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Identifying the factors that influence species diversification is fundamental to our understanding of the evolutionary processes underlying extant biodiversity. Behavioural innovation, coupled with the social transmission of new behaviours, has been proposed to increase rates of evolutionary diversification, as novel behaviours expose populations to new selective regimes. Thus, it is believed that behavioural flexibility may play an important role in driving evolutionary diversification across animals. We test this hypothesis within the primates, a taxonomic group with considerable among-lineage variation in both species diversity and behavioural flexibility. We employ a time cut-off in our phylogeny to help account for biases associated with recent taxonomic reclassifications and compare three alternative measures of diversification rate that consider different phylogenetic depths. We find that the presence of behavioural innovation and social learning are positively correlated with diversification rates among primate genera, but not at shallower phylogenetic depths. Given that we find stronger associations when examining older rather than more recent diversification events, we suggest that extinction resistance, as opposed to speciation, may be an important mechanism linking behavioural flexibility and primate diversification. Our results contrast with work linking behavioural flexibility with diversification of birds at various phylogenetic depths. We offer a possible dispersal-mediated explanation for these conflicting patterns, such that the influence behavioural flexibility plays in dictating evolutionary trajectories differs across clades. Our results suggest that behavioural flexibility may act through several different pathways to shape the evolutionary trajectories of lineages.

The Tree of Life will be irrevocably reshaped as anthropogenic extinctions continue to unfold. Theory suggests that lineage evolutionary dynamics, such as age since origination, historical extinction filters and speciation rates, have influenced ancient extinction patterns – but whether these factors also contribute to modern extinction risk is largely unknown. We examine evolutionary legacies in contemporary extinction risk for over 4000 genera, representing ~30,000 species, from the major tetrapod groups: amphibians, birds, turtles and crocodiles, squamate reptiles and mammals. We find consistent support for the hypothesis that extinction risk is elevated in lineages with higher recent speciation rates. We subsequently test, and find modest support for, a primary mechanism driving this pattern: that rapidly diversifying clades predominantly comprise range-restricted, and extinction-prone, species. These evolutionary patterns in current imperilment may have important consequences for how we manage the erosion of biological diversity across the Tree of Life.

In the simplest phylogenetic diversification model (the pure-birth Yule process), lineages split independently at a constant rate λ for time t. The length of a randomly chosen edge (either interior or pendant) in the resulting tree has an expected value that rapidly converges to as t grows, and thus is essentially independent of t. However, the behaviour of the length L of the longest pendant edge reveals remarkably different behaviour: L converges to t/2 as the expected number of leaves grows. Extending this model to allow an extinction rate μ (where μ < λ), we also establish a similar result for birth-death trees, except that t/2 is replaced by t/2 · (1 – μ/λ). This ‘complete’ tree may contain subtrees that have died out before time t; for the ‘reduced tree’ that just involves the leaves present at time t and their direct ancestors, the longest pendant edge length L again converges to t/2. Thus, there is likely to be at least one extant species whose associated pendant branch attaches to the tree approximately half-way back in time to the origin of the entire clade. We also briefly consider the length of the shortest edges. Our results are relevant to phylogenetic diversity indices in biodiversity conservation, and to quantifying the length of aligned sequences required to correctly infer a tree. We compare our theoretical results with simulations, and with the branch lengths from a recent phylogenetic tree of all mammals.

When prioritizing populations for conservation of a given species, it is unclear whether the distribution of standing genetic variation can be used as a suitable proxy for the distribution of useful adaptive genetic variation. We tested whether using genome-wide and putatively adaptive genetic variation give similar prioritization results. We identified adaptive loci via their association with either environmental factors or phenotypic traits using two genomic data sets: yellow warblers (Setophaga petechia) across North America and lodgepole pines (Pinus contorta) in western Canada. We measured pairwise differentiation among populations using a principal components analysis and used a phylogenetic approach (NeighborNet networks) coupled with a measure of evolutionary distinctiveness (Shapley value) to attribute a priority rank to each population. Overall, we found that prioritization rankings using adaptive variation alone were not significantly divergent from rankings based on genome-wide genetic variation. Our testing framework might be of immediate use to conservation practitioners collecting next-generation sequencing data, and we call for further investigation in other species. Our results suggest that we may not need to pursue the contingent step of identifying adaptive variation in species of concern before prioritizing populations, i.e. a naive approach of using genome-wide genetic variation might be a suitable proxy for identifying local adaptation.

Based on the number of words per meaning across the Indo-European Swadesh list,Pagel et al. (2007)suggest that frequency of use is a general mechanism of linguistic evolution. We test this claim using within-language change. From the IDS (Key & Comrie 2015) we compiled a comparative word list of 1,147 cognate pairs for Classical Latin and Modern Spanish, and 1,231 cognate pairs for Classical and Modern Greek. We scored the amount of change for each cognate pair in the two language histories according to a novel 6-point scale reflecting increasing levels of change from regular sound change to external borrowing. We find a weak negative correlation between frequency of use and lexical change for both the Latin-Spanish and Classical-Modern Greek language developments, but post hoc tests reveal that low frequency of use of borrowed words drive these patterns, casting some doubt on frequency of use as a general mechanism of language change.

