Extinctions in ancient and modern seas

Back to the future? Late Holocene marine food web structure in a warm climatic phase as a predictor of trophodynamics in a warmer South-Western Atlantic Ocean

Stable carbon and nitrogen isotope ratios in the skeletal elements of both ancient and modern marine species from the Beagle Channel were used to compare the structure of Late Holocene and modern food webs, and predict potential changes as a result of a Sea Surface Temperature (SST) increase in the region. Complementary, ancient and modern shells of limpets and mussels were isotopically analysed to explore changes in the isotopic baseline and compare marine food webs through time after an appropriate correction for baseline shifts. Results confirmed a declining pattern of marine primary productivity during the Late Holocene in the Beagle Channel. In general, the isotopic niches overlapped largely in the ancient food web in comparison to the current marine one, with the exception of that of cormorants (Phalacrocorax sp.). Our data suggest that all the species that have undergone intense human exploitation (Arctocephalus australis, Otaria flavescens and Merluccius sp.) significantly increased their trophic levels. The most important finding of this work was the very high isotopic overlap between snoek (Thyrsites atun) and hake (Merluccius sp.) during the Late Holocene. Increasing SST as a result of global warming could favour the recolonization of the southern South-Western Atlantic Ocean by snoek from the South-Eastern Pacific Ocean, with a potential impact on the landings of the economically important Argentine and Austral hake. These findings highlight the relevance of using zooarchaeological remains for providing predictions about marine food webs changes in the near future.

Marine Metazoan Modern Mass Extinction: Improving Predictions by Integrating Fossil, Modern, and Physiological Data

Evolution, extinction, and dispersion are fundamental processes affecting marine biodiversity. Until recently, studies of extant marine systems focused mainly on evolution and dispersion, with extinction receiving less attention. Past extinction events have, however, helped shape the evolutionary history of marine ecosystems, with ecological and evolutionary legacies still evident in modern seas. Current anthropogenic global changes increase extinction risk and pose a significant threat to marine ecosystems, which are critical for human use and sustenance. The evaluation of these threats and the likely responses of marine ecosystems requires a better understanding of evolutionary processes that affect marine ecosystems under global change. Here, we discuss how knowledge of ( a) changes in biodiversity of ancient marine ecosystems to past extinctions events, ( b) the patterns of sensitivity and biodiversity loss in modern marine taxa, and ( c) the physiological mechanisms underpinning species' sensitivity to global change can be exploited and integrated to advance our critical thinking in this area.

Eocene sand tiger sharks (Lamniformes, Odontaspididae) from the Bolca Konservat-Lagerstätte, Italy: palaeobiology, palaeobiogeography and evolutionary significance

Here we report the first record of one of the most common and widespread Palaeogene selachians, the sand tiger shark Brachycarcharias, from the Ypresian Bolca Konservat-Lagerstätte. The combination of dental character of the 15 isolated teeth collected from the Pesciara and Monte Postale sites (e.g. anterior teeth up to 25 mm with fairly low triangular cusp decreasing regularly in width; one to two pairs of well-developed lateral cusplets; root with broadly separated lobes; upper teeth with a cusp bent distally) supports their assignment to the odontaspidid Brachycarcharias lerichei (Casier, 1946), a species widely spread across the North Hemisphere during the early Palaeogene. The unambiguous first report of this lamniform shark in the Eocene Bolca Konservat-Lagerstätte improves our knowledge concerning the diversity and palaeobiology of the cartilaginous fishes of this palaeontological site, and provides new insights about the biotic turnovers that involved the high trophic levels of the marine settings after the end-Cretaceous extinction.

