Once envisioned, learned, and appreciated, the nomenclatural approach proposed by Humphrey and Parkes (1959), as modified by Howell et al. (2003), is scientifically more precise, allows the recognition of all inserted moults, and is easier to apply consistently to all taxa and by all parties interested in the study of moult in birds. – We thank Lauren Helton of the Institute for Bird Populations for preparing the figure with the phylogenetic tree (Figure 1). – Peter Pyle is generally supported by The Institute for Bird Populations but not specifically for this project. The same can be stated for the three co-authors regarding their institutions. Peter Pyle: Conceptualization (equal); Investigation (equal); Visualization (equal); Writing – original draft (equal). Steve N. G. Howell: Investigation (supporting); Writing – review and editing (supporting). Danny I. Rogers: Investigation (supporting); Writing – review and editing (supporting). Chris Corben: Investigation (supporting); Writing – review and editing (supporting). The peer review history for this article is available at https://publons.com/publon/10.1111/jav.03169. This article contains no additional data. A theoretical evolutionary approach to moult in birds from reptiles, using the four moult strategies defined by Howell et al. (2003; see also Howell 2010). See Box 1 for details. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article. A theoretical evolutionary approach to moult in birds from reptiles, using the four moult strategies defined by Howell et al. (2003, Howell 2010). The phylogenetic tree is based primarily on that of del Hoyo and Collar (2014, 2016), with a few exceptions (e.g. parrots and falcons are here placed basal to passerines; Suh et al. 2011). This phylogenetic concept of avian lineages has been and will continue to be revised as new data on systematics accumulate; however, we are confident that, for the purposes of our hypotheses, this tree serves as an adequate template to demonstrate an evolutionary approach to moults. The four strategies are ‘simple basic strategy' (SBS; no preformative or prealternate moults), ‘complex basic strategy' (CBS; a preformative moult but no prealternate moults), ‘simple alternate strategy' (SAS; a single moult in the first cycle and prealternate moults in later cycles), and ‘complex alternate strategy' (CAS; a preformative moult in the first cycle and prealternate moults in all cycles); presupplemental moults may also occur within taxa exhibiting complex strategies. Note that current taxa at the end of each lineage can exhibit more than one strategy. In lineages (other than CBS) in which this occurs, we show SBS, SAS, and/or CAS if any one extant species exhibits or appears to exhibit this strategy. We wish to emphasize that, despite these strategies and accompanying H–P terms having unambiguous definitions based on the principles of evolution, our understanding of precisely how moults have evolved from basal to derived taxa is still progressing. The following syntheses should be regarded as our own interpretations of how moults may have evolved and can be considered as working hypotheses. All birds have prebasic moults, which we consider an ancestral endogenous process that forms a structural framework to illustrate the evolutionary approach to moulting strategies using Humphrey–Parkes (H–P) nomenclature (Humphrey and Parkes 1959). Here we hypothesise that preformative moults may have also evolved from reptiles, as they are present in most bird taxa including basal lineages such as ratites (in Tinamiformes, at least; Davies 2002, Johnson and Wolfe 2018; and we suspect in Apterygiformes) as well as Galloanseres, Columbiformes, and Podicipediformes (Pyle 2005a, 2007, 2008, 2022a). Inserted preformative moults may have occurred in reptiles and vertebrates as body size developed quickly in the first year of life or, if not, they appear to have evolved during the basal stages of avian evolution. As such, we therefore provisionally hypothesise that the CBS is ancestral to all modern birds. Further study on the moults of reptiles and feathered dinosaurs (c.f. Kiat et al. 2020, 2021a,b2021), as well as the poorly known moulting strategies of ratites (Marchant and Higgins 1990, Davies 2002), could shed further light on this hypothesis. Along bird lineages, preformative moults may be lost and prealternate moults can be gained through evolution. Although the absence of a preformative moult in a species can be difficult to confirm (c.f. Pyle 2005b, 2008), it appears not to occur in at least some lineages, which thus exhibit the SBS. These include albatrosses (Diomedidae; Pyle 2008), storm-petrels (Oceanitidae and Hydrobatidae; Cramp and Simmons 1977, Marchant and Higgins 1990, Pyle 2008, Howell 2010, 2012), penguins (Sphenisciformes; Marchant and Higgins 1990), New World vultures (Cathartidae; Pyle 2008, Chandler et al. 2010), some Halcyoninae kingfishers (Alcedinidae; Pyle et al. 2016), and the Ivory Gull Pagophila eburnea (Howell 2001a). Barn owls (Tytonidae) may also show a SBS depending on the interpretation of first-cycle moults (c.f. Howell 2010, Pyle 2022b). As these current-day taxa all occur along lineages that basally exhibit the CBS, we propose that the preformative moult has been lost evolutionarily along these lineages, rather than the SBS being ancestral. Juvenile feathering in most bird taxa is