British Columbia has the greatest biological diversity of any province or territory in Canada. Yet increasing numbers of species in British Columbia are threatened with extinction. The current patchwork of provincial laws and regulations has not effectively prevented species declines. Recently, the Provincial Government has committed to enacting an endangered species law. Drawing upon our scientific and legal expertise, we offer recommendations for key features of endangered species legislation that build upon strengths and avoid weaknesses observed elsewhere. We recommend striking an independent Oversight Committee to provide recommendations about listing species, organize Recovery Teams, and monitor the efficacy of actions taken. Recovery Teams would evaluate and prioritize potential actions for individual species or groups of species that face common threats or live in a common area, based on best available evidence (including natural and social science and Indigenous Knowledge). Our recommendations focus on implementing an adaptive approach, with ongoing and transparent monitoring and reporting, to reduce delays between determining when a species is at risk and taking effective actions to save it. We urge lawmakers to include this strong evidentiary basis for species recovery as they tackle the scientific and socioeconomic challenges of building an effective species at risk Act. Au Canada, c’est en Colombie-Britannique que la biodiversité est la plus élevée. Pourtant, un nombre croissant de ces espèces sont menacées. L’actuel enchevêtrement de lois et de règlements provinciaux ne parvient pas à en prévenir le déclin. Récemment, le gouvernement provincial s’est engagé à adopter une loi sur les espèces en péril. En nous appuyant sur notre expertise légale et scientifique et sur les succès et échecs connus ailleurs, nous proposons les éléments clés que devrait présenter cette loi. Nous recommandons la formation d’un Comité indépendant de surveillance qui évaluera le statut des espèces, organisera les Équipes de rétablissement et estimera l’efficacité des mesures de protection adoptées. Les Équipes de rétablissement prioriseront les actions possibles pour chaque espèce ou groupe d’espèces subissant les mêmes menaces ou habitant la même région en s’appuyant sur les meilleures informations disponibles (sciences naturelles et sociales et savoirs autochtones). Nos recommandations visent à établir une approche adaptative, incluant un suivi régulier et transparent, afin de réduire les délais entre l’établissement du statut et la mise en œuvre d’actions de rétablissement. Nous exhortons les législateurs et législatrices à tenir compte de cette approche basée sur les éléments probants relatifs au rétablissement des espèces.

Faced with the challenge of saving as much diversity as possible given financial and time constraints, conservation biologists are increasingly prioritizing species on the basis of their overall contribution to evolutionary diversity. Metrics such as EDGE (Evolutionary Distinct and Globally Endangered) have been used to set such evolutionarily based conservation priorities for a number of taxa, such as mammals, birds, corals, amphibians, and sharks. Each application of EDGE has required some form of correction to account for species whose positions within the tree of life are unknown. Perhaps the most advanced of these corrections is phylogenetic imputation, but to date there has been no systematic assessment of both the sensitivity of EDGE scores to a phylogeny missing species, and the impact of using imputation to correct for species missing from the tree. Here, we perform such an assessment, by simulating phylogenies, removing some species to make the phylogeny incomplete, imputing the position of those species, and measuring (1) how robust ED scores are for the species that are not removed and (2) how accurate the ED scores are for those removed and then imputed. We find that the EDGE ranking for species on a tree is remarkably robust to missing species from that tree, but that phylogenetic imputation for missing species, while unbiased, does not accurately reconstruct species’ evolutionary distinctiveness. On the basis of these results, we provide clear guidance for EDGE scoring in the face of phylogenetic uncertainty.

The Monarch butterfly eastern population (Danaus plexippus) is in decline primarily due to habitat loss. Current habitat restoration programs focus on re-establishing milkweed, the primary food resource for Monarch caterpillars, in the central United States of America. However, individual components of the Monarch life cycle function as part of an integrated whole. Here we develop the MOBU-SDyM, a migration-wide systems dynamics model of the Monarch butterfly migratory cycle to explore alternative management strategies’ impacts. Our model offers several advances over previous efforts, considering complex variables such as dynamic temperature-dependent developmental times, dynamic habitat availability, and weather-related mortality across the entire range. We first explored whether the predominant focus of milkweed restoration in the mid-range of the Monarch’s migration could be overestimating the Monarch’s actual habitat requirements. Second, we examined the robustness of using the recommended 1.2–1.6 billion milkweed stems as a policy objective when accounting for factors such as droughts, changes in temperature, and the stems’ effective usability by the Monarchs. Third, we used the model to estimate the number and distribution of stems across the northern, central, and southern regions of the breeding range needed to reach a self-sustainable long-term Monarch population of six overwintering hectares. Our analysis revealed that concentrating milkweed growth in the central region increases the size of the overwintering colonies more so than equivalent growth in the south region, with growth in the northern region having a negligible effect. However, even though simulating an increase in milkweed stems in the south did not play a key role in increasing the size of the overwintering colonies, it plays a paramount role in keeping the population above a critically small size. Abiotic factors considerably influenced the actual number of stems needed, but, in general, our estimates of required stems were 43–91% larger than the number of stems currently set as a restoration target: our optimal allocation efforts were 7.35, 92, and 0.15% to the south, central, and northern regions, respectively. Systems dynamics’ analytical and computational strengths provided us with new avenues to investigate the Monarch’s migration as a complex biological system and to contribute to more robust restoration policies for this unique species.

