Species diversity as a surrogate for conservation of phylogenetic and functional diversity in terrestrial vertebrates across the Americas

Advancing EDGE Zones to identify spatial conservation priorities of tetrapod evolutionary history

The biodiversity crisis is pruning the Tree of Life in a way that threatens billions of years of evolutionary history and there is a need to understand where the greatest losses are predicted to occur. We therefore present threatened evolutionary history mapped for all tetrapod groups and describe patterns of Evolutionarily Distinct and Globally Endangered (EDGE) species. Using a complementarity procedure with uncertainty incorporated for 33,628 species, we identify 25 priority tetrapod EDGE Zones, which are insufficiently protected and disproportionately exposed to high human pressure. Tetrapod EDGE Zones are spread over five continents, 33 countries, and 117 ecoregions. Together, they occupy 0.723% of the world's surface but harbour one-third of the world's threatened evolutionary history and EDGE tetrapod species, half of which is endemic. These EDGE Zones highlight areas of immediate concern for researchers, practitioners, policymakers, and communicators looking to safeguard the tetrapod Tree of Life.

Long term declines in the functional diversity of sharks in the coastal oceans of eastern Australia

Human impacts lead to widespread changes in the abundance, diversity and traits of shark assemblages, altering the functioning of coastal ecosystems. The functional consequences of shark declines are often poorly understood due to the absence of empirical data describing long-term change. We use data from the Queensland Shark Control Program in eastern Australia, which has deployed mesh nets and baited hooks across 80 beaches using standardised methodologies since 1962. We illustrate consistent declines in shark functional richness quantified using both ecological (e.g., feeding, habitat and movement) and morphological (e.g., size, morphology) traits, and this corresponds with declining ecological functioning. We demonstrate a community shift from targeted apex sharks to a greater functional richness of non-target species. Declines in apex shark functional richness and corresponding changes in non-target species may lead to an anthropogenically induced trophic cascade. We suggest that repairing diminished shark populations is crucial for the stability of coastal ecosystems.

Global multifaceted biodiversity patterns, centers, and conservation needs in angiosperms

The Convention on Biological Diversity seeks to conserve at least 30% of global land and water areas by 2030, which is a challenge but also an opportunity to better preserve biodiversity, including flowering plants (angiosperms). Herein, we compiled a large database on distributions of over 300,000 angiosperm species and the key functional traits of 67,024 species. Using this database, we constructed biodiversity-environment models to predict global patterns of taxonomic, phylogenetic, and functional diversity in terrestrial angiosperms and provide a comprehensive mapping of the three diversity facets. We further evaluated the current protection status of the biodiversity centers of these diversity facets. Our results showed that geographical patterns of the three facets of plant diversity exhibited substantial spatial mismatches and nonoverlapping conservation priorities. Idiosyncratic centers of functional diversity, particularly of herbaceous species, were primarily distributed in temperate regions and under weaker protection compared with other biodiversity centers of taxonomic and phylogenetic facets. Our global assessment of multifaceted biodiversity patterns and centers highlights the insufficiency and unbalanced conservation among the three diversity facets and the two growth forms (woody vs. herbaceous), thus providing directions for guiding the future conservation of global plant diversity.

The stability and collapse of marine ecosystems during the Permian-Triassic mass extinction

The history of Earth's biodiversity is punctuated episodically by mass extinctions. These are characterized by major declines of taxon richness, but the accompanying ecological collapse has rarely been evaluated quantitatively. The Permian-Triassic mass extinction (PTME; ∼252 mya), as the greatest known extinction, permanently altered marine ecosystems and paved the way for the transition from Paleozoic to Mesozoic evolutionary faunas. Thus, the PTME offers a window into the relationship between taxon richness and ecological dynamics of ecosystems during a severe extinction. However, the accompanying ecological collapse through the PTME has not been evaluated in detail. Here, using food-web models and a marine paleocommunity dataset spanning the PTME, we show that after the first extinction phase, community stability decreased only slightly despite the loss of more than half of taxonomic diversity, while community stability significantly decreased in the second phase. Thus, taxonomic and ecological changes were unequivocally decoupled, with species richness declining severely ∼61 ka earlier than the collapse of marine ecosystem stability, implying that in major catastrophes, a biodiversity crash may be the harbinger of a more devastating ecosystem collapse.

