Has the Earth's sixth mass extinction already arrived?

Explaining bathymetric diversity patterns in marine benthic invertebrates and demersal fishes: physiological contributions to adaptation of life at depth

Bathymetric biodiversity patterns of marine benthic invertebrates and demersal fishes have been identified in the extant fauna of the deep continental margins. Depth zonation is widespread and evident through a transition between shelf and slope fauna from the shelf break to 1000 m, and a transition between slope and abyssal fauna from 2000 to 3000 m; these transitions are characterised by high species turnover. A unimodal pattern of diversity with depth peaks between 1000 and 3000 m, despite the relatively low area represented by these depths. Zonation is thought to result from the colonisation of the deep sea by shallow-water organisms following multiple mass extinction events throughout the Phanerozoic. The effects of low temperature and high pressure act across hierarchical levels of biological organisation and appear sufficient to limit the distributions of such shallow-water species. Hydrostatic pressures of bathyal depths have consistently been identified experimentally as the maximum tolerated by shallow-water and upper bathyal benthic invertebrates at in situ temperatures, and adaptation appears required for passage to deeper water in both benthic invertebrates and demersal fishes. Together, this suggests that a hyperbaric and thermal physiological bottleneck at bathyal depths contributes to bathymetric zonation. The peak of the unimodal diversity-depth pattern typically occurs at these depths even though the area represented by these depths is relatively low. Although it is recognised that, over long evolutionary time scales, shallow-water diversity patterns are driven by speciation, little consideration has been given to the potential implications for species distribution patterns with depth. Molecular and morphological evidence indicates that cool bathyal waters are the primary site of adaptive radiation in the deep sea, and we hypothesise that bathymetric variation in speciation rates could drive the unimodal diversity-depth pattern over time. Thermal effects on metabolic-rate-dependent mutation and on generation times have been proposed to drive differences in speciation rates, which result in modern latitudinal biodiversity patterns over time. Clearly, this thermal mechanism alone cannot explain bathymetric patterns since temperature generally decreases with depth. We hypothesise that demonstrated physiological effects of high hydrostatic pressure and low temperature at bathyal depths, acting on shallow-water taxa invading the deep sea, may invoke a stress-evolution mechanism by increasing mutagenic activity in germ cells, by inactivating canalisation during embryonic or larval development, by releasing hidden variation or mutagenic activity, or by activating or releasing transposable elements in larvae or adults. In this scenario, increased variation at a physiological bottleneck at bathyal depths results in elevated speciation rate. Adaptation that increases tolerance to high hydrostatic pressure and low temperature allows colonisation of abyssal depths and reduces the stress-evolution response, consequently returning speciation of deeper taxa to the background rate. Over time this mechanism could contribute to the unimodal diversity-depth pattern.

Assemblage time series reveal biodiversity change but not systematic loss

The extent to which biodiversity change in local assemblages contributes to global biodiversity loss is poorly understood. We analyzed 100 time series from biomes across Earth to ask how diversity within assemblages is changing through time. We quantified patterns of temporal α diversity, measured as change in local diversity, and temporal β diversity, measured as change in community composition. Contrary to our expectations, we did not detect systematic loss of α diversity. However, community composition changed systematically through time, in excess of predictions from null models. Heterogeneous rates of environmental change, species range shifts associated with climate change, and biotic homogenization may explain the different patterns of temporal α and β diversity. Monitoring and understanding change in species composition should be a conservation priority.

Declines in large wildlife increase landscape-level prevalence of rodent-borne disease in Africa

Populations of large wildlife are declining on local and global scales. The impacts of this pulse of size-selective defaunation include cascading changes to smaller animals, particularly rodents, and alteration of many ecosystem processes and services, potentially involving changes to prevalence and transmission of zoonotic disease. Understanding linkages between biodiversity loss and zoonotic disease is important for both public health and nature conservation programs, and has been a source of much recent scientific debate. In the case of rodent-borne zoonoses, there is strong conceptual support, but limited empirical evidence, for the hypothesis that defaunation, the loss of large wildlife, increases zoonotic disease risk by directly or indirectly releasing controls on rodent density. We tested this hypothesis by experimentally excluding large wildlife from a savanna ecosystem in East Africa, and examining changes in prevalence and abundance of Bartonella spp. infection in rodents and their flea vectors. We found no effect of wildlife removal on per capita prevalence of Bartonella infection in either rodents or fleas. However, because rodent and, consequently, flea abundance doubled following experimental defaunation, the density of infected hosts and infected fleas was roughly twofold higher in sites where large wildlife was absent. Thus, defaunation represents an elevated risk in Bartonella transmission to humans (bartonellosis). Our results (i) provide experimental evidence of large wildlife defaunation increasing landscape-level disease prevalence, (ii) highlight the importance of susceptible host regulation pathways and host/vector density responses in biodiversity-disease relationships, and (iii) suggest that rodent-borne disease responses to large wildlife loss may represent an important context where this relationship is largely negative.