Herbivore grazing is an important determinant of plant community assemblages. Thus, it is essential to understand its impact to direct conservation efforts in regions where herbivores are managed. While the impacts of reindeer (Rangifer tarandus) grazing on plant biodiversity and community composition in the Fennoscandian tundra are well studied, the impact of reindeer grazing on phylogenetic community structure is not. We used data from a multiyear quasi‐experimental study in northern Fennoscandia to analyze the effect of reindeer grazing on plant community diversity including its phylogenetic structure. Our study design used a permanent fence constructed in the 1960s and temporary fences constructed along the permanent fence to expose plant communities to three different grazing regimes: light (almost never grazed), pulse (grazed every other year), and press (chronic grazing for over 40 years). Similar to previous studies on low productivity ecosystems in this region, the species richness and evenness of plant communities with pulse and press grazing did not differ from communities with light grazing. Also consistent with previous studies in this region, we observed a transition from shrub‐dominated communities with light grazing to graminoid‐dominated communities with pulse and press grazing. Interestingly, communities with pulse, but not press, grazing were more phylogenetically dispersed than communities with light grazing. If grazing pulses can increase the phylogenetic diversity of plant communities, our result suggests changes in reindeer management allowing for pulses of grazing to increase phylogenetic diversity of plant communities., We used data from a multiyear experimental study in northern Fennoscandia to analyze the effect of reindeer (Rangifer tarandus) grazing on plant community diversity including its phylogenetic structure. Interestingly, communities with pulse, but not press, grazing were more phylogenetically dispersed than communities with light grazing. Our results have important implications for our understanding of how herbivore grazing drives plant community assembly and for the management of reindeer in Fennoscandia if pulses of grazing can increase the phylogenetic diversity of plant communities.

Herbivore grazing is an important determinant of plant community assemblages. We used data from a multi-year experimental study in Northern Fennoscandia to analyze the effect of reindeer (Rangifer tarandus) grazing on plant community diversity including its phylogenetic structure. Similar to previous studies on low productivity ecosystems in this region, we found no effect of grazing on plant biodiversity and a transition from dwarf shrubs to graminoids with pulse (i.e. grazed every other year) and press (i.e. grazed every year) grazing. Interestingly, communities with pulse grazing were more phylogenetically dispersed than communities with press grazing and lightly grazed communities. We argue that the indirect effects of reindeer grazing (e.g. interspecific competition and soil nutrient availability) may work in opposition of the direct effects (i.e. physical removal of species) and that the phylogenetic structure of the resulting community will depend upon the relative strengths of the direct and indirect effects. This interpretation suggests that the indirect effects of reindeer grazing in our study region are more important than the direct effects in driving community assembly for plant communities that are exposed to pulse grazing. Our results have important implications for the management of reindeer in Fennoscandia if pulses of grazing can increase the phylogenetic diversity of plant communities.

The extent to which phylogenetic diversity (PD) captures feature diversity (FD) is a topical and controversial question in biodiversity conservation. In this short paper, we formalize this question and establish a precise mathematical condition for FD (based on discrete characters) to coincide with PD. In this way, we make explicit the two main reasons why the two diversity measures might disagree for given data; namely, the presence of certain patterns of feature evolution and loss, and using temporal branch lengths for PD in settings that may not be appropriate (e.g., due to rapid evolution of certain features over short periods of time). Our article also explores the relationship between the “Fair Proportion” index of PD and a simple index of FD (both of which correspond to Shapley values in cooperative game theory). In a second mathematical result, we show that the two indices can take identical values for any phylogenetic tree, provided the branch lengths in the tree are chosen appropriately. [Evolutionary distinctiveness; feature diversity; phylogenetic diversity; shapley value.]

Humans continue to alter terrestrial ecosystems, but our understanding of how biodiversity responds is still limited. Anthropogenic habitat conversion has been associated with the loss of evolutionarily distinct bird species at local scales, but whether this evolutionary pattern holds across other clades is unknown. We collate a global dataset on amphibian assemblages in intact forests and nearby human-modified sites to assess whether evolutionary history influences susceptibility to land conversion. We found that evolutionarily distinct amphibian species are disproportionately lost when forested habitats are converted to alternative land-uses. We tested the hypothesis that grassland-associated amphibian lineages have both higher diversification and are pre-adapted to human landscapes, but found only weak evidence supporting this. The loss of evolutionarily distinct amphibians with land conversion suggests that preserving remnant forests will be vital if we aim to preserve the amphibian tree of life in the face of mounting anthropogenic pressures.

