Elevational distribution and extinction risk in birds

Mountainous regions are hotspots of terrestrial biodiversity. Unlike islands, which have been the focus of extensive research on extinction dynamics, fewer studies have examined mountain ranges even though they face increasing threats from human pressures – notably habitat conversion and climate change. Limits to the taxonomic and geographical extent and resolution of previously available information have precluded an explicit assessment of the relative role of elevational distribution in determining extinction risk. We use a new global species-level avian database to quantify the influence of elevational distribution (range, maximum and midpoint) on extinction risk in birds at the global scale. We also tested this relationship within biogeographic realms, higher taxonomic levels, and across phylogenetic contrasts. Potential confounding variables (i.e. phylogenetic, distributional, morphological, life history and niche breadth) were also tested and controlled for. We show that the three measures of elevational distribution are strong negative predictors of avian extinction risk, with elevational range comparable and complementary to that of geographical range size. Extinction risk was also found to be positively associated with body weight, development and adult survival, but negatively associated with reproduction and niche breadth. The robust and consistent findings from this study demonstrate the importance of elevational distribution as a key driver of variation in extinction dynamics in birds. Our results also highlight elevational distribution as a missing criterion in current schemes for quantifying extinction risk and setting species conservation priorities in birds. Further research is recommended to test for generality across non-avian taxa, which will require an advance in our knowledge of species’ current elevational ranges and increased efforts to digitise and centralise such data.

Association of extinction risk of saproxylic beetles with ecological degradation of forests in Europe

To reduce future loss of biodiversity and to allocate conservation funds effectively, the major drivers behind large-scale extinction processes must be identified. A promising approach is to link the red-list status of species and specific traits that connect species of functionally important taxa or guilds to resources they rely on. Such traits can be used to detect the influence of anthropogenic ecosystem changes and conservation efforts on species, which allows for practical recommendations for conservation. We modeled the German Red List categories as an ordinal index of extinction risk of 1025 saproxylic beetles with a proportional-odds linear mixed-effects model for ordered categorical responses. In this model, we estimated fixed effects for intrinsic traits characterizing species biology, required resources, and distribution with phylogenetically correlated random intercepts. The model also allowed predictions of extinction risk for species with no red-list category. Our model revealed a higher extinction risk for lowland and large species as well as for species that rely on wood of large diameter, broad-leaved trees, or open canopy. These results mirror well the ecological degradation of European forests over the last centuries caused by modern forestry, that is the conversion of natural broad-leaved forests to dense conifer-dominated forests and the loss of old growth and dead wood. Therefore, conservation activities aimed at saproxylic beetles in all types of forests in Central and Western Europe should focus on lowlands, and habitat management of forest stands should aim at increasing the amount of dead wood of large diameter, dead wood of broad-leaved trees, and dead wood in sunny areas.

Estimating the normal background rate of species extinction

A key measure of humanity's global impact is by how much it has increased species extinction rates. Familiar statements are that these are 100-1000 times pre-human or background extinction levels. Estimating recent rates is straightforward, but establishing a background rate for comparison is not. Previous researchers chose an approximate benchmark of 1 extinction per million species per year (E/MSY). We explored disparate lines of evidence that suggest a substantially lower estimate. Fossil data yield direct estimates of extinction rates, but they are temporally coarse, mostly limited to marine hard-bodied taxa, and generally involve genera not species. Based on these data, typical background loss is 0.01 genera per million genera per year. Molecular phylogenies are available for more taxa and ecosystems, but it is debated whether they can be used to estimate separately speciation and extinction rates. We selected data to address known concerns and used them to determine median extinction estimates from statistical distributions of probable values for terrestrial plants and animals. We then created simulations to explore effects of violating model assumptions. Finally, we compiled estimates of diversification-the difference between speciation and extinction rates for different taxa. Median estimates of extinction rates ranged from 0.023 to 0.135 E/MSY. Simulation results suggested over- and under-estimation of extinction from individual phylogenies partially canceled each other out when large sets of phylogenies were analyzed. There was no evidence for recent and widespread pre-human overall declines in diversity. This implies that average extinction rates are less than average diversification rates. Median diversification rates were 0.05-0.2 new species per million species per year. On the basis of these results, we concluded that typical rates of background extinction may be closer to 0.1 E/MSY. Thus, current extinction rates are 1,000 times higher than natural background rates of extinction and future rates are likely to be 10,000 times higher.