Oil in the Sahara: mapping anthropogenic threats to Saharan biodiversity from space

Deserts are among the most poorly monitored and understood biomes in the world, with evidence suggesting that their biodiversity is declining fast. Oil exploration and exploitation can constitute an important threat to fragmented and remnant desert biodiversity, yet little is known about where and how intensively such developments are taking place. This lack of information hinders local efforts to adequately buffer and protect desert wildlife against encroachment from anthropogenic activity. Here, we investigate the use of freely available satellite imagery for the detection of features associated with oil exploration in the African Sahelo-Saharan region. We demonstrate how texture analyses combined with Landsat data can be employed to detect ground-validated exploration sites in Algeria and Niger. Our results show that site detection via supervised image classification and prediction is generally accurate. One surprising outcome of our analyses is the relatively high level of site omission errors in Niger (43%), which appears to be due to non-detection of potentially small-scale, temporary exploration activity: we believe the repeated implementation of our framework could reduce the severity of potential methodological limitations. Overall, our study provides a methodological basis for the mapping of anthropogenic threats associated with oil exploitation that can be conducted across desert regions.

Applications and implications of ecological energetics

The ecological processes that are crucial to an animal's growth, survival, and reproductive fitness have energetic costs. The imperative for an animal to meet these costs within the energetic constraints of the environment drives many aspects of animal ecology and evolution, yet has largely been overlooked in traditional ecological paradigms. The field of 'ecological energetics' is bringing comparative physiology out of the laboratory and, for the first time, is becoming broadly accessible to field ecologists addressing real-world questions at many spatial and temporal scales. In an era of unprecedented global environmental challenges, ecological energetics opens up the tantalising prospect of a more predictive, mechanistic understanding of the drivers of threatened species decline, delivering process-based modelling approaches to natural resource management.

The ethics of reviving long extinct species

There now appears to be a plausible pathway for reviving species that have been extinct for several decades, centuries, or even millennia. I conducted an ethical analysis of de-extinction of long extinct species. I assessed several possible ethical considerations in favor of pursuing de-extinction: that it is a matter of justice; that it would reestablish lost value; that it would create new value; and that society needs it as a conservation last resort. I also assessed several possible ethical arguments against pursuing de-extinction: that it is unnatural; that it could cause animal suffering; that it could be ecologically problematic or detrimental to human health; and that it is hubristic. There are reasons in favor of reviving long extinct species, and it can be ethically acceptable to do so. However, the reasons in favor of pursuing de-extinction do not have to do with its usefulness in species conservation; rather, they concern the status of revived species as scientific and technological achievements, and it would be ethically problematic to promote de-extinction as a significant conservation strategy, because it does not prevent species extinctions, does not address the causes of extinction, and could be detrimental to some species conservation efforts. Moreover, humanity does not have a responsibility or obligation to pursue de-extinction of long extinct species, and reviving them does not address any urgent problem. Therefore, legitimate ecological, political, animal welfare, legal, or human health concerns associated with a de-extinction (and reintroduction) must be thoroughly addressed for it to be ethically acceptable.

Stability of soil microbial structure and activity depends on microbial diversity

Despite the central role of microbes in soil processes, empirical evidence concerning the effect of their diversity on soil stability remains controversial. Here, we addressed the ecological insurance hypothesis by examining the stability of microbial communities along a gradient of soil microbial diversity in response to mercury pollution and heat stress. Diversity was manipulated by dilution extinction approach. Structural and functional stabilities of microbial communities were assessed from patterns of genetic structure and soil respiration after the stress. Dilution led to the establishment of a consistent diversity gradient, as revealed by 454 sequencing of ribosomal genes. Diversity stability was enhanced in species-rich communities whatever the stress whereas functional stability was improved with increasing diversity after heat stress, but not after mercury pollution. This discrepancy implies that the relevance of ecological insurance for soil microbial communities might depend on the type of stress. Our results also suggest that the significance of microbial diversity for soil functional stability might increase with available soil resources. This could have strong repercussions in the current 'global changes' context because it suggests that the combined increased frequencies of extreme climatic events, nutrient loading and biotic exploitation may amplify the functional consequences of diversity decrease.

Does recognized genetic management in supportive breeding prevent genetic changes in life-history traits?

Supportive breeding is one of the last resort conservation strategies to avoid species extinction. Management of captive populations is challenging because several harmful genetic processes need to be avoided. Several recommendations have been proposed to limit these deleterious effects, but empirical assessments of these strategies remain scarce. We investigated the outcome of a genetic management in a supportive breeding for the Houbara Bustard. At the phenotypic level, we found an increase over generations in the mean values of gamete production, body mass and courtship display rate. Using an animal model, we found that phenotypic changes reflected genetic changes as evidenced by an increase in breeding values for all traits. These changes resulted from selection acting on gamete production and to a lesser extent on courtship display. Selection decreased over years for female gametes, emphasizing the effort of managers to increase the contribution of poor breeders to offspring recruited in the captive breeding. Our results shed light on very fast genetic changes in an exemplary captive programme that follows worldwide used recommendations and emphasizes the need of more empirical evidence of the effects of genetic guidelines on the prevention of genetic changes in supportive breeding.