Climate change is causing rapid shifts in species’ range limits, leading to poleward expansions and range losses toward the equator. However, ‘climate debt’, the gap between required and realized range shifts under changing climates, can accumulate when species are unable to track shifting conditions sufficiently rapidly to keep pace with climate changes. Currently, we do not know the rate at which species will keep pace via dispersal to track their climate envelopes, yet understanding potential differences in climate debt is central to estimating how climate change will influence extinction risk. Here, we use historical observations of 155 butterfly species found in Canada to construct climate‐based environmental niche models for each species and then compare projections with observed modern distributions to quantify climate debts. This approach suggests that high levels of climate debt are accumulating within the vast majority of these species. Such failure to track changing climates may arise from some combination of interspecific interactions such as particular food availability for specialists, abiotic barriers such as mountain ranges, or species’ intrinsic dispersal capacities. Our linear models relating climate debt to a variety of biological predictors suggest that the debts we documented are accumulating independently of dispersal ability, diet breadth, and phylogeny. A proxy for range size is the only significant predictor of climate debt, with species with narrower ranges accumulating more debt: this suggests that species with narrow ranges may be at risk from both a reduction of suitable habitat in their current range and the failure to colonize newly available habitat. Identifying the factors, whether intrinsic or imposed by local environmental conditions, that limit species’ capacities to colonize areas beyond their historical limits is vital to conservation planning.

It has long been asserted that samples of taxa that span more of the Tree of Life contain more features that humans find useful. This has now been tested at a global scale: across 13,500 plant genera and nearly 9,500 uses, the prediction holds, supporting a macroevolutionary perspective on biodiversity conservation.

Many of the traits associated with elevated rates of speciation, including niche specialization and having small and isolated populations, are similarly linked with an elevated risk of extinction. This suggests that rapidly speciating lineages may also be more extinction prone. Empirical tests of a speciation-extinction correlation are rare because assessing paleontological extinction rates is difficult. However, the modern biodiversity crisis allows us to observe patterns of extinction in real time, and if this hypothesis is true then we would expect young clades that have recently diversified to have high contemporary extinction risk. Here, we examine evolutionary patterns of modern extinction risk across over 300 genera within one of the most threatened vertebrate classes, the Amphibia. Consistent with predictions, rapidly diversifying amphibian clades also had a greater share of threatened species. Curiously, this pattern is not reflected in other tetrapod classes and may reflect a greater propensity to speciate through peripheral isolation in amphibians, which is partly supported by a negative correlation between diversification rate and mean geographic range size. This clustered threat in rapidly diversifying amphibian genera means that protecting a small number of species can achieve large gains in preserving amphibian phylogenetic diversity. Nonindependence between speciation and extinction rates has many consequences for patterns of biodiversity and how we may choose to conserve it.

It is often claimed that conserving evolutionary history is more efficient than species-based approaches for capturing the attributes of biodiversity that benefit people. This claim underpins academic analyses and recommendations about the distribution and prioritization of species and areas for conservation, but evolutionary history is rarely considered in practical conservation activities. One impediment to implementation is that arguments related to the human-centric benefits of evolutionary history are often vague and the underlying mechanisms poorly explored. Herein we identify the arguments linking the prioritization of evolutionary history with benefits to people, and for each we explicate the purported mechanism, and evaluate its theoretical and empirical support. We find that, even after 25 years of academic research, the strength of evidence linking evolutionary history to human benefits is still fragile. Most – but not all – arguments rely on the assumption that evolutionary history is a useful surrogate for phenotypic diversity. This surrogacy relationship in turn underlies additional arguments, particularly that, by capturing more phenotypic diversity, evolutionary history will preserve greater ecosystem functioning, capture more of the natural variety that humans prefer, and allow the maintenance of future benefits to humans. A surrogate relationship between evolutionary history and phenotypic diversity appears reasonable given theoretical and empirical results, but the strength of this relationship varies greatly. To the extent that evolutionary history captures unmeasured phenotypic diversity, maximizing the representation of evolutionary history should capture variation in species characteristics that are otherwise unknown, supporting some of the existing arguments. However, there is great variation in the strength and availability of evidence for benefits associated with protecting phenotypic diversity. There are many studies finding positive biodiversity–ecosystem functioning relationships, but little work exists on the maintenance of future benefits or the degree to which humans prefer sets of species with high phenotypic diversity or evolutionary history. Although several arguments link the protection of evolutionary history directly with the reduction of extinction rates, and with the production of relatively greater future biodiversity via increased adaptation or diversification, there are few direct tests. Several of these putative benefits have mismatches between the relevant spatial scales for conservation actions and the spatial scales at which benefits to humans are realized. It will be important for future work to fill in some of these gaps through direct tests of the arguments we define here. Fil: Tucker, Caroline M.. University of North Carolina; Estados Unidos Fil: Aze, Tracy. University Of Leeds.; Reino Unido Fil: Cadotte, Marc W.. University of Toronto; Canadá Fil: Cantalapiedra, Juan L.. Universidad de Alcalá; España Fil: Chisholm, Chelsea. Universite de Lausanne; Suiza Fil: Díaz, Sandra Myrna. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentina Fil: Grenyer, Richard. University of Oxford; Reino Unido Fil: Huang, Danwei. National Singapore University; Singapur Fil: Mazel, Florent. University of British Columbia; Canadá Fil: Pearse, William D.. University of Utah; Estados Unidos Fil: Pennell, Matthew W.. University of British Columbia; Canadá Fil: Winter, Marten. German Centre for Integrative Biodiversity Research; Alemania Fil: Mooers, Arne O.. University Fraser Simon; Canadá