Environmental and topographic drivers of amphibian phylogenetic diversity and endemism in the Iberian Peninsula

Understanding the ecological and evolutionary processes driving biodiversity patterns and allowing their persistence is of utmost importance. Many hypotheses have been proposed to explain spatial diversity patterns, including water-energy availability, habitat heterogeneity, and historical climatic refugia. The main goal of this study is to identify if general spatial drivers of species diversity patterns of phylogenetic diversity (PD) and phylogenetic endemism (PE) at the global scale are also predictive of PD and PE at regional scales, using Iberian amphibians as a case study. Our main hypothesis assumes that topography along with contemporary and historical climate are drivers of phylogenetic diversity and endemism, but that the strength of these predictors may be weaker at the regional scale than it tends to be at the global scale. We mapped spatial patterns of Iberian amphibians' phylogenetic diversity and endemism, using previously published phylogenetic and distribution data. Furthermore, we compiled spatial data on topographic and climatic variables related to the water-energy availability, topography, and historical climatic instability hypotheses. To test our hypotheses, we used Spatial Autoregressive Models and selected the best model to explain diversity patterns based on Akaike Information Criterion. Our results show that, out of the variables tested in our study, water-energy availability and historical climate instability are the most important drivers of amphibian diversity in Iberia. However, as predicted, the strength of these predictors in our case study is weaker than it tends to be at global scales. Thus, additional drivers should also be investigated and we suggest caution when interpreting these predictors as surrogates for different components of diversity.

Preserving the woody plant tree of life in China under future climate and land-cover changes

The tree of life (TOL) is severely threatened by climate and land-cover changes. Preserving the TOL is urgent, but has not been included in the post-2020 global biodiversity framework. Protected areas (PAs) are fundamental for biological conservation. However, we know little about the effectiveness of existing PAs in preserving the TOL of plants and how to prioritize PA expansion for better TOL preservation under future climate and land-cover changes. Here, using high-resolution distribution maps of 8732 woody species in China and phylogeny-based Zonation, we find that current PAs perform poorly in preserving the TOL both at present and in 2070s. The geographical coverage of TOL branches by current PAs is approx. 9%, and less than 3% of the identified priority areas for preserving the TOL are currently protected. Interestingly, the geographical coverage of TOL branches by PAs will be improved from 9% to 52-79% by the identified priority areas for PA expansion. Human pressures in the identified priority areas are high, leading to high cost for future PA expansion. We thus suggest that besides nature reserves and national parks, other effective area-based conservation measures should be considered. Our study argues for the inclusion of preserving the TOL in the post-2020 conservation framework, and provides references for decision-makers to preserve the Earth's evolutionary history.

High exposure of global tree diversity to human pressure

Safeguarding Earth's tree diversity is a conservation priority due to the importance of trees for biodiversity and ecosystem functions and services such as carbon sequestration. Here, we improve the foundation for effective conservation of global tree diversity by analyzing a recently developed database of tree species covering 46,752 species. We quantify range protection and anthropogenic pressures for each species and develop conservation priorities across taxonomic, phylogenetic, and functional diversity dimensions. We also assess the effectiveness of several influential proposed conservation prioritization frameworks to protect the top 17% and top 50% of tree priority areas. We find that an average of 50.2% of a tree species' range occurs in 110-km grid cells without any protected areas (PAs), with 6,377 small-range tree species fully unprotected, and that 83% of tree species experience nonnegligible human pressure across their range on average. Protecting high-priority areas for the top 17% and 50% priority thresholds would increase the average protected proportion of each tree species' range to 65.5% and 82.6%, respectively, leaving many fewer species (2,151 and 2,010) completely unprotected. The priority areas identified for trees match well to the Global 200 Ecoregions framework, revealing that priority areas for trees would in large part also optimize protection for terrestrial biodiversity overall. Based on range estimates for >46,000 tree species, our findings show that a large proportion of tree species receive limited protection by current PAs and are under substantial human pressure. Improved protection of biodiversity overall would also strongly benefit global tree diversity.