Fish functional traits correlated with environmental variables in a temperate biodiversity hotspot

The global biodiversity crisis has invigorated the search for generalized patterns in most disciplines within the natural sciences. Studies based on organismal functional traits attempt to broaden implications of results by identifying the response of functional traits, instead of taxonomic units, to environmental variables. Determining the functional trait responses enables more direct comparisons with, or predictions for, communities of different taxonomic composition. The North American freshwater fish fauna is both diverse and increasingly imperiled through human mediated disturbances, including climate change. The Tennessee River, USA, contains one of the most diverse assemblages of freshwater fish in North America and has more imperiled species than other rivers, but there has been no trait-based study of community structure in the system. We identified 211 localities in the upper Tennessee River that were sampled by the Tennessee Valley Authority between 2009 and 2011 and compiled fish functional traits for the observed species and environmental variables for each locality. Using fourth corner analysis, we identified significant correlations between many fish functional traits and environmental variables. Functional traits associated with an opportunistic life history strategy were correlated with localities subject to greater land use disturbance and less flow regulation, while functional traits associated with a periodic life history strategy were correlated with localities subject to regular disturbance and regulated flow. These are patterns observed at the continental scale, highlighting the generalizability of trait-based methods. Contrary to studies that found no community structure differences when considering riparian buffer zones, we found that fish functional traits were correlated with different environmental variables between analyses with buffer zones vs. entire catchment area land cover proportions. Using existing databases and fourth corner analysis, our results support the broad application potential for trait-based methods and indicate trait-based methods can detect environmental filtering by riparian zone land cover.

A stratigraphical basis for the Anthropocene?

Recognition of intimate feedback mechanisms linking changes across the atmosphere, biosphere, geosphere and hydrosphere demonstrates the pervasive nature of humankind's influence, perhaps to the point that we have fashioned a new geological epoch, the Anthropocene. To what extent will these changes be evident as long-lasting signatures in the geological record?

To establish the Anthropocene as a formal chronostratigraphical unit it is necessary to consider a spectrum of indicators of anthropogenically induced environmental change, and to determine how these show as stratigraphic signals that can be used to characterize an Anthropocene unit and to recognize its base. It is important to consider these signals against a context of Holocene and earlier stratigraphic patterns. Here we review the parameters used by stratigraphers to identify chronostratigraphical units and how these could apply to the definition of the Anthropocene. The onset of the range of signatures is diachronous, although many show maximum signatures which post-date 1945, leading to the suggestion that this date may be a suitable age for the start of the Anthropocene.

Can an Anthropocene Series be defined and recognized?

We consider the Anthropocene as a physical, chronostratigraphic unit across terrestrial and marine sedimentary facies, from both a present and a far future perspective, provisionally using an approximately 1950 CE base that approximates with the ‘Great Acceleration’, worldwide sedimentary incorporation of A-bomb-derived radionuclides and light nitrogen isotopes linked to the growth in fertilizer use, and other markers. More or less effective recognition of such a unit today (with annual/decadal resolution) is facies-dependent and variably compromised by the disturbance of stratigraphic superposition that commonly occurs at geologically brief temporal scales, and that particularly affects soils, deep marine deposits and the pre-1950 parts of current urban areas. The Anthropocene, thus, more than any other geological time unit, is locally affected by such blurring of its chronostratigraphic boundary with Holocene strata. Nevertheless, clearly separable representatives of an Anthropocene Series may be found in lakes, land ice, certain river/delta systems, in the widespread dredged parts of shallow-marine systems on continental shelves and slopes, and in those parts of deep-water systems where human-rafted debris is common. From a far future perspective, the boundary is likely to appear geologically instantaneous and stratigraphically significant.

Non-random biodiversity loss underlies predictable increases in viral disease prevalence

Disease dilution (reduced disease prevalence with increasing biodiversity) has been described for many different pathogens. Although the mechanisms causing this phenomenon remain unclear, the disassembly of communities to predictable subsets of species, which can be caused by changing climate, land use or invasive species, underlies one important hypothesis. In this case, infection prevalence could reflect the competence of the remaining hosts. To test this hypothesis, we measured local host species abundance and prevalence of four generalist aphid-vectored pathogens (barley and cereal yellow dwarf viruses) in a ubiquitous annual grass host at 10 sites spanning 2000 km along the North American West Coast. In laboratory and field trials, we measured viral infection as well as aphid fecundity and feeding preference on several host species. Virus prevalence increased as local host richness declined. Community disassembly was non-random: ubiquitous hosts dominating species-poor assemblages were among the most competent for vector production and virus transmission. This suggests that non-random biodiversity loss led to increased virus prevalence. Because diversity loss is occurring globally in response to anthropogenic changes, such work can inform medical, agricultural and veterinary disease research by providing insights into the dynamics of pathogens nested within a complex web of environmental forces.