Historical species losses in bumblebee evolution

Investigating how species coped with past environmental changes informs how modern species might face human-induced global changes, notably via the study of historical extinction, a dominant feature that has shaped current biodiversity patterns. The genus Bombus, which comprises 250 mostly cold-adapted species, is an iconic insect group sensitive to current global changes. Through a combination of habitat loss, pathogens and climate change, bumblebees have experienced major population declines, and several species are threatened with extinction. Using a time-calibrated tree of Bombus, we analyse their diversification dynamics and test hypotheses about the role of extinction during major environmental changes in their evolutionary history. These analyses support a history of fluctuating species dynamics with two periods of historical species loss in bumblebees. Dating estimates gauge that one of these events started after the middle Miocene climatic optimum and one during the early Pliocene. Both periods are coincident with global climate change that may have extirpated Bombus species. Interestingly, bumblebees experienced high diversification rates during the Plio-Pleistocene glaciations. We also found evidence for a major species loss in the past one million years that may be continuing today.

Origins, bottlenecks, and present-day diversity: patterns of morphospace occupation in marine bivalves

It has long been known that species should not be distributed randomly in morphospace (a multidimensional trait space), even under simple models of evolution. However, recent studies suggest that position in morphospace can affect aspects of evolution such as the durations of clades and the species richness of their constituent taxa. Here we investigate the dynamics of morphospace occupancy in living and fossil marine bivalves using shell size and aspect ratio, two functionally important traits. Multiple lines of evidence indicate that the center of a family's morphospace today represents a location where taxonomic diversity is maximized, apparently owing to lower extinction rates. Within individual bivalve families, species with narrow geographic ranges are distributed throughout the morphospace but widespread species, which are generally expected to be extinction resistant, tend to be concentrated near the center. The morphospace centers of most species-rich families today (defined as the median value for all species in the family) tend to be close to the positions of the family founders, further suggesting an association between position in morphospace and net diversification rates. However, trajectories of individual subclades (genera) are inconsistent with the center of morphospace being an evolutionary attractor.

Drivers of extinction risk in African mammals: the interplay of distribution state, human pressure, conservation response and species biology

Although conservation intervention has reversed the decline of some species, our success is outweighed by a much larger number of species moving towards extinction. Extinction risk modelling can identify correlates of risk and species not yet recognized to be threatened. Here, we use machine learning models to identify correlates of extinction risk in African terrestrial mammals using a set of variables belonging to four classes: species distribution state, human pressures, conservation response and species biology. We derived information on distribution state and human pressure from satellite-borne imagery. Variables in all four classes were identified as important predictors of extinction risk, and interactions were observed among variables in different classes (e.g. level of protection, human threats, species distribution ranges). Species biology had a key role in mediating the effect of external variables. The model was 90% accurate in classifying extinction risk status of species, but in a few cases the observed and modelled extinction risk mismatched. Species in this condition might suffer from an incorrect classification of extinction risk (hence require reassessment). An increased availability of satellite imagery combined with improved resolution and classification accuracy of the resulting maps will play a progressively greater role in conservation monitoring.

Replicated radiations of the alpine genus Androsace (Primulaceae) driven by range expansion and convergent key innovations

AIM

We still have limited understanding of the contingent and deterministic factors that have fostered the evolutionary success of some species lineages over others. We investigated how the interplay of intercontinental migration and key innovations promoted diversification of the genus Androsace.