A global reptile assessment highlights shared conservation needs of tetrapods

Comprehensive assessments of species’ extinction risks have documented the extinction crisis¹ and underpinned strategies for reducing those risks². Global assessments reveal that, among tetrapods, 40.7% of amphibians, 25.4% of mammals and 13.6% of birds are threatened with extinction³. Because global assessments have been lacking, reptiles have been omitted from conservation-prioritization analyses that encompass other tetrapods^4–7. Reptiles are unusually diverse in arid regions, suggesting that they may have different conservation needs⁶. Here we provide a comprehensive extinction-risk assessment of reptiles and show that at least 1,829 out of 10,196 species (21.1%) are threatened—confirming a previous extrapolation⁸ and representing 15.6 billion years of phylogenetic diversity. Reptiles are threatened by the same major factors that threaten other tetrapods—agriculture, logging, urban development and invasive species—although the threat posed by climate change remains uncertain. Reptiles inhabiting forests, where these threats are strongest, are more threatened than those in arid habitats, contrary to our prediction. Birds, mammals and amphibians are unexpectedly good surrogates for the conservation of reptiles, although threatened reptiles with the smallest ranges tend to be isolated from other threatened tetrapods. Although some reptiles—including most species of crocodiles and turtles—require urgent, targeted action to prevent extinctions, efforts to protect other tetrapods, such as habitat preservation and control of trade and invasive species, will probably also benefit many reptiles.

An extinction-risk assessment of reptiles shows that at least 21.1% of species are threatened by factors such as agriculture, logging, urban development and invasive species, and that efforts to protect birds, mammals and amphibians probably also benefit many reptiles.

Increasing taxonomic diversity and spatial resolution clarifies opportunities for protecting US imperiled species

Continental- and regional-scale assessments of gaps in protected area networks typically use relatively coarse range maps for well documented species groups, creating uncertainty about the fate of unexamined biodiversity and providing insufficient guidance for land managers. By building habitat suitability models for a taxonomically diverse group of 2216 imperiled plants and animals, we revealed comprehensive and detailed protection opportunities in the conterminous United States. Summing protection-weighted range-size rarity (PWRSR, the product of the percent of modeled habitat outside of protected areas and the inverse of modeled habitat extent) uncovered novel patterns of biodiversity importance. Concentrations of unprotected imperiled species in places such as the northern Sierra Nevada, central and northern Arizona, the Rocky Mountains of Utah and Colorado, southeastern Texas, southwestern Arkansas, and Florida's Lake Wales Ridge have rarely if ever been featured in continental- and regional-scale analyses. Inclusion of diverse taxa (vertebrates, freshwater mussels, crayfishes, bumble bees, butterflies, skippers, and vascular plants) partially drove these new patterns. When analyses were restricted to groups typically included in previous studies (birds, mammals, and amphibians), up to 53% of imperiled species in other groups were left out. The finer resolution of modeled inputs (990 m) also resulted in a more geographically dispersed pattern. For example, 90% of the human population of the conterminous United States lives within 50 km of modeled habitat for one or more species with high PWRSR scores. Over one-half of the habitat for 818 species occurs within federally lands managed for biodiversity protection; an additional 360 species have over one-half of their modeled habitat on federal multiple use land. Freshwater animals occur in places with poorer landscape condition but with less exposure to climate change than other groups, suggesting that habitat restoration is an important conservation strategy for these species. The results provide fine-scale, taxonomically diverse inputs for local and regional priority-setting and show that although protection efforts are still widely needed on private lands, notable gains can be achieved by increasing protection status on selected federal lands.

Areas of global importance for conserving terrestrial biodiversity, carbon and water

To meet the ambitious objectives of biodiversity and climate conventions, the international community requires clarity on how these objectives can be operationalized spatially and how multiple targets can be pursued concurrently. To support goal setting and the implementation of international strategies and action plans, spatial guidance is needed to identify which land areas have the potential to generate the greatest synergies between conserving biodiversity and nature's contributions to people. Here we present results from a joint optimization that minimizes the number of threatened species, maximizes carbon retention and water quality regulation, and ranks terrestrial conservation priorities globally. We found that selecting the top-ranked 30% and 50% of terrestrial land area would conserve respectively 60.7% and 85.3% of the estimated total carbon stock and 66% and 89.8% of all clean water, in addition to meeting conservation targets for 57.9% and 79% of all species considered. Our data and prioritization further suggest that adequately conserving all species considered (vertebrates and plants) would require giving conservation attention to ~70% of the terrestrial land surface. If priority was given to biodiversity only, managing 30% of optimally located land area for conservation may be sufficient to meet conservation targets for 81.3% of the terrestrial plant and vertebrate species considered. Our results provide a global assessment of where land could be optimally managed for conservation. We discuss how such a spatial prioritization framework can support the implementation of the biodiversity and climate conventions.