Alternative prioritization strategies have been proposed to safeguard biodiversity over macroevolutionary time scales. The first prioritizes the most distantly related species-maximizing phylogenetic diversity (PD)-in the hopes of capturing at least some lineages that will successfully diversify into the future. The second prioritizes lineages that are currently speciating, in the hopes that successful lineages will continue to generate species into the future. These contrasting schemes also map onto contrasting predictions about the role of slow diversifiers in the production of biodiversity over palaeontological time scales. We consider the performance of the two schemes across 10 dated species-level palaeo-phylogenetic trees ranging from Foraminifera to dinosaurs. We find that prioritizing PD for conservation generally led to fewer subsequent lineages, while prioritizing diversifiers led to modestly more subsequent diversity, compared with random sets of lineages. Importantly for conservation, the tree shape when decisions are made cannot predict which scheme will be most successful. These patterns are inconsistent with the notion that long-lived lineages are the source of new species. While there may be sound reasons for prioritizing PD for conservation, long-term species production might not be one of them., This paper is a product of the sCAP working group supported by sDiv, the Synthesis Centre of the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig (DFGFZT 118), and by the Canadian Institute for Ecology and Evolution. M.W.C., A.Ø.M. and M.W.P. acknowledge generous support from NSERC Canada. D.H. acknowledges the National Research Foundation, Prime Minister’s Office, Singapore under its Marine Science R&D Programme (MSRDP-P03); F.M. was supported by an NSERC Accelerator Grant to A.Ø.M. and an NSERC Banting Postdoctoral Fellowship; J.L.C. was funded by the Humboldt Foundation, the German Research Foundation (DFG, AOBJ: 637491) and the Talent Attraction Program of the Madrid Government (2017-P1/AMB-5298).

The original version of this Article contained a plotting error in Figure 3g. The Serranidae and Siganidae families were misplaced in the plotted phylogeny. This error has now been corrected in the PDF and HTML versions of the Article. For comparison, the original, incorrect version of Figure 3g is presented in the associated Author Correction.

[Excerpt] Academic biologists have long advocated for conserving phylogenetic diversity (PD), often (but not exclusively) on the basis that PD is a useful proxy for “feature diversity”, defined as the variety of forms and functions represented in set of organisms (see below for an extended discussion of this definition)1,2,3,4. In a recent paper5, we assess the extent to which this proxy (which we coined the “phylogenetic gambit”) holds in three empirical datasets (terrestrial mammals, birds, and tropical marine fishes) when using functional traits and functional diversity (FD) to operationalize feature diversity. Owen et al.6 offer a criticism of our methods for quantifying feature diversity with FD and disagree with our conclusions. We are grateful that Owen et al.6 have engaged thoughtfully with our work, but we believe there are more points of agreement than Owen et al.6 imply.

Bumble bees are globally important pollinators, especially in temperate regions, and evidence suggests that many species are declining. One recent high profile study by Soroye et al. (2020) applied occupancy models to dated historical collection data to quantify declines across North America and Europe. The authors modelled 66 species across a set of sites spanning both North America and Europe, rather than confining species to sites where they might be expected to occur. In addition, they inferred non-detections for time intervals where there is no evidence that the site was visited (by forcing every site to have exactly 3 visits in each era). We use simulated data to (i) investigate the validity of methods used in that study and (ii) test whether a multi-species framework that incorporates species' ranges and site visitation histories produces better estimates. We show that the method used by Soroye et al. (2020) yields biased estimates of declines, whereas our framework does not. We use such a model to provide revised and appreciably lower estimates for bumble bee community declines, with species-specific trends more closely matching classifications from IUCN. The species level trends we provide can help inform future species-at-risk assessments. Well-parameterized occupancy models may be a powerful tool for assessing species-wide trends using curated historical collection data.

The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub-disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub-disciplines hampers potential meta-analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo-diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo-diversity metrics based on their mathematical form within these three dimensions and identify ‘anchor’ representatives: for α-diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices.

International audience; A recommendation of Tanentzap A J, Igea J, Johnston MG, and Larcombe MJ. Range size dynamics can explain why evolutionarily age and diversification rate correlate with contemporary extinction risk in plants. bioRxiv 152215 (2018), ver. 5 peer-reviewed and recommended by PCI Evol Biol.

Population decline is a process, yet estimates of current extinction rates often consider just the final step of that process by counting numbers of species lost in historical times. This neglects the increased extinction risk that affects a large proportion of species, and consequently underestimates the effective extinction rate. Here, we model observed trajectories through IUCN Red List extinction risk categories for all bird species globally over 28 years, and estimate an overall effective extinction rate of 2.17 × 10 −4 /species/year. This is six times higher than the rate of outright extinction since 1500, as a consequence of the large number of species whose status is deteriorating. We very conservatively estimate that global conservation efforts have reduced the effective extinction rate by 40%, but mostly through preventing critically endangered species from going extinct rather than by preventing species at low risk from moving into higher-risk categories. Our findings suggest that extinction risk in birds is accumulating much more than previously appreciated, but would be even greater without conservation efforts.