LOCATION

Mountain ranges and cold steppes of the Northern Hemisphere.

METHODS

We reconstructed ancestral biogeographical ranges at regional and continental scales by means of a dispersal-extinction-cladogenesis analysis using dated Bayesian phylogenies and contrasting two migration scenarios. Based on diversification analyses under two frameworks, we tested the influence of life form on speciation rates and whether diversification has been diversity-dependent.

RESULTS

We found that three radiations occurred in this genus, at different periods and on different continents, and that life form played a critical role in the history of Androsace. Short-lived ancestors first facilitated the expansion of the genus' range from Asia to Europe, while cushions, which appeared independently in Asia and Europe, enhanced species diversification in alpine regions. One long-distance dispersal event from Europe to North America led to the diversification of the nested genus Douglasia. We found support for a model in which speciation of the North American-European clade is diversity-dependent and close to its carrying capacity, and that the diversification dynamics of the North American subclade are uncoupled from this and follow a pure birth process.

MAIN CONCLUSIONS

The contingency of past biogeographical connections combined with the evolutionary determinism of convergent key innovations may have led to replicated radiations of Androsace in three mountain regions of the world. The repeated emergence of the cushion life form was a convergent key innovation that fostered radiation into alpine habitats. Given the large ecological similarity of Androsace species, allopatry may have been the main mode of speciation.

Using landscape history to predict biodiversity patterns in fragmented landscapes

Landscape ecology plays a vital role in understanding the impacts of land-use change on biodiversity, but it is not a predictive discipline, lacking theoretical models that quantitatively predict biodiversity patterns from first principles. Here, we draw heavily on ideas from phylogenetics to fill this gap, basing our approach on the insight that habitat fragments have a shared history. We develop a landscape ‘terrageny’, which represents the historical spatial separation of habitat fragments in the same way that a phylogeny represents evolutionary divergence among species. Combining a random sampling model with a terrageny generates numerical predictions about the expected proportion of species shared between any two fragments, the locations of locally endemic species, and the number of species that have been driven locally extinct. The model predicts that community similarity declines with terragenetic distance, and that local endemics are more likely to be found in terragenetically distinctive fragments than in large fragments. We derive equations to quantify the variance around predictions, and show that ignoring the spatial structure of fragmented landscapes leads to over-estimates of local extinction rates at the landscape scale. We argue that ignoring the shared history of habitat fragments limits our ability to understand biodiversity changes in human-modified landscapes.

A Global Trend towards the Loss of Evolutionarily Unique Species in Mangrove Ecosystems

The mangrove biome stands out as a distinct forest type at the interface between terrestrial, estuarine, and near-shore marine ecosystems. However, mangrove species are increasingly threatened and experiencing range contraction across the globe that requires urgent conservation action. Here, we assess the spatial distribution of mangrove species richness and evolutionary diversity, and evaluate potential predictors of global declines and risk of extinction. We found that human pressure, measured as the number of different uses associated with mangroves, correlated strongly, but negatively, with extinction probability, whereas species ages were the best predictor of global decline, explaining 15% of variation in extinction risk. Although the majority of mangrove species are categorised by the IUCN as Least Concern, our finding that the more threatened species also tend to be those that are more evolutionarily unique is of concern because their extinction would result in a greater loss of phylogenetic diversity. Finally, we identified biogeographic regions that are relatively species-poor but rich in evolutionary history, and suggest these regions deserve greater conservation priority. Our study provides phylogenetic information that is important for developing a unified management plan for mangrove ecosystems worldwide.

Recovering speciation and extinction dynamics based on phylogenies

Phylogenetic trees of only extant species contain information about the underlying speciation and extinction pattern. In this review, I provide an overview over the different methodologies that recover the speciation and extinction dynamics from phylogenetic trees. Broadly, the methods can be divided into two classes: (i) methods using the phylogenetic tree shapes (i.e. trees without branch length information) allowing us to test for speciation rate variation and (ii) methods using the phylogenetic trees with branch length information allowing us to quantify speciation and extinction rates. I end the article with an overview on limitations, open questions and challenges of the reviewed methodology.