The effects of ecological selection on species diversity and trait distribution: predictions and an empirical test

Ecological selection is a major driver of community assembly. Selection is classified as stabilizing when species with intermediate trait values gain the highest reproductive success, whereas selection is considered directional when fitness is highest for species with extreme trait values. Previous studies have investigated the effects of different selection types on trait distribution, but the effects of selection on species diversity have remained unclear. Here, we propose a framework for inferring the type and strength of selection by studying species diversity and trait distribution together against null expectations. We use a simulation model to confirm our prediction that directional selection should lead to lower species diversity than stabilizing selection despite a similar effect on trait community-weighted variance. We apply the framework to a mesocosm system of annual plants to test whether differences in species diversity between two habitats that vary in productivity are related to differences in selection on seed mass. We show that, in both habitats, species diversity was lower than the null expectation, but that species diversity was lower in the more productive habitat. We attribute this difference to strong directional selection for large-seeded species in the productive habitat as indicated by trait community-weighted-mean being higher and community-weighted variance being lower than the null expectations. In the less productive habitat, we found that community-weighted variance was higher than expected by chance, suggesting that seed mass could be a driver of niche partitioning under such conditions. Altogether, our results suggest that viewing species diversity and trait distribution as interrelated patterns driven by the same process, ecological selection, is helpful in understanding community assembly.

Degree of anisogamy is unrelated to the intensity of sexual selection

Males and females often display different behaviours and, in the context of reproduction, these behaviours are labelled sex roles. The Darwin–Bateman paradigm argues that the root of these differences is anisogamy (i.e., differences in size and/or function of gametes between the sexes) that leads to biased sexual selection, and sex differences in parental care and body size. This evolutionary cascade, however, is contentious since some of the underpinning assumptions have been questioned. Here we investigate the relationships between anisogamy, sexual size dimorphism, sex difference in parental care and intensity of sexual selection using phylogenetic comparative analyses of 64 species from a wide range of animal taxa. The results question the first step of the Darwin–Bateman paradigm, as the extent of anisogamy does not appear to predict the intensity of sexual selection. The only significant predictor of sexual selection is the relative inputs of males and females into the care of offspring. We propose that ecological factors, life-history and demography have more substantial impacts on contemporary sex roles than the differences of gametic investments between the sexes.

Sympatric and independently evolving lineages in the Thoropa miliaris - T. taophora species complex (Anura: Cycloramphidae)

Species delimitation can be challenging and affected by subjectivity. Sibling lineages that occur in sympatry constitute good candidates for species delimitation regardless of the adopted species concept. The Thoropa miliaris + T. taophora species complex exhibits high genetic diversity distributed in several lineages that occur sympatrically in the southeastern Atlantic Forest of Brazil. We used 414 loci obtained by anchored hybrid enrichment to characterize genetic variation in the Thoropa miliaris species group (T. saxatilis, T megatympanum, T. miliaris, and T. taophora), combining assignment analyses with traditional and coalescent phylogeny reconstruction. We also investigated evolutionary independence in co-occurring lineages by estimating gene flow, and validated lineages under the multispecies coalescent. We recovered most previously described lineages as unique populations in assignment analyses; exceptions include two lineages within T. miliaris that are further substructured, and the merging of all T. taophora lineages. We found very low probabilities of gene flow between sympatric lineages, suggesting independent evolution. Species tree inferences and species delimitation yielded resolved relationships and indicate that all lineages constitute putative species that diverged during the Pliocene and Pleistocene, later than previously estimated.