The evolutionary paths towards complexity: a metabolic perspective

As sessile organisms, land plants have exploited their metabolic systems to produce a panoply of structurally and functionally diverse natural chemicals and polymers to adapt to challenging ecosystems. Many of these core and specialized metabolites confer chemical shields against a multitude of abiotic stresses, while others play important roles in plants' interactions with their biotic environments. Plant specialized metabolites can be viewed as complex traits in the sense that the biosynthesis of these molecules typically requires multistep metabolic pathways comprising numerous specific enzymes belonging to diverse protein fold families. Resolving the evolutionary trajectories underlying the emergence of these specialized metabolic pathways will impact a fundamental question in biology – how do complex traits evolve in a Darwinian fashion? Here, I discuss several general patterns observed in rapidly evolving specialized metabolic systems in plants, and surmise mechanistic features at enzyme, pathway and organismal levels that rationalize the remarkable malleability of these systems through stepwise evolution. Future studies, focused on fine sampling of metabolic enzymes and pathways in phylogenetically related plant species, or employing directed evolution strategies in synthetic systems, will significantly broaden our perspective on how biological complexity arises at the metabolic level.

Generalized drivers in the mammalian endangerment process

An important challenge for conservation today is to understand the endangerment process and identify any generalized patterns in how threats occur and aggregate across taxa. Here we use a global database describing main current external threats in mammals to evaluate the prevalence of distinct threatening processes, primarily of anthropogenic origin, and to identify generalized drivers of extinction and their association with vulnerability status and intrinsic species' traits. We detect several primary threat combinations that are generally associated with distinct species. In particular, large and widely distributed mammals are affected by combinations of direct exploitation and threats associated with increasing landscape modification that go from logging to intense human land-use. Meanwhile, small, narrowly distributed species are affected by intensifying levels of landscape modification but are not directly exploited. In general more vulnerable species are affected by a greater number of threats, suggesting increased extinction risk is associated with the accumulation of external threats. Overall, our findings show that endangerment in mammals is strongly associated with increasing habitat loss and degradation caused by human land-use intensification. For large and widely distributed mammals there is the additional risk of being hunted.

Threat to the point: improving the value of comparative extinction risk analysis for conservation action

Comparative extinction risk analysis is a common approach for assessing the relative plight of biodiversity and making conservation recommendations. However, the usefulness of such analyses for conservation practice has been questioned. One reason for underperformance may be that threats arising from global environmental changes (e.g., habitat loss, invasive species, climate change) are often overlooked, despite being widely regarded as proximal drivers of species' endangerment. We explore this problem by (i) reviewing the use of threats in this field and (ii) quantitatively investigating the effects of threat exclusion on the interpretation and potential application of extinction risk model results. We show that threat variables are routinely (59%) identified as significant predictors of extinction risk, yet while most studies (78%) include extrinsic factors of some kind (e.g., geographic or bioclimatic information), the majority (63%) do not include threats. Despite low overall usage, studies are increasingly employing threats to explain patterns of extinction risk. However, most continue to employ methods developed for the analysis of heritable traits (e.g., body size, fecundity), which may be poorly suited to the treatment of nonheritable predictors including threats. In our global mammal and continental amphibian extinction risk case studies, omitting threats reduced model predictive performance, but more importantly (i) reduced mechanistic information relevant to management; (ii) resulted in considerable disagreement in species classifications (12% and 5% for amphibians and mammals, respectively, translating to dozens and hundreds of species); and (iii) caused even greater disagreement (20-60%) in a downstream conservation application (species ranking). We conclude that the use of threats in comparative extinction risk analysis is important and increasing but currently in the early stages of development. Priorities for future studies include improving uptake, availability, quality and quantification of threat data, and developing analytical methods that yield more robust, relevant and tangible products for conservation applications.

Modeling extinction risk of endemic birds of mainland china

The extinction risk of endemic birds of mainland China was modeled over evolutionary time. Results showed that extinction risk of endemic birds in mainland China always tended to be similar within subclades over the evolutionary time of species divergence, and the overall evolution of extinction risk of species presented a conservatism pattern, as evidenced by the disparity-through-time plot. A constant-rate evolutionary model was the best one to quantify the evolution of extinction risk of endemic birds of mainland China. Thus, there was no rate shifting pattern for the evolution of extinction risk of Chinese endemic birds over time. In a summary, extinction risk of endemic birds of mainland China is systematically quantified under the evolutionary framework in the present work.

Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals

O'Leary et al. (O'Leary et al. 2013 Science339, 662–667. (doi:10.1126/science.1229237)) performed a fossil-only dating analysis of mammals, concluding that the ancestor of placentals post-dated the Cretaceous–Palaeogene boundary, contradicting previous palaeontological and molecular studies that placed the ancestor in the Cretaceous. They incorrectly used fossil ages as species divergence times for crown groups, while in fact the former should merely form minimum-age bounds for the latter. Statistical analyses of the fossil record have shown that crown groups are significantly older than the oldest ingroup fossil, so that fossils do not directly reflect the true ages of clades. Here, we analyse a 20 million nucleotide genome-scale alignment in conjunction with a probabilistic interpretation of the fossil ages from O'Leary et al. Our combined analysis of fossils and molecules demonstrates that Placentalia originated in the Cretaceous.