Are species' responses to global change predicted by past niche evolution?

Predicting how and when adaptive evolution might rescue species from global change, and integrating this process into tools of biodiversity forecasting, has now become an urgent task. Here, we explored whether recent population trends of species can be explained by their past rate of niche evolution, which can be inferred from increasingly available phylogenetic and niche data. We examined the assemblage of 409 European bird species for which estimates of demographic trends between 1970 and 2000 are available, along with a species-level phylogeny and data on climatic, habitat and trophic niches. We found that species' proneness to demographic decline is associated with slow evolution of the habitat niche in the past, in addition to certain current-day life-history and ecological traits. A similar result was found at a higher taxonomic level, where families prone to decline have had a history of slower evolution of climatic and habitat niches. Our results support the view that niche conservatism can prevent some species from coping with environmental change. Thus, linking patterns of past niche evolution and contemporary species dynamics for large species samples may provide insights into how niche evolution may rescue certain lineages in the face of global change.

Oceanographic controls on the diversity and extinction of planktonic foraminifera

Understanding the links between long-term biological evolution, the ocean-atmosphere system and plate tectonics is a central goal of Earth science. Although environmental perturbations of many different kinds are known to have affected long-term biological evolution, particularly during major mass extinction events, the relative importance of physical environmental factors versus biological interactions in governing rates of extinction and origination through geological time remains unknown. Here we use macrostratigraphic data from the Atlantic Ocean basin to show that changes in global species diversity and rates of extinction among planktonic foraminifera have been linked to tectonically and climatically forced changes in ocean circulation and chemistry from the Jurassic period to the present. Transient environmental perturbations, such as those that occurred after the asteroid impact at the end of the Cretaceous period approximately 66 million years ago, and the Eocene/Oligocene greenhouse-icehouse transition approximately 34 million years ago, are superimposed on this general long-term relationship. Rates of species origination, by contrast, are not correlated with corresponding macrostratigraphic quantities, indicating that physiochemical changes in the ocean-atmosphere system affect evolution principally by driving the synchronous extinction of lineages that originated owing to more protracted and complex interactions between biological and environmental factors.

Deep-time phylogenetic clustering of extinctions in an evolutionarily dynamic clade (Early Jurassic ammonites)

Conservation biologists and palaeontologists are increasingly investigating the phylogenetic distribution of extinctions and its evolutionary consequences. However, the dearth of palaeontological studies on that subject and the lack of methodological consensus hamper our understanding of that major evolutionary phenomenon. Here we address this issue by (i) reviewing the approaches used to quantify the phylogenetic selectivity of extinctions and extinction risks; (ii) investigating with a high-resolution dataset whether extinctions and survivals were phylogenetically clustered among early Pliensbachian (Early Jurassic) ammonites; (iii) exploring the phylogenetic and temporal maintenance of this signal. We found that ammonite extinctions were significantly clumped phylogenetically, a pattern that prevailed throughout the 6.6 Myr-long early Pliensbachian interval. Such a phylogenetic conservatism did not alter – or may even have promoted – the evolutionary success of this major cephalopod clade. However, the comparison of phylogenetic autocorrelation among studies remains problematic because the notion of phylogenetic conservatism is scale-dependent and the intensity of the signal is sensitive to temporal resolution. We recommend a combined use of Moran's I, Pearson's ϕ and Fritz and Purvis' D statistics because they highlight different facets of the phylogenetic pattern of extinctions and/or survivals.