The decline of mammal functional and evolutionary diversity worldwide

Biodiversity is declining worldwide. Because species interact with one another and with their environment, losses of particular organisms alter the function of ecosystems. Our understanding of the global rates and specific causes of functional decline remains limited, however. Species losses also reduce the cumulative amount of extant evolutionary history ("phylogenetic diversity" [PD]) in communities-our biodiversity heritage. Here we provide a global assessment of how each known anthropogenic threat is driving declines in functional diversity (FD) and PD, using terrestrial mammals as a case study. We find that habitat loss and harvest (e.g., legal hunting, poaching, snaring) are by far the biggest drivers of ongoing FD and PD loss. Declines in FD in high-biodiversity countries, particularly in Southeast Asia and South America, are greater than would be expected if species losses were random with respect to ecological function. Among functional guilds, herbivores are disproportionately likely to be declining from harvest, with important implications for plant communities and nutrient cycling. Frugivores are particularly likely to be declining from both harvest and habitat loss, with potential ramifications for seed dispersal and even forest carbon storage. Globally, phylogenetically unique species do not have an elevated risk of decline, but in areas such as Australia and parts of Southeast Asia, both habitat loss and harvest are biased toward phylogenetically unique species. Enhanced conservation efforts, including a renewed focus on harvest sustainability, are urgently needed to prevent the deterioration of ecosystem function, especially in the South American and equatorial Asian tropics.

Protecting Biodiversity (in All Its Complexity): New Models and Methods

We are facing a biodiversity crisis at the same time as we are acquiring an unprecedented view of the world's biodiversity. Vast new datasets (e.g., species distributions, traits, phylogenies, and interaction networks) hold knowledge to better comprehend the depths of biodiversity change, reliably anticipate these changes, and inform conservation actions. To harness this information for conservation, we need to integrate the largely independent fields of biodiversity modeling and conservation. We highlight new developments in each respective field, early examples of how they are being brought together, and ideas for a future synthesis such that conservation decisions can be made with fuller awareness of the biodiversity at stake.

The trinity of ecological contrasts: a case study on rich insect assemblages by means of species, functional and phylogenetic diversity measures

BACKGROUND

The 'classical' concept of species diversity was extended in the last decades into other dimensions focusing on the functional and phylogenetic diversity of communities. These measures are often argued to allow a deeper understanding of the mechanisms shaping community assembly along environmental gradients. Because of practical impediments, thus far only very few studies evaluated the performance of these diversity measures on large empirical data sets. Here, data on species-rich riparian moth communities under different flood regimes and from three different rivers has been used to compare the power of various diversity measures to uncover ecological contrasts.

RESULTS

Contrary to the expectation, classical metrics of species diversity (Hill numbers N1, N2 and N_inf) and evenness (Buzas-Gibson's E and Pielous's J) turned out to be the most powerful measures in unravelling the two gradients investigated in this study (e.g. flood regime and region). Several measures of functional and phylogenetic diversity tended to depict either only one or none of these contrasts. Rao's Q behaved similarly as species diversity and evenness. NTI and NRI showed a similar pattern among each other but, were different to all the other measures. Functional Divergence also behaved idiosyncratically across the 28 moth communities. The community weighted means of nearly all individual functional traits showed significant ecological patterns, supporting the relevance of the selected traits in shaping assemblage compositions.

CONCLUSIONS

Species diversity and evenness measures turned out to be the most powerful metrics and clearly reflected both investigated environmental contrasts. This poses the question when it is useful to compile the additional data necessary for the calculation of additional diversity measures, since assembling trait bases and community phylogenies often requires a high work load. Apart from these methodological issues, most of the diversity measures related to communities of terrestrial insects like moths increased in forests that still are subject to flooding dynamics. This emphasizes the high conservation value of riparian forests and the importance of keeping and restoring river dynamics as a means of fostering also terrestrial biodiversity in floodplain areas.