Vintage venoms: proteomic and pharmacological stability of snake venoms stored for up to eight decades

For over a century, venom samples from wild snakes have been collected and stored around the world. However, the quality of storage conditions for "vintage" venoms has rarely been assessed. The goal of this study was to determine whether such historical venom samples are still biochemically and pharmacologically viable for research purposes, or if new sample efforts are needed. In total, 52 samples spanning 5 genera and 13 species with regional variants of some species (e.g., 14 different populations of Notechis scutatus) were analysed by a combined proteomic and pharmacological approach to determine protein structural stability and bioactivity. When venoms were not exposed to air during storage, the proteomic results were virtually indistinguishable from that of fresh venom and bioactivity was equivalent or only slightly reduced. By contrast, a sample of Acanthophis antarcticus venom that was exposed to air (due to a loss of integrity of the rubber stopper) suffered significant degradation as evidenced by the proteomics profile. Interestingly, the neurotoxicity of this sample was nearly the same as fresh venom, indicating that degradation may have occurred in the free N- or C-terminus chains of the proteins, rather than at the tips of loops where the functional residues are located. These results suggest that these and other vintage venom collections may be of continuing value in toxin research. This is particularly important as many snake species worldwide are declining due to habitat destruction or modification. For some venoms (such as N. scutatus from Babel Island, Flinders Island, King Island and St. Francis Island) these were the first analyses ever conducted and these vintage samples may represent the only venom ever collected from these unique island forms of tiger snakes. Such vintage venoms may therefore represent the last remaining stocks of some local populations and thus are precious resources. These venoms also have significant historical value as the Oxyuranus venoms analysed include samples from the first coastal taipan (Oxyuranus scutellatus) collected for antivenom production (the snake that killed the collector Kevin Budden), as well as samples from the first Oxyuranus microlepidotus specimen collected after the species' rediscovery in 1976. These results demonstrate that with proper storage techniques, venom samples can retain structural and pharmacological stability. This article is part of a Special Issue entitled: Proteomics of non-model organisms.

BIOLOGICAL SIGNIFICANCE

Endoreduplicative standards for calibration of flow cytometric C-Value measurements

It has been estimated that there are, globally, as many as 400,000 species of the angiosperms (the flowering plants). Of these, a minimal proportion has been characterized at the cytological level. Urgency is required in initiating a systematic and comprehensive census, due to species extinction as a consequence of anthropogenic activities. Fundamental to eukaryotes is the 2C-value, the amount of DNA contained within the nucleus of the unreduced gametes. Flow cytometry provides an ideal method for determining C-values, but the values archived in the Kew Plant C-value Database represent <2% of these species. Complicating the issue is a proliferation of different, and inconsistent standards for C-value measurements utilizing flow cytometry, and variability associated with different instrument platforms and using different staining procedures. In previous work, the use of flow cytometry for analysis of plant nuclear DNA contents for species spanning much of the range of genome sizes found in the angiosperms was described. For this work, an endoreduplicative species (Arabidopsis thaliana L.) was particularly helpful as an internal standard for genome size calibration. Such a standard is compromised if it overlaps in DNA content than that of the species whose genome size is sought. This report describes the use of a second species displaying endoreduplication, Capsicum annuum L., for similar standardization. The results (a) indicate accurate reporting of nuclear DNA contents across a range 0.32-423.68 pg, (b) confirm that endoreduplication increases nuclear DNA contents by complete replication of the genome, and (c) provide a means for quality control of linearity in instrumentation over defined dynamic ranges.

Assessing "dangerous climate change": required reduction of carbon emissions to protect young people, future generations and nature

We assess climate impacts of global warming using ongoing observations and paleoclimate data. We use Earth's measured energy imbalance, paleoclimate data, and simple representations of the global carbon cycle and temperature to define emission reductions needed to stabilize climate and avoid potentially disastrous impacts on today's young people, future generations, and nature. A cumulative industrial-era limit of ∼500 GtC fossil fuel emissions and 100 GtC storage in the biosphere and soil would keep climate close to the Holocene range to which humanity and other species are adapted. Cumulative emissions of ∼1000 GtC, sometimes associated with 2°C global warming, would spur "slow" feedbacks and eventual warming of 3-4°C with disastrous consequences. Rapid emissions reduction is required to restore Earth's energy balance and avoid ocean heat uptake that would practically guarantee irreversible effects. Continuation of high fossil fuel emissions, given current knowledge of the consequences, would be an act of extraordinary witting intergenerational injustice. Responsible policymaking requires a rising price on carbon emissions that would preclude emissions from most remaining coal and unconventional fossil fuels and phase down emissions from conventional fossil fuels.

Plant-pollinator coextinctions and the loss of plant functional and phylogenetic diversity

Plant-pollinator coextinctions are likely to become more frequent as habitat alteration and climate change continue to threaten pollinators. The consequences of the resulting collapse of plant communities will depend partly on how quickly plant functional and phylogenetic diversity decline following pollinator extinctions. We investigated the functional and phylogenetic consequences of pollinator extinctions by simulating coextinctions in seven plant-pollinator networks coupled with independent data on plant phylogeny and functional traits. Declines in plant functional diversity were slower than expected under a scenario of random extinctions, while phylogenetic diversity often decreased faster than expected by chance. Our results show that plant functional diversity was relatively robust to plant-pollinator coextinctions, despite the underlying rapid loss of evolutionary history. Thus, our study suggests the possibility of uncoupled responses of functional and phylogenetic diversity to species coextinctions, highlighting the importance of considering both dimensions of biodiversity explicitly in ecological studies and when planning for the conservation of species and interactions.