Threatened reef corals of the world

A substantial proportion of the world's living species, including one-third of the reef-building corals, are threatened with extinction and in pressing need of conservation action. In order to reduce biodiversity loss, it is important to consider species' contribution to evolutionary diversity along with their risk of extinction for the purpose of setting conservation priorities. Here I reconstruct the most comprehensive tree of life for the order Scleractinia (1,293 species) that includes all 837 living reef species, and employ a composite measure of phylogenetic distinctiveness and extinction risk to identify the most endangered lineages that would not be given top priority on the basis of risk alone. The preservation of these lineages, not just the threatened species, is vital for safeguarding evolutionary diversity. Tests for phylogeny-associated patterns show that corals facing elevated extinction risk are not clustered on the tree, but species that are susceptible, resistant or resilient to impacts such as bleaching and disease tend to be close relatives. Intensification of these threats or extirpation of the endangered lineages could therefore result in disproportionate pruning of the coral tree of life.

The ghosts of mammals past: biological and geographical patterns of global mammalian extinction across the Holocene

Although the recent historical period is usually treated as a temporal base-line for understanding patterns of mammal extinction, mammalian biodiversity loss has also taken place throughout the Late Quaternary. We explore the spatial, taxonomic and phylogenetic patterns of 241 mammal species extinctions known to have occurred during the Holocene up to the present day. To assess whether our understanding of mammalian threat processes has been affected by excluding these taxa, we incorporate extinct species data into analyses of the impact of body mass on extinction risk. We find that Holocene extinctions have been phylogenetically and spatially concentrated in specific taxa and geographical regions, which are often not congruent with those disproportionately at risk today. Large-bodied mammals have also been more extinction-prone in most geographical regions across the Holocene. Our data support the extinction filter hypothesis, whereby regional faunas from which susceptible species have already become extinct now appear less threatened; they may also suggest that different processes are responsible for driving past and present extinctions. We also find overall incompleteness and inter-regional biases in extinction data from the recent fossil record. Although direct use of fossil data in future projections of extinction risk is therefore not straightforward, insights into extinction processes from the Holocene record are still useful in understanding mammalian threat.

Reconciling molecular phylogenies with the fossil record

Historical patterns of species diversity inferred from phylogenies typically contradict the direct evidence found in the fossil record. According to the fossil record, species frequently go extinct, and many clades experience periods of dramatic diversity loss. However, most analyses of molecular phylogenies fail to identify any periods of declining diversity, and they typically infer low levels of extinction. This striking inconsistency between phylogenies and fossils limits our understanding of macroevolution, and it undermines our confidence in phylogenetic inference. Here, we show that realistic extinction rates and diversity trajectories can be inferred from molecular phylogenies. To make this inference, we derive an analytic expression for the likelihood of a phylogeny that accommodates scenarios of declining diversity, time-variable rates, and incomplete sampling; we show that this likelihood expression reliably detects periods of diversity loss using simulation. We then study the cetaceans (whales, dolphins, and porpoises), a group for which standard phylogenetic inferences are strikingly inconsistent with fossil data. When the cetacean phylogeny is considered as a whole, recently radiating clades, such as the Balaneopteridae, Delphinidae, Phocoenidae, and Ziphiidae, mask the signal of extinctions. However, when isolating these groups, we infer diversity dynamics that are consistent with the fossil record. These results reconcile molecular phylogenies with fossil data, and they suggest that most extant cetaceans arose from four recent radiations, with a few additional species arising from clades that have been in decline over the last ~10 Myr.

Seeing the forest for the trees: the limitations of phylogenies in comparative biology. (American Society of Naturalists Address)

The past 30 years have seen a revolution in comparative biology. Before that time, systematics was not at the forefront of the biological sciences, and few scientists considered phylogenetic relationships when investigating evolutionary questions. By contrast, systematic biology is now one of the most vigorous disciplines in biology, and the use of phylogenies not only is requisite in macroevolutionary studies but also has been applied to a wide range of topics and fields that no one could possibly have envisioned 30 years ago. My message is simple: phylogenies are fundamental to comparative biology, but they are not the be-all and end-all. Phylogenies are powerful tools for understanding the past, but like any tool, they have their limitations. In addition, phylogenies are much more informative about pattern than they are about process. The best way to fully understand the past-both pattern and process-is to integrate phylogenies with other types of historical data as well as with direct studies of evolutionary process.