Evaluating policy-relevant surrogate taxa for biodiversity conservation: a case study from British Columbia, Canada

Conservation efforts often lead to a small proportion of species receiving a disproportionate amount of attention. This bias in funding may help or hinder broader goals of biodiversity conservation depending on the surrogacy value of the well-funded species. Surrogate species are selected to represent other taxa in a shared environment when it would be costly or impractical to obtain information on individual taxa. We compared the surrogacy value of common groups of taxa implicated in conservation — game species, carnivores, non-game species, and other species. Using a publicly available data set of species–habitat associations, we compared the surrogacy value for 1012 species and 64 habitat types in British Columbia, Canada. We used a conditional entropy metric to quantify pairwise associations between species via their occurrence in different habitat types. Our analysis reveals that game and non-game species surrogacy groups do not significantly differ in either the frequency of captured pairwise associations or their coverage of species. These results suggest that funding game species conservation is likely conferring some benefits to non-game species, but optimal habitat-based conservation outcomes will come from a combination of taxa. This analysis provides an important step in influencing management decisions for the preservation of biodiversity in British Columbia.

Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation

Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all approximately 6,000 living species of mammals, we developed credible sets of trees that capture root-to-tip uncertainty in topology and divergence times. Our "backbone-and-patch" approach to tree building applies a newly assembled 31-gene supermatrix to two levels of Bayesian inference: (1) backbone relationships and ages among major lineages, using fossil node or tip dating, and (2) species-level "patch" phylogenies with nonoverlapping in-groups that each correspond to one representative lineage in the backbone. Species unsampled for DNA are either excluded ("DNA-only" trees) or imputed within taxonomic constraints using branch lengths drawn from local birth-death models ("completed" trees). Joining time-scaled patches to backbones results in species-level trees of extant Mammalia with all branches estimated under the same modeling framework, thereby facilitating rate comparisons among lineages as disparate as marsupials and placentals. We compare our phylogenetic trees to previous estimates of mammal-wide phylogeny and divergence times, finding that (1) node ages are broadly concordant among studies, and (2) recent (tip-level) rates of speciation are estimated more accurately in our study than in previous "supertree" approaches, in which unresolved nodes led to branch-length artifacts. Credible sets of mammalian phylogenetic history are now available for download at http://vertlife.org/phylosubsets, enabling investigations of long-standing questions in comparative biology.

Exploring the Concept of Lineage Diversity across North American Forests

Lineage diversity can refer to the number of genetic lineages within species or to the number of deeper evolutionary lineages, such as genera or families, within a community or assemblage of species. Here, we study the latter, which we refer to as assemblage lineage diversity (ALD), focusing in particular on its richness dimension. ALD is of interest to ecologists, evolutionary biologists, biogeographers, and those setting conservation priorities, but despite its relevance, it is not clear how to best quantify it. With North American tree assemblages as an example, we explore and compare different metrics that can quantify ALD. We show that both taxonomic measures (e.g., family richness) and Faith’s phylogenetic diversity (PD) are strongly correlated with the number of lineages in recent evolutionary time, but have weaker correlations with the number of lineages deeper in the evolutionary history of an assemblage. We develop a new metric, time integrated lineage diversity (TILD), which serves as a useful complement to PD, by giving equal weight to old and recent lineage diversity. In mapping different ALD metrics across the contiguous United States, both PD and TILD reveal high ALD across large areas of the eastern United States, but TILD gives greater value to the southeast Coastal Plain, southern Rocky Mountains and Pacific Northwest, while PD gives relatively greater value to the southern Appalachians and Midwest. Our results demonstrate the value of using multiple metrics to quantify ALD, in order to highlight areas of both recent and older evolutionary diversity.

Projected losses of global mammal and bird ecological strategies

Species, and their ecological strategies, are disappearing. Here we use species traits to quantify the current and projected future ecological strategy diversity for 15,484 land mammals and birds. We reveal an ecological strategy surface, structured by life-history (fast-slow) and body mass (small-large) as one major axis, and diet (invertivore-herbivore) and habitat breadth (generalist-specialist) as the other. We also find that of all possible trait combinations, only 9% are currently realized. Based on species' extinction probabilities, we predict this limited set of viable strategies will shrink further over the next 100 years, shifting the mammal and bird species pool towards small, fast-lived, highly fecund, insect-eating, generalists. In fact, our results show that this projected decline in ecological strategy diversity is much greater than if species were simply lost at random. Thus, halting the disproportionate loss of ecological strategies associated with highly threatened animals represents a key challenge for conservation.