Faced with the challenge of saving as much diversity as possible given financial and time constraints, conservation biologists are increasingly prioritizing species on the basis of their overall contribution to evolutionary diversity. Metrics such as EDGE (Evolutionary Distinct and Globally Endangered) have been used to set such evolutionarily-based conservation priorities for a number of taxa, such as mammals, birds, corals, amphibians, and sharks. Each application of EDGE has required some form of correction to account for species whose position within the tree of life are unknown. Perhaps the most advanced of these corrections is phylogenetic imputation, but to date there has been no systematic assessment of both the sensitivity of EDGE scores to a phylogeny missing species, and the impact of using imputation to correct for species missing from the tree. Here we perform such an assessment, by simulating phylogenies, removing some species to make the phylogeny incomplete, imputating the position of those species, and measuring (1) how robust ED scores are for the species that are not removed and (2) how accurate the ED scores are for those removed and then imputed. We find that the EDGE ranking for species on a tree is remarkably robust to missing species from that tree, but that phylogenetic imputation for missing species, while unbiased, does not accurately reconstruct species’ evolutionary distinctiveness. On the basis of these results, we provide clear guidance for EDGE scoring in the face of phylogenetic uncertainty.

New species of marine fishes are found to emerge at a faster rate in high-latitude oceans, which have lower densities of species, than in the species-rich tropics. Are the tropics too crowded for new species to take hold? New species of marine fishes are found to emerge at a faster rate in high-latitude oceans, which have lower densities of species, than in the species-rich tropics. Are the tropics too crowded for new species to take hold?

Zoos have played a pivotal role in the successful reinforcement and reintroduction of species threatened with extinction, but prioritization is required in the face of increasing need and limited capacity. One means of prioritizing between species of equal threat status when establishing new breeding programs is the consideration of evolutionary distinctness (ED). More distinct species have fewer close relatives such that their extinction would result in a greater overall loss to the Tree of Life. Considering global ex situ holdings of birds (a group with a complete and well-detailed evolutionary tree), we investigate the representation of at-risk and highly evolutionarily distinct species in global zoo holdings. We identified a total of 2,236 bird species indicated by the Zoological Information Management System as being held in zoological institutions worldwide. As previously reported, imperiled species (defined as those possessing endangered or critically endangered threat status) in this database are less likely to be held in zoos than non-imperiled species. However, we find that species possessing ED scores within the top 10% of all bird species are more likely to be held in zoos than other species, possibly because they possess unique characteristics that have historically made them popular exhibits. To assist with the selection of high priority ED species for future zoo conservation programs, we provide a list of imperiled species currently not held in zoos, ranked by ED. This list highlights species representing particular priorities for ex situ conservation planners, and represents a practical tool for improving the conservation value of zoological collections.

In the face of the biodiversity crisis, it is argued that we should prioritize species in order to capture high functional diversity (FD). Because species traits often reflect shared evolutionary history, many researchers have advocated for a “phylogenetic gambit”: maximizing phylogenetic diversity (PD) should indirectly capture FD. For the first time, we empirically test this gambit using data from >15,000 vertebrate species and ecologically-relevant traits. Maximizing PD results in an average gain of 18% of FD relative to random choice. However, this average gain hides the fact that in over 1/3 of the comparisons, maximum PD sets contain less FD than randomly chosen sets of species. These results suggest that, while maximizing PD protection can help to protect FD, it represents a risky strategy.Statement of authorshipFM, MP, MC, SD, GVDR, RG, AOM, CT and WP conceived the design of the study. FM and GVDR conducted the analysis. FM, RG, MP and WP interpreted the results and wrote the first draft of the manuscript. All authors edited the final version.Data accessibility statementMost of the data is publicly available (see methods). The Fish data is available upon request.Code accessibility statementR functions developed in this paper are available at https://github.com/FloMazel/FD_PD_Max

Western North America contains a mosaic of indigenous and introduced red fox (Vulpes vulpes) populations. Historically, native red foxes occurred in subalpine zones of the Cascade, Rocky, and Sierra Nevada mountain ranges, and in the desert-like Sacramento Valley of California. The origins of red foxes observed in the Intermountain West since the early 1900s are unclear, potentially representing native population relicts from the last ice age, dispersers from adjacent mountain populations, or early fur-farm escapees. These foxes carry a native 696-bp mitochondrial haplotype (A-19), which was also the most basal and widespread among western populations and thus equally consistent with ancient and contemporary origins. Here, to increase resolution, we sequenced an additional 3,308 bp (totaling 4,004bp) of the mitochondrial genome corresponding to A-19 and related haplotypes (O-24 and D-19) from historical and modern samples collected throughout western North America. The expanded sequences revealed previous...