Phylogenetically clustered extinction risks do not substantially prune the Tree of Life

Anthropogenic activities have increased the rate of biological extinction many-fold. Recent empirical studies suggest that projected extinction may lead to extensive loss to the Tree of Life, much more than if extinction were random. One suggested cause is that extinction risk is heritable (phylogenetically patterned), such that entire higher groups will be lost. We show here with simulation that phylogenetically clustered extinction risks are necessary but not sufficient for the extensive loss of phylogenetic diversity (PD) compared to random extinction. We simulated Yule trees and evolved extinction risks at various levels of heritability (measured using Pagel's ). At most levels of heritability ( in range of 0 to 10), mean values of extinction risk (range 0.25 to 0.75), tree sizes (64 to 128 tips), tree balance and temporal heterogeneity of diversification rates (Yule and coalescent trees), extinction risks do not substantially increase the loss of PD in these trees when compared to random extinction. The maximum loss of PD (20% above random) was only associated with the combination of extremely excessive values of phylogenetic signal, high mean species' extinction probabilities, and extreme (coalescent) tree shapes. Interestingly, we also observed a decline in the rate of increase in the loss of PD at high phylogenetic clustering of extinction risks. Our results suggest that the interplay between various aspects of tree shape and a predisposition of higher extinction risks in species-poor clades is required to explain the substantial pruning of the Tree of Life.

Direct and indirect effects of biological factors on extinction risk in fossil bivalves

Biological factors, such as abundance and body size, may contribute directly to extinction risk and indirectly through their influence on other biological characteristics, such as geographic range size. Paleontological data can be used to explicitly test many of these hypothesized relationships, and general patterns revealed through analysis of the fossil record can help refine predictive models of extinction risk developed for extant species. Here, I use structural equation modeling to tease apart the contributions of three canonical predictors of extinction--abundance, body size, and geographic range size--to the duration of bivalve species in the early Cenozoic marine fossil record of the eastern United States. I find that geographic range size has a strong direct effect on extinction risk and that an apparent direct effect of abundance can be explained entirely by its covariation with geographic range. The influence of geographic range on extinction risk is manifest across three ecologically disparate bivalve clades. Body size also has strong direct effects on extinction risk but operates in opposing directions in different clades, and thus, it seems to be decoupled from extinction risk in bivalves as a whole. Although abundance does not directly predict extinction risk, I reveal weak indirect effects of both abundance and body size through their positive influence on geographic range size. Multivariate models that account for the pervasive covariation between biological factors and extinction are necessary for assessing causality in evolutionary processes and making informed predictions in applied conservation efforts.

Selectivity of terrestrial gastropod extinctions on an oceanic archipelago and insights into the anthropogenic extinction process

Anthropogenic impacts have led to widespread extinctions of species on oceanic islands but the nature of many of these extinctions remains poorly known. Here we investigate extinction selectivities of terrestrial gastropods from the Ogasawara archipelago in the northwest Pacific, where anthropogenic threats have changed over time, shifting primarily from the effects of habitat loss to predation by a variety of different predators. Across all of the islands, extinct species had significantly smaller geographic ranges compared with species that are still alive, but among the surviving species, ranges of those that are currently declining due to human impacts do not differ significantly from those that are not threatened. Extinctions were selective with respect to spire index (SI) of shells, a trait of potential functional importance, but the relationship between body size and extinction vulnerability varied among extinction agents, some of which were strongly size selective, whereas others were not. Overall, whereas anthropogenic impacts have resulted in nonrandom losses of phenotypic diversity, the patterns of selectivity are complex, vary among islands, and with the type of threat. As extinction agents have changed historically, so has the pattern of loss. Because of the changing nature of anthropogenic impacts, resiliency to one type of threat does not guarantee long-term survival of species and future patterns of biodiversity loss on these islands are likely to be different from those in the past.