Global meta-analysis reveals no net change in local-scale plant biodiversity over time

Global biodiversity is in decline. This is of concern for aesthetic and ethical reasons, but possibly also for practical reasons, as suggested by experimental studies, mostly with plants, showing that biodiversity reductions in small study plots can lead to compromised ecosystem function. However, inferring that ecosystem functions will decline due to biodiversity loss in the real world rests on the untested assumption that such loss is actually occurring at these small scales in nature. Using a global database of 168 published studies and >16,000 nonexperimental, local-scale vegetation plots, we show that mean temporal change in species diversity over periods of 5-261 y is not different from zero, with increases at least as likely as declines over time. Sites influenced primarily by plant species' invasions showed a tendency for declines in species richness, whereas sites undergoing postdisturbance succession showed increases in richness over time. Other distinctions among studies had little influence on temporal richness trends. Although maximizing diversity is likely important for maintaining ecosystem function in intensely managed systems such as restored grasslands or tree plantations, the clear lack of any general tendency for plant biodiversity to decline at small scales in nature directly contradicts the key assumption linking experimental results to ecosystem function as a motivation for biodiversity conservation in nature. How often real world changes in the diversity and composition of plant communities at the local scale cause ecosystem function to deteriorate, or actually to improve, remains unknown and is in critical need of further study.

Implications of Time-Averaged Death Assemblages for Ecology and Conservation Biology

Biologists increasingly appreciate the importance of community-level attributes in the functioning and temporal turnover of ecosystems, but data other than species richness are difficult to acquire over the habitat-to-regional and decadal-to-millennial scales needed to recognize biodiversity change, discriminate between natural and anthropogenic drivers, and inform theoretical and applied ecology. Death assemblages (DAs)—the actively accumulating organic remains encountered in present-day seabeds and landscapes, as distinct from permanently buried fossil assemblages—are an underexploited source of historical information at precisely these scales. Meta-analyses, dynamic modeling, and individual case studies, particularly of mollusks and mammals, reveal that DAs differ from censused living assemblages (LAs) primarily because they are temporally coarse, time-averaged samples, contrary to concerns that postmortem bias dominates. Temporal pooling predictably damps the ability of DAs to detect small-scale variation, but promotes their ability to inventory rare species; estimate the abundance structure of the metacommunity; document range changes; evaluate historic habitat use; and identify now-absent species, community states, and anthropogenically shifted baselines.

Life history of the Glanville fritillary butterfly in fragmented versus continuous landscapes

Habitat loss and fragmentation threaten the long-term viability of innumerable species of plants and animals. At the same time, habitat fragmentation may impose strong natural selection and lead to evolution of life histories with possible consequences for demographic dynamics. The Baltic populations of the Glanville fritillary butterfly (Melitaea cinxia) inhabit regions with highly fragmented habitat (networks of small dry meadows) as well as regions with extensive continuous habitat (calcareous alvar grasslands). Here, we report the results of common garden studies on butterflies originating from two highly fragmented landscapes (FL) in Finland and Sweden and from two continuous landscapes (CL) in Sweden and Estonia, conducted in a large outdoor cage (32 by 26 m) and in the laboratory. We investigated a comprehensive set of 51 life-history traits, including measures of larval growth and development, flight performance, and adult reproductive behavior. Seventeen of the 51 traits showed a significant difference between fragmented versus CL. Most notably, the growth rate of postdiapause larvae and several measures of flight capacity, including flight metabolic rate, were higher in butterflies from fragmented than CL. Females from CL had shorter intervals between consecutive egg clutches and somewhat higher life-time egg production, but shorter longevity, than females from FL. These results are likely to reflect the constant opportunities for oviposition in females living in continuous habitats, while the more dispersive females from FL allocate more resources to dispersal capacity at the cost of egg maturation rate. This study supports theoretical predictions about small population sizes and high rate of population turnover in fragmented habitats selecting for increased rate of dispersal, but the results also indicate that many other life-history traits apart from dispersal are affected by the degree of habitat fragmentation.

Fire promotes pollinator visitation: implications for ameliorating declines of pollination services

Pollinators serve critical roles for the functioning of terrestrial ecosystems, and have an estimated annual value of over $150 billion for global agriculture. Mounting evidence from agricultural systems reveals that pollinators are declining in many regions of the world, and with a lack of information on whether pollinator communities in natural systems are following similar trends, identifying factors which support pollinator visitation and services are important for ameliorating the effects of the current global pollinator crisis. We investigated how fire affects resource structure and how that variation influences floral pollinator communities by comparing burn versus control treatments in a southeastern USA old-field system. We hypothesized and found a positive relationship between fire and plant density of a native forb, Verbesina alternifolia, as well as a significant difference in floral visitation of V. alternifolia between burn and control treatments. V. alternifolia density was 44% greater and floral visitation was 54% greater in burned treatments relative to control sites. When the density of V. alternifolia was experimentally reduced in the burn sites to equivalent densities observed in control sites, floral visitation in burned sites declined to rates found in control sites. Our results indicate that plant density is a proximal mechanism by which an imposed fire regime can indirectly impact floral visitation, suggesting its usefulness as a tool for management of pollination services. Although concerns surround the negative impacts of management, indirect positive effects may provide an important direction to explore for managing future ecological and conservation issues. Studies examining the interaction among resource concentration, plant apparency, and how fire affects the evolutionary consequences of altered patterns of floral visitation are overdue.