Empirical two-part models describe the relationship between conservation spending, human development pressures and biodiversity loss and can inform sustainable development strategies by predicting the effects of financing decisions on future biodiversity losses. Financial investments into conservation are often held back by a lack of certainty over the benefits of spending more. Anthony Waldron and colleagues assess the impact of conservation spending on biodiversity between 1996 and 2008 in 109 countries that signed up to the Convention on Biological Diversity. They find that conservation spending over this period reduced national-level biodiversity loss by 29%, on average. They also find that the funding needed to achieve specific conservation goals rises with socioeconomic pressures. The authors develop a predictive model of biodiversity decline, which takes into account the effects of human development pressures and conservation financing. They propose that this could help to predict the funding that each country needs to achieve specific biodiversity policy goals, including those laid out in the Convention on Biological Diversity and the broader United Nations Sustainable Development Goals. Halting global biodiversity loss is central to the Convention on Biological Diversity and United Nations Sustainable Development Goals1,2, but success to date has been very limited3,4,5. A critical determinant of success in achieving these goals is the financing that is committed to maintaining biodiversity6,7,8,9; however, financing decisions are hindered by considerable uncertainty over the likely impact of any conservation investment6,7,8,9. For greater effectiveness, we need an evidence-based model10,11,12 that shows how conservation spending quantitatively reduces the rate of biodiversity loss. Here we demonstrate such a model, and empirically quantify how conservation investment reduced biodiversity loss in 109 countries (signatories to the Convention on Biological Diversity and Sustainable Development Goals), by a median average of 29% per country between 1996 and 2008 We also show that biodiversity changes in signatory countries can be predicted with high accuracy, using a dual model that balances the effects of conservation investment against those of economic, agricultural and population growth (human development pressures)13,14,15,16,17,18. Decision-makers can use this model to forecast the improvement that any proposed biodiversity budget would achieve under various scenarios of human development pressure, and then compare these forecasts to any chosen policy target. We find that the impact of spending decreases as human development pressures grow, which implies that funding may need to increase over time. The model offers a flexible tool for balancing the Sustainable Development Goals of human development and maintaining biodiversity, by predicting the dynamic changes in conservation finance that will be needed as human development proceeds.

The fungal pathogen Batrachochytrium dendrobatidis (B. dendrobatidis) has emerged as a major agent of amphibian extinction, requiring conservation intervention for many susceptible species. Identifying susceptible species is challenging, but many aspects of species biology are predicted to influence the evolution of host resistance, tolerance, or avoidance strategies towards disease. In turn, we may expect species exhibiting these distinct strategies to differ in their ability to survive epizootic disease outbreaks. Here, we test for phylogenetic and trait‐based patterns of B. dendrobatidis infection risk and infection intensity among 302 amphibian species by compiling a global data set of B. dendrobatidis infection surveys across 95 sites. We then use best‐fit models that associate traits, taxonomy and environment with B. dendrobatidis infection risk and intensity to predict host disease mitigation strategies (tolerance, resistance, avoidance) for 122 Neotropical amphibian species that experienced epizootic B. dendrobatidis outbreaks, and noted species persistence or extinction from these events. Aspects of amphibian species life history, habitat use and climatic niche were consistently linked to variation in B. dendrobatidis infection patterns across sites around the world. However, predicted B. dendrobatidis infection risk and intensity based on site environment and species traits did not reveal a consistent pattern between the predicted host disease mitigation strategy and extinction outcome. This suggests that either tolerant or resistant species may have no advantage in ameliorating disease during epizootic events, or that other factors drive the persistence of amphibian populations during chytridiomycosis outbreaks. These results suggest that using a trait‐based approach may allow us to identify species with resistance or tolerance to endemic B. dendrobatidis infections, but that this approach may be insufficient to ultimately identify species at risk of extinction from epizootics.

Ambitious global conservation targets have been set to manage increasing threats to amphibians. Ex situ institutions (broadly, ‘zoos’) are playing an expanding role in meeting these targets. Here, we examine the extent to which zoos house species representing the greatest overall conservation priority by testing how eight variables relating to extinction risk – International Union for the Conservation of Nature status, habitat specialization, obligate stream breeding, geographic range size, body size and island, high-altitude and tropical endemism – vary between amphibian species held in zoos and their close relatives not held in zoos. Based on 253 species found in zoos that could be confidently paired with close relatives not in zoos, and in contrast to reported patterns for birds and mammals, we find that amphibians currently held in zoos are equally as threatened as their close relatives not found in zoos. This result is entirely driven by the inclusion of data on species holdings from Amphibian Ark (AArk), an organization that helps to coordinate conservation activities in many ‘non-traditional’ institutions, as well as in ‘traditional’ commercial zoos. Such networks of small non-traditional institutions thus make meaningful contributions to ex situ conservation, and the establishment of other taxa-specific organizations modelled on AArk might be considered. That said, our results indicate that the ex situ network is still not prioritizing range-restricted habitat specialists, species that possess greater overall extinction risk in the near future. We strongly encourage zoos to continue increasing their holdings of amphibian species, but to pay greater attention to these species of particular conservation concern.