Extinction risk and diversification are linked in a plant biodiversity hotspot

It is widely recognized that we are entering an extinction event on a scale approaching the mass extinctions seen in the fossil record. Present-day rates of extinction are estimated to be several orders of magnitude greater than background rates and are projected to increase further if current trends continue. In vertebrates, species traits, such as body size, fecundity, and geographic range, are important predictors of vulnerability. Although plants are the basis for life on Earth, our knowledge of plant extinctions and vulnerabilities is lagging. Here, we disentangle the underlying drivers of extinction risk in plants, focusing on the Cape of South Africa, a global biodiversity hotspot. By comparing Red List data for the British and South African floras, we demonstrate that the taxonomic distribution of extinction risk differs significantly between regions, inconsistent with a simple, trait-based model of extinction. Using a comprehensive phylogenetic tree for the Cape, we reveal a phylogenetic signal in the distribution of plant extinction risks but show that the most threatened species cluster within short branches at the tips of the phylogeny--opposite to trends in mammals. From analyzing the distribution of threatened species across 11 exemplar clades, we suggest that mode of speciation best explains the unusual phylogenetic structure of extinction risks in plants of the Cape. Our results demonstrate that explanations for elevated extinction risk in plants of the Cape flora differ dramatically from those recognized for vertebrates. In the Cape, extinction risk is higher for young and fast-evolving plant lineages and cannot be explained by correlations with simple biological traits. Critically, we find that the most vulnerable plant species are nonetheless marching towards extinction at a more rapid pace but, surprisingly, independently from anthropogenic effects. Our results have important implications for conservation priorities and cast doubts on the utility of current Red List criteria for plants in regions such as the Cape, where speciation has been rapid, if our aim is to maximize the preservation of the tree-of-life.

The importance of phylogeny to the study of phenological response to global climate change

Climate change has resulted in major changes in the phenology--i.e. the timing of seasonal activities, such as flowering and bird migration--of some species but not others. These differential responses have been shown to result in ecological mismatches that can have negative fitness consequences. However, the ways in which climate change has shaped changes in biodiversity within and across communities are not well understood. Here, we build on our previous results that established a link between plant species' phenological response to climate change and a phylogenetic bias in species' decline in the eastern United States. We extend a similar approach to plant and bird communities in the United States and the UK that further demonstrates that climate change has differentially impacted species based on their phylogenetic relatedness and shared phenological responses. In plants, phenological responses to climate change are often shared among closely related species (i.e. clades), even between geographically disjunct communities. And in some cases, this has resulted in a phylogenetically biased pattern of non-native species success. In birds, the pattern of decline is phylogenetically biased but is not solely explained by phenological response, which suggests that other traits may better explain this pattern. These results illustrate the ways in which phylogenetic thinking can aid in making generalizations of practical importance and enhance efforts to predict species' responses to future climate change.

Selectivity in mammalian extinction risk and threat types: a new measure of phylogenetic signal strength in binary traits

The strength of phylogenetic signal in extinction risk can give insight into the mechanisms behind species' declines. Nevertheless, no existing measure of phylogenetic pattern in a binary trait, such as extinction-risk status, measures signal strength in a way that can be compared among data sets. We developed a new measure for phylogenetic signal of binary traits, D, which simulations show gives robust results with data sets of more than 50 species, even when the proportion of threatened species is low. We applied D to the red-list status of British birds and the world's mammals and found that the threat status for both groups exhibited moderately strong phylogenetic clumping. We also tested the hypothesis that the phylogenetic pattern of species threatened by harvesting will be more strongly clumped than for those species threatened by either habitat loss or invasive species because the life-history traits mediating the effects of harvesting show strong evolutionary pattern. For mammals, our results supported our hypothesis; there was significant but weaker phylogenetic signal in the risk caused by the other two drivers (habitat loss and invasive species). We conclude that D is likely to be a useful measure of the strength of phylogenetic pattern in many binary traits.