weaker and less durable than that of later plumages, probably because there is a selective advantage to rapid growth of juvenile plumage, therefore shortening the period of high mortality rates in which birds are unable to fly. Preformative moults therefore appear to be necessary to replace juvenile plumage that is not durable enough to remain functional throughout the first cycle. In contrast, taxa exhibiting the SBS share the trait of having relatively protected and long natal stages, often in burrows or cavities, where chicks are at low risk from predation and are also fed protein-rich food. In such species, selection may favour slow growth of a durable juvenile plumage that will remain functional until the second cycle, precluding the need for a preformative moult (Howell 2010). Such traits are shared by diurnal raptors (Accipitridae and Falconidae) and petrels (Procellariidae), families previously thought to exhibit the SBS (Cramp and Simmons 1977, Marchant and Higgins 1990, Forsman 1999) but for which limited preformative moults have recently been identified in some or most taxa (Pyle 2005b, 2008). The preformative moults within these families may be vestigial carryovers from ancestral taxa exhibiting the CBS, and could be lost in the future, or perhaps they have redeveloped along lineages in which the preformative moult was lost. Derived lineages such as some cavity nesting passerines and woodpeckers also share the traits of relatively protected natal stages where chicks are at low risk from predation but continue to undergo preformative moults. It is possible that not enough time has elapsed for these species to lose the preformative moult evolutionarily, although note that some taxa of kingfishers do appear to have lost the preformative moult (Pyle et al. 2016). Inserted prealternate moults have evolved independently along various bird lineages, including basal taxa such as ptarmigan (Galliformes, Lagopus; Pyle 2007), ducks (Anatidae; Pyle 2005a, 2013), grebes (Podicipediformes; Pyle 2008), and waders or shorebirds (Charadriidae and Scolopacidae), as well as derived taxa such as many passerines (Passeriformes). Prealternate moults, therefore, should not be considered homologous across all birds (Howell et al. 2004, Pyle 2022b). These moults appear to have initially evolved to replace worn feathers, with some taxa later taking advantage of them for purposes of sexual selection or predation avoidance (Howell 2010, Pyle 2022a). In many species among various lineages (e.g. grebes, divers, waders or shorebirds, and several passerine branches), males or both sexes gain more colourful alternate feathering to better attract mates. In other taxa, such as ducks and perhaps skuas (jaegers), alternate feathering has become less colourful or more cryptic given surrounding habitat preferences, to better avoid predation (Pyle 2005a, Pyle and Reid 2016). Still in other species, alternate feathering resembles basic feathering in colour patterns. Despite subsequent selection for alternate feather colouration, the initial evolution of prealternate moults appears to have occurred independently along many lineages as behavioural changes, including migration strategies (below), resulted in the need to replace exposed feathers more than once on an annual basis. In some derived lineages (e.g. among waders and some passerines), different genera or even species within genera can have or lack prealternate moults. In such cases, further study may reveal whether or not prealternate moults have been recently gained among taxa that have alternate plumages, or recently lost in species that lack them. Divers (loons; Gaviiformes), Pelecaniformes, some larger gulls (among Laridae), and some alcids (Alcididae) have evolved prealternate moults in the second and later basic cycles but apparently undergo only one moult in the first cycle (Pyle 2008, 2008; Howell 2001b, 2010), and thus exhibit the SAS. The SAS may have evolved in one of several ways (Howell and Pyle 2015). In one scenario, lineages that exhibited a CBS may have gained a prealternate moult in the second and later cycles but not in the first cycle. It is possible that such an evolutionary history has occurred for divers and Pelecaniformes, as well as ibises and spoonbills (Threskiornithidae). In these species, development of colourful plumages for mate selection may have resulted in the retention of an inserted prealternate moult in birds of breeding age but not those of pre-breeding ages. This may not be the case for those Procellariiformes and other species exhibiting the SBS, which may rely more on vocalizations (e.g. petrels, kingfishers) or dance and/or flight displays (e.g. albatrosses, New World vultures) for mate selection. Prealternate moults have recently been documented in a few migratory hummingbirds (Trochilidae) and, although H–P nomenclature has been debated for these species (Howell 2010, Pyle 2022a), it is possible that a prealternate moult evolved in the second and later cycles but not the first (Sieburth and Pyle 2018, Pyle 2022c). Another scenario leading to the SAS would be the loss of either the preformative moult or the first prealternate moult (or a merging of these two moults) along a lineage exhibiting the CAS. Such an evolutionary history may have occurred for some alcids, as proposed by Pyle (2009), as well as for larger gulls (Howell and Corben 2000) and