The competency debate over small cetacean regulation at the International Whaling Commission (IWC) is legal in nature, yet has been in a political stalemate for years. In this article we argue that the IWC has the competence to regulate small cetaceans and that the commercial whaling of ‘small cetaceans’ is a violation of the moratorium on commercial whaling. We present hybrid legal and scientific arguments and counter-arguments for the treaty interpretation of the International Convention for the Regulation of Whaling and, given recent precedent, advocate that the International Court of Justice be called upon to resolve this matter.

Summary Background Integrated, efficient, and global prioritization approaches are necessary to manage the ongoing loss of species and their associated function. "Evolutionary distinctness" measures a species' contribution to the total evolutionary history of its clade and is expected to capture uniquely divergent genomes and functions. Here we demonstrate how such a metric identifies species and regions of particular value for safeguarding evolutionary diversity. Results Among the world's 9,993 recognized bird species, evolutionary distinctness is very heterogeneously distributed on the phylogenetic tree and varies little with range size or threat level. Species representing the most evolutionary history over the smallest area (those with greatest "evolutionary distinctness rarity") as well as some of the most imperiled distinct species are often concentrated outside the species-rich regions and countries, suggesting they may not be well captured by current conservation planning. We perform global cross-species and spatial analyses and generate minimum conservation sets to assess the benefits of the presented species-level metrics. We find that prioritizing imperiled species by their evolutionary distinctness and geographic rarity is a surprisingly effective and spatially economical way to maintain the total evolutionary information encompassing the world's birds. We identify potential conservation gaps in relation to the existing reserve network that in particular highlight islands as effective priority areas. Conclusions The presented distinctness metrics are effective yet easily communicable and versatile tools to assist objective global conservation decision making. Given that most species will remain ecologically understudied, combining growing phylogenetic and spatial data may be an efficient way to retain vital aspects of biodiversity.

Phylogenetic trees that include all member lineages are necessary for many questions in macroevolution, biogeography and conservation. Currently, producing such trees when genetic data or phenotypic characters for some tips are missing generally involves assigning missing species to the root of theirmost exclusive clade, essentially grafting them onto existing and static topologies as polytomies. 2. We describe an R package, ‘PASTIS’, that enables a two-stage Bayesian method usingMrBayes version 3.2 (or higher) to incorporate lineages lacking genetic data at the tree inference stage. The inputs include a consensus topology, a set of taxonomic statements (e.g. placing species in genera and aligning some genera with each other or placing subspecies within species) and user-defined priors on edge lengths and topologies. PASTIS produces input files for execution inMrBayes that will produce a posterior distribution of complete ultrametric trees that captures uncertainty under a homogeneous birth-death prior model of diversification and placement constraints. If the age distribution of a focal node is known (e.g. from fossils), the ultrametric tree distribution can be converted to a set of dated trees.We also provide functions to visualize the placement ofmissing taxa in the posterior distribution. 3. The PASTIS approach is not limited to the level of species and could equally be applied to higher or lower levels of organization (e.g. accounting for all recognized subspecies or populations within a species) given an appropriate choice of priors on branching times.

Zoos and related institutions make important contributions to the conservation of global biodiversity. However, resource constraints have led to certain faunal groupings being better represented in ex situ breeding programmes than others. Some broad patterns of faunal representation in zoos have been identified, although finer-scale differences within taxonomical families remain poorly understood, as do the influence of many geographical and ecological factors. Using a novel paired-species comparison approach, we investigate for the first time how seven of these variables can influence the current representation of mammal and bird species in zoos. Using data from 550 high-quality zoos worldwide, we identified 165 mammal and 228 bird species held in zoos that could be paired with clearly identifiable closest relatives not currently held in zoos. These matched pairs were then compared for threat level, zoogeographical distribution (including global hotspot endemism), spatial range, body mass, island habitat and altitudinal range. Results indicate that mammal and bird species in zoos are, on average, not only larger than their close relatives not held in zoos, but also possess larger spatial ranges, are less likely to be endemic and are distributed in lower-risk geographical regions. Importantly, they also tend to be less, rather than more, threatened with extinction. Multivariate models confirm that many of these correlated predictors act independently. We suggest that key mechanisms which can increase the inherent conservation risk of mammal and bird species can also act as barriers to their representation in zoos, and that this may contribute to a disparity between where ex situ resources are spent and where they are most needed.

Inadequate funding levels are a major impediment to effective global biodiversity conservation and are likely associated with recent failures to meet United Nations biodiversity targets. Some countries are more severely underfunded than others and therefore represent urgent financial priorities. However, attempts to identify these highly underfunded countries have been hampered for decades by poor and incomplete data on actual spending, coupled with uncertainty and lack of consensus over the relative size of spending gaps. Here, we assemble a global database of annual conservation spending. We then develop a statistical model that explains 86% of variation in conservation expenditures, and use this to identify countries where funding is robustly below expected levels. The 40 most severely underfunded countries contain 32% of all threatened mammalian diversity and include neighbors in some of the world’s most biodiversity-rich areas (Sundaland, Wallacea, and Near Oceania). However, very modest increases in international assistance would achieve a large improvement in the relative adequacy of global conservation finance. Our results could therefore be quickly applied to limit immediate biodiversity losses at relatively little cost.