Explaining geographic gradients in winter selection of landscapes by boreal caribou with implications under global changes in Eastern Canada

Many animal species exhibit broad-scale latitudinal or longitudinal gradients in their response to biotic and abiotic components of their habitat. Although knowing the underlying mechanism of these patterns can be critical to the development of sound measures for the preservation or recovery of endangered species, few studies have yet identified which processes drive the existence of geographical gradients in habitat selection. Using extensive spatial data of broad latitudinal and longitudinal extent, we tested three hypotheses that could explain the presence of geographical gradients in landscape selection of the endangered boreal woodland caribou (Rangifer tarandus caribou) during winter in Eastern Canadian boreal forests: 1) climate-driven selection, which postulates that geographic gradients are surrogates for climatic gradients; 2) road-driven selection, which proposes that boreal caribou adjust their selection for certain habitat classes as a function of proximity to roads; and 3) an additive effect of both roads and climate. Our data strongly supported road-driven selection over climate influences. Thus, direct human alteration of landscapes drives boreal caribou distribution and should likely remain so until the climate changes sufficiently from present conditions. Boreal caribou avoided logged areas two-fold more strongly than burnt areas. Limiting the spread of road networks and accounting for the uneven impact of logging compared to wildfire should therefore be integral parts of any habitat management plan and conservation measures within the range of the endangered boreal caribou. The use of hierarchical spatial models allowed us to explore the distribution of spatially-structured errors in our models, which in turn provided valuable insights for generating alternative hypotheses about processes responsible for boreal caribou distribution.

Understanding mechanisms of rarity in pteridophytes: competition and climate change threaten the rare fern Asplenium scolopendrium var. americanum (Aspleniaceae)

PREMISE OF THE STUDY

Understanding the ecology of rare species can inform aspects of conservation strategies; however, the mechanisms of rarity remain elusive for most pteridophytes, which possess independent and ecologically distinct gametophyte and sporophyte generations. To elucidate factors contributing to recent declines of the rare fern Asplenium scolopendrium var. americanum, we studied the ecology and ecophysiology of its gametophyte generation, focusing on responses to competition, temperature, and water stress.

METHODS

Gametophytes of A. scolopendrium var. americanum, its widespread European relative A. scolopendrium var. scolopendrium, and five co-occurring fern species were grown from spores. Gametophytes were grown at 20°C and 25°C, and germination rates, intra- and interspecific competition, desiccation tolerance, and sporophyte production were determined for all species.

KEY RESULTS

Gametophytes of A. scolopendrium var. americanum had the lowest rates of germination and sporophyte production among all species studied and exhibited the greatest sensitivity to interspecific competition, temperature increases, and desiccation. Mature gametophytes of A. scolopendrium var. americanum grown at 25°C were 84.6% smaller than those grown at 20°C, and only 1.5% produced sporophytes after 200 d in culture. Similar responses were not observed in other species studied.

CONCLUSIONS

The recent declines and current status of populations of A. scolopendrium var. americanum are linked to its gametophyte's limited capacity to tolerate competition and physiological stress linked to climate change. This is the first study to develop a mechanistic understanding of rarity and decline in a fern and demonstrates the importance of considering the ecology of the gametophyte in plants with independent sporophyte and gametophyte generations.

Morphological divergence and flow-induced phenotypic plasticity in a native fish from anthropogenically altered stream habitats

Understanding population-level responses to human-induced changes to habitats can elucidate the evolutionary consequences of rapid habitat alteration. Reservoirs constructed on streams expose stream fishes to novel selective pressures in these habitats. Assessing the drivers of trait divergence facilitated by these habitats will help identify evolutionary and ecological consequences of reservoir habitats. We tested for morphological divergence in a stream fish that occupies both stream and reservoir habitats. To assess contributions of genetic-level differences and phenotypic plasticity induced by flow variation, we spawned and reared individuals from both habitats types in flow and no flow conditions. Body shape significantly and consistently diverged in reservoir habitats compared with streams; individuals from reservoirs were shallower bodied with smaller heads compared with individuals from streams. Significant population-level differences in morphology persisted in offspring but morphological variation compared with field-collected individuals was limited to the head region. Populations demonstrated dissimilar flow-induced phenotypic plasticity when reared under flow, but phenotypic plasticity in response to flow variation was an unlikely explanation for observed phenotypic divergence in the field. Our results, together with previous investigations, suggest the environmental conditions currently thought to drive morphological change in reservoirs (i.e., predation and flow regimes) may not be the sole drivers of phenotypic change.