for Gaviiformes and Pelicaniformes as mentioned above. Among gulls (Laridae), for example, basal taxa, such as those in genera Chroicocephalus and Leucophaeus (Pons et al. 2005), exhibit a CAS whereas the more derived white-headed gulls (genus Larus) exhibit the SAS (Howell and Dunn 2007, Pyle 2008). Having lost the first prealternate moult or having had it merge with the preformative moult in ancestral species was perhaps due to the increased energy and longer period needed to replace feathers in larger gulls. Likewise, among alcids (Alcidae), larger species such as those of genus Fratercula may have lost the prealternate moult or had it merge with the preformative moult during the first cycle (Howell and Pyle 2005, Pyle 2008, 2008). No non-passerine taxa among more derived lineages (e.g. Strigidae, Picidae and Psitaciiformes) and no species of passerine (Passeriformes) has been documented with either the SBS or the SAS. The CAS, involving a preformative moult in the first cycle and prealternate moults in both first and later cycles, likely resulted primarily from the evolution of inserted prealternate moults into all cycles. All taxa in which the CAS is exhibited by at least some species, including those among Podicipediformes, Galloanseraes, Charadriiformes, and Gruiformes, appear to have evolved along lineages in which the CBS was basal and still occurs in many species within these groups. Passerines share a common ancestor which likely exhibited the CBS, given that it is shown by most passerines, and taxa immediately ancestral to passerines, such as parrots (Psittaciformes) and falcons (Falconidae). Moreover, basal passerine lineages such as New Zealand wrens (Acanthisittidae), broadbills (Calyptomenidae), pittas (Pittidae), antbirds (Thamnophilidae), ovenbirds (Furnariidae), tityras (Tityridae), and lyrebirds (Menuridae), all exhibit the CBS. It appears that the CAS has evolved many times within Passeriformes, including along basal Passeriform lineages such as fairywrens (Maluridae), tyrannid flycatchers (Tyrannidae), and vireos (Vireonidae), as well as derived (including terminal) lineages such as cardinals (Cardinalidae), sunbirds (Nectariniidae), finches (Fringillidae), wood-warblers (Parulidae), and tanagers (Thraupidae). However, the CBS has also been maintained among terminal taxa, such as penduline-tits (Remizidae), bulbuls (Pycnonotidae), mockingbirds (Mimidae), and elachuras (Elachuridae), with no evidence that prealternate moults have evolved along their lineages. The CAS appears to have evolved more often in highly migratory than in resident (including most tropical) species of birds, perhaps due to the increased effects of solar radiation on exposed feathers on an annual basis, requiring feathers to be replaced more than once per cycle to maintain functionality (Pyle 1998, Howell 2010, Kiat et al. 2019, Terrill et al. 2020, Guallar et al. 2021, Kiat and Izhaki 2021). For similar reasons, it also appears to have evolved in some resident species found in harsher habitats such as saltmarshes, scrub, and thornforests, which can contribute to rapid feather wear (Willoughby 1991, Howell 2010, Pyle 2022a).

Abstract Aichi Target 12 of the Convention on Biological Diversity (CBD) contains the aim to ‘prevent extinctions of known threatened species’. To measure the degree to which this was achieved, we used expert elicitation to estimate the number of bird and mammal species whose extinctions were prevented by conservation action in 1993–2020 (the lifetime of the CBD) and 2010–2020 (the timing of Aichi Target 12). We found that conservation action prevented 21–32 bird and 7–16 mammal extinctions since 1993, and 9–18 bird and two to seven mammal extinctions since 2010. Many remain highly threatened and may still become extinct. Considering that 10 bird and five mammal species did go extinct (or are strongly suspected to) since 1993, extinction rates would have been 2.9–4.2 times greater without conservation action. While policy commitments have fostered significant conservation achievements, future biodiversity action needs to be scaled up to avert additional extinctions.

Sea-level rise (SLR) will greatly alter littoral ecosystems, causing habitat change and loss for coastal species. Habitat loss is widely used as a measurement of the risk of extinction, but because many coastal species are migratory, the impact of habitat loss will depend not only on its extent, but also on where it occurs. Here, we develop a novel graph-theoretic approach to measure the vulnerability of a migratory network to the impact of habitat loss from SLR based on population flow through the network. We show that reductions in population flow far exceed the proportion of habitat lost for 10 long-distance migrant shorebirds using the East Asian-Australasian Flyway. We estimate that SLR will inundate 23-40% of intertidal habitat area along their migration routes, but cause a reduction in population flow of up to 72 per cent across the taxa. This magnifying effect was particularly strong for taxa whose migration routes contain bottlenecks-sites through which a large fraction of the population travels. We develop the bottleneck index, a new network metric that positively correlates with the predicted impacts of habitat loss on overall population flow. Our results indicate that migratory species are at greater risk than previously realized.