Epidemic disease decimates amphibian abundance, species diversity, and evolutionary history in the highlands of central Panama

Amphibian populations around the world are experiencing unprecedented declines attributed to a chytrid fungal pathogen, Batrachochytrium dendrobatidis. Despite the severity of the crisis, quantitative analyses of the effects of the epidemic on amphibian abundance and diversity have been unavailable as a result of the lack of equivalent data collected before and following disease outbreak. We present a community-level assessment combining long-term field surveys and DNA barcode data describing changes in abundance and evolutionary diversity within the amphibian community of El Copé, Panama, following a disease epidemic and mass-mortality event. The epidemic reduced taxonomic, lineage, and phylogenetic diversity similarly. We discovered that 30 species were lost, including five undescribed species, representing 41% of total amphibian lineage diversity in El Copé. These extirpations represented 33% of the evolutionary history of amphibians within the community, and variation in the degree of population loss and decline among species was random with respect to the community phylogeny. Our approach provides a fast, economical, and informative analysis of loss in a community whether measured by species or phylogenetic diversity.

Geographical variation in predictors of mammalian extinction risk: big is bad, but only in the tropics

Whereas previous studies have investigated correlates of extinction risk either at global or regional scales, our study explicitly models regional effects of anthropogenic threats and biological traits across the globe. Using phylogenetic comparative methods with a newly-updated supertree of 5020 extant mammals, we investigate the impact of species traits on extinction risk within each WWF ecoregion. Our analyses reveal strong geographical variation in the influence of traits on risk: notably, larger species are at higher risk only in tropical regions. We then relate these patterns to current and recent-historical human impacts across ecoregions using spatial modelling. The body-mass results apparently reflect historical declines of large species outside the tropics due to large-scale land conversion. Narrow-ranged and rare species tend to be at high risk in areas of high current human impacts. The interactions we describe between biological traits and anthropogenic threats increase understanding of the processes determining extinction risk.

Ecomorphological selectivity among marine teleost fishes during the end-Cretaceous extinction

Despite the attention focused on mass extinction events in the fossil record, patterns of extinction in the dominant group of marine vertebrates-fishes-remain largely unexplored. Here, I demonstrate ecomorphological selectivity among marine teleost fishes during the end-Cretaceous extinction, based on a genus-level dataset that accounts for lineages predicted on the basis of phylogeny but not yet sampled in the fossil record. Two ecologically relevant anatomical features are considered: body size and jaw-closing lever ratio. Extinction intensity is higher for taxa with large body sizes and jaws consistent with speed (rather than force) transmission; resampling tests indicate that victims represent a nonrandom subset of taxa present in the final stage of the Cretaceous. Logistic regressions of the raw data reveal that this nonrandom distribution stems primarily from the larger body sizes of victims relative to survivors. Jaw mechanics are also a significant factor for most dataset partitions but are always less important than body size. When data are corrected for phylogenetic nonindependence, jaw mechanics show a significant correlation with extinction risk, but body size does not. Many modern large-bodied, predatory taxa currently suffering from overexploitation, such billfishes and tunas, first occur in the Paleocene, when they appear to have filled the functional space vacated by some extinction victims.

The Red Queen and the Court Jester: species diversity and the role of biotic and abiotic factors through time

Evolution may be dominated by biotic factors, as in the Red Queen model, or abiotic factors, as in the Court Jester model, or a mixture of both. The two models appear to operate predominantly over different geographic and temporal scales: Competition, predation, and other biotic factors shape ecosystems locally and over short time spans, but extrinsic factors such as climate and oceanographic and tectonic events shape larger-scale patterns regionally and globally, and through thousands and millions of years. Paleobiological studies suggest that species diversity is driven largely by abiotic factors such as climate, landscape, or food supply, and comparative phylogenetic approaches offer new insights into clade dynamics.