Technology as a geological phenomenon: implications for human well-being

The technosphere, the interlinked set of communication, transportation, bureaucratic and other systems that act to metabolize fossil fuels and other energy resources, is considered to be an emerging global paradigm, with similarities to the lithosphere, atmosphere, hydrosphere and biosphere. The technosphere is of global extent, exhibits large-scale appropriation of mass and energy resources, shows a tendency to co-opt for its own use information produced by the environment, and is autonomous. Unlike the older paradigms, the technosphere has not yet evolved the ability to recycle its own waste stream. Unless or until it does so, its status as a paradigm remains provisional. Humans are ‘parts’ of the technosphere – subcomponents essential for system function. Viewed from the inside by its human parts, the technosphere is perceived as a derived and controlled construct. Viewed from outside as a geological phenomenon, the technosphere appears as a quasi-autonomous system whose dynamics constrains the behaviour of its human parts. A geological perspective on technology suggests why strategies to limit environmental damage that consider only the needs of people are likely to fail without parallel consideration of the requirements of technology, especially its need for an abundant supply of energy.

Palaeontological evidence for defining the Anthropocene

Palaeontology formed the basis for defining most of the geological eras, periods, epochs and ages that are commonly recognized. By the same token, the Anthropocene can be defined by diverse palaeontological criteria, in accordance with commonly accepted biostratigraphic practice. The most useful Anthropocene biostratigraphic zones will be assemblage and abundance zones based on mixes of native and non-native species in both the marine and terrestrial realms, although lineage zones based on evolution of crop plants may also have utility. Also useful are human-produced trace fossils, which have resulted in prominent biohorizons that can mark the onset of the Anthropocene, especially the paved road system, widespread through terrestrial regions, and microplastics, ubiquitous in near-shore and deep-water marine sediments. Most of these palaeontological criteria support placing the Holocene–Anthropocene boundary near 1950. Continuation of current extinction rates would produce an extinction biohorizon on the scale of the Big Five mass extinctions within a few centuries, but enhanced conservation measures could prevent making mass extinction an Anthropocene signature. A grand challenge for palaeontologists now is to define Anthropocene biostratigraphic zones rigorously, not only as a necessary precursor to formalizing the epoch, but also to more fully understand how humans have restructured the biosphere.

Body size and extinction risk in terrestrial mammals above the species level

Mammalian body mass strongly correlates with life history and population properties at the scale of mouse to elephant. Large body size is thus often associated with elevated extinction risk. I examined the North American fossil record (28-1 million years ago) of 276 terrestrial genera to uncover the relationship between body size and extinction probability above the species level. Phylogenetic comparative analysis revealed no correlation between sampling-adjusted durations and body masses ranging 7 orders of magnitude, an observation that was corroborated by survival analysis. Most of the ecological and temporal groups within the data set showed the same lack of relationship. Size-biased generic extinctions do not constitute a general feature of the Holarctic mammalian faunas in the Neogene. Rather, accelerated loss of large mammals occurred during intervals that experienced combinations of regional aridification and increased biomic heterogeneity within continents. The latter phenomenon is consistent with the macroecological prediction that large geographic ranges are critical to the survival of large mammals in evolutionary time. The frequent lack of size selectivity in generic extinctions can be reconciled with size-biased species loss if extinctions of large and small mammals at the species level are often driven by ecological perturbations of different spatial and temporal scales, while those at the genus level are more synchronized in time as a result of fundamental, multiscale environmental shifts.

The alligator gut microbiome and implications for archosaur symbioses

Among vertebrate gastrointestinal microbiome studies, complete representation of taxa is limited, particularly among reptiles. Here, we provide evidence for previously unrecognized host-microbiome associations along the gastrointestinal tract from the American alligator, a crown archosaur with shared ancestry to extinct taxa, including dinosaurs. Microbiome compositional variations reveal that the digestive system consists of multiple, longitudinally heterogeneous microbiomes that strongly correlate to specific gastrointestinal tract organs, regardless of rearing histories or feeding status. A core alligator gut microbiome comprised of Fusobacteria, but depleted in Bacteroidetes and Proteobacteria common to mammalians, is compositionally unique from other vertebrate gut microbiomes, including other reptiles, fish, and herbivorous and carnivorous mammals. As such, modern alligator gut microbiomes advance our understanding of archosaur gut microbiome evolution, particularly if conserved host ecology has retained archosaur-specific symbioses over geologic time.

Trophic flexibility and the persistence of understory birds in intensively logged rainforest

Effects of logging on species composition in tropical rainforests are well known but may fail to reveal key changes in species interactions. We used nitrogen stable-isotope analysis of 73 species of understory birds to quantify trophic responses to repeated intensive logging of rainforest in northern Borneo and to test 4 hypotheses: logging has significant effects on trophic positions and trophic-niche widths of species, and the persistence of species in degraded forest is related to their trophic positions and trophic-niche widths in primary forest. Species fed from higher up the food chain and had narrower trophic-niche widths in degraded forest. Species with narrow trophic-niche widths in primary forest were less likely to persist after logging, a result that indicates a higher vulnerability of dietary specialists to local extinction following habitat disturbance. Persistence of species in degraded forest was not related to a species' trophic position. These results indicate changes in trophic organization that were not apparent from changes in species composition and highlight the importance of focusing on trophic flexibility over the prevailing emphasis on membership of static feeding guilds. Our results thus support the notion that alterations to trophic organization and interactions within tropical forests may be a pervasive and functionally important hidden effect of forest degradation.