Knowing where species occur is fundamental to many ecological and environmental applications. Species distribution models (SDMs) are typically based on correlations between species occurrence data and environmental predictors, with ecological processes captured only implicitly. However, there is a growing interest in approaches that explicitly model processes such as physiology, dispersal, demography and biotic interactions. These models are believed to offer more robust predictions, particularly when extrapolating to novel conditions. Many process-explicit approaches are now available, but it is not clear how we can best draw on this expanded modelling toolbox to address ecological problems and inform management decisions. Here, we review a range of process-explicit models to determine their strengths and limitations, as well as their current use. Focusing on four common applications of SDMs - regulatory planning, extinction risk, climate refugia and invasive species - we then explore which models best meet management needs. We identify barriers to more widespread and effective use of process-explicit models and outline how these might be overcome. As well as technical and data challenges, there is a pressing need for more thorough evaluation of model predictions to guide investment in method development and ensure the promise of these new approaches is fully realised.

Abstract Innumerable approaches to analyse genetic data are now available to guide conservation, ecological and agricultural projects. However, streamlined and accessible tools are needed to bring these approaches within the reach of a broader user base. dartR was released in 2018 to lessen the intrinsic complexity of analysing single nucleotide polymorphisms (SNPs) and dominant markers (presence/absence of amplified sequence tags) by providing user‐friendly data quality control and marker selection functions. dartR users have grown steadily since its release and provided valuable feedback on their interaction with the package allowing us to enhance dartR capabilities. Here, we present Version 2 of dartR . In this version, we substantially increased the number of available functions from 45 to 144. In addition to improved functionality, we focused on enhancing the user experience by extending plot customisation, function standardisation, increasing user support and function speed. dartR provides functions for various stages in analysing genetic data, from data manipulation to reporting. dartR provides many functions for importing, exporting and linking to other packages, to provide an easy‐to‐navigate conduit between data generation and analysis options already available via other packages. We also implemented simulation functions whose results can be analysed seamlessly with several other dartR functions. As more methods and approaches mature to inform conservation, we envision that accessible platforms to analyse genetic data will play a crucial role in translating science into practice.

Summary Angiosperm trees often dominate forests growing in resource‐rich habitats, whereas conifers are generally restricted to less productive habitats. It has been suggested that conifers may be displaced by angiosperms except where competition is less intense, because conifer seedlings are inherently slow growing, and are outpaced by faster‐growing angiosperm species. Here we investigate whether competition with ferns and deeply shading trees also contributes to a failure of conifers to regenerate in resource‐rich habitats. We examined how changes in soil nutrient availability and drainage affected vegetation along the retrogressive stages of a soil chronosequence in southern New Zealand. Vegetation composition shifted from angiosperm‐tree dominance on ‘recent’ alluvial terraces (< 24 ky), via coniferous‐tree dominance on older marine terraces (79–121 ky), to coniferous‐shrub dominance on the oldest marine terraces (291 ky). Soil drainage deteriorated along the sequence, and N : P leaves and N : P soil indicate increasing P‐limitation. Conifer species appear to be adapted to persistence on infertile and poorly drained soils. The floor of the relatively fertile alluvial forests was deeply shaded (∼1% light transmission) by dense groves of tree‐ferns and ground‐ferns, and by large‐leaved subcanopy trees. Few seedlings of any type were found on the forest floor, even in tree‐fall gaps, and establishment was restricted to rotting logs and tree‐fern trunks. Angiosperms were particularly successful at colonizing these raised surfaces. Less shade was cast by the conifer‐dominated forests on infertile marine terraces (∼5% light transmission), which lacked tall ferns. There were many opportunities for conifer establishment, with high seedling densities recorded on the forest floor and on logs. By contrast, angiosperm seedlings were mainly restricted to logs. Our results suggest that several mechanisms act in concert to reduce regeneration opportunities for conifers in productive habitats. In particular, we suggest that tall ferns and deep shade are responsible for a restriction of regeneration opportunities in relatively productive forests in New Zealand, diminishing the opportunities for conifers to escape the competitive effects of fast‐growing angiosperms. Thus ‘crocodiles’ may alter the outcome of the race between ‘hares’ and ‘tortoises’.