Eocene sand tiger sharks (Lamniformes, Odontaspididae) from the Bolca Konservat-Lagerstätte, Italy: palaeobiology, palaeobiogeography and evolutionary significance

Here we report the first record of one of the most common and widespread Palaeogene selachians, the sand tiger shark Brachycarcharias, from the Ypresian Bolca Konservat-Lagerstätte. The combination of dental character of the 15 isolated teeth collected from the Pesciara and Monte Postale sites (e.g. anterior teeth up to 25 mm with fairly low triangular cusp decreasing regularly in width; one to two pairs of well-developed lateral cusplets; root with broadly separated lobes; upper teeth with a cusp bent distally) supports their assignment to the odontaspidid Brachycarcharias lerichei (Casier, 1946), a species widely spread across the North Hemisphere during the early Palaeogene. The unambiguous first report of this lamniform shark in the Eocene Bolca Konservat-Lagerstätte improves our knowledge concerning the diversity and palaeobiology of the cartilaginous fishes of this palaeontological site, and provides new insights about the biotic turnovers that involved the high trophic levels of the marine settings after the end-Cretaceous extinction.

History is written by the victors: The effect of the push of the past on the fossil record

Survivorship biases can generate remarkable apparent rate heterogeneities through time in otherwise homogeneous birth‐death models of phylogenies. They are a potential explanation for many striking patterns seen in the fossil record and molecular phylogenies. One such bias is the “push of the past”: clades that survived a substantial length of time are likely to have experienced a high rate of early diversification. This creates the illusion of a secular rate slow‐down through time that is, rather, a reversion to the mean. An extra effect increasing early rates of lineage generation is also seen in large clades. These biases are important but relatively neglected influences on many aspects of diversification patterns in the fossil record and elsewhere, such as diversification spikes after mass extinctions and at the origins of clades; they also influence rates of fossilization, changes in rates of phenotypic evolution and even molecular clocks. These inevitable features of surviving and/or large clades should thus not be generalized to the diversification process as a whole without additional study of small and extinct clades, and raise questions about many of the traditional explanations of the patterns seen in the fossil record.

Extinction risk in extant marine species integrating palaeontological and biodistributional data

Extinction risk assessments of marine invertebrate species remain scarce, which hinders effective management of marine biodiversity in the face of anthropogenic impacts. To help close this information gap, in this paper we provide a metric of relative extinction risk that combines palaeontological data, in the form of extinction rates calculated from the fossil record, with two known correlates of risk in the modern day: geographical range size and realized thermal niche. We test the performance of this metric-Palaeontological Extinction Risk In Lineages (PERIL)-using survivorship analyses of Pliocene bivalve faunas from California and New Zealand, and then use it to identify present-day hotspots of extinction vulnerability for extant shallow-marine Bivalvia. Areas of the ocean where concentrations of bivalve species with higher PERIL scores overlap with high levels of climatic or anthropogenic stressors should be considered of most immediate concern for both conservation and management.

Cracking the Code of Biodiversity Responses to Past Climate Change

How individual species and entire ecosystems will respond to future climate change are among the most pressing questions facing ecologists. Past biodiversity dynamics recorded in the paleoecological archives show a broad array of responses, yet significant knowledge gaps remain. In particular, the relative roles of evolutionary adaptation, phenotypic plasticity, and dispersal in promoting survival during times of climate change have yet to be clarified. Investigating the paleo-archives offers great opportunities to understand biodiversity responses to future climate change. In this review we discuss the mechanisms by which biodiversity responds to environmental change, and identify gaps of knowledge on the role of range shifts and tolerance. We also outline approaches at the intersection of paleoecology, genomics, experiments, and predictive models that will elucidate the processes by which species have survived past climatic changes and enhance predictions of future changes in biological diversity.

Temperature is a poor proxy for synergistic climate forcing of plankton evolution

Changes in biodiversity at all levels from molecules to ecosystems are often linked to climate change, which is widely represented univariately by temperature. A global environmental driving mechanism of biodiversity dynamics is thus implied by the strong correlation between temperature proxies and diversity patterns in a wide variety of fauna and flora. Yet climate consists of many interacting variables. Species probably respond to the entire climate system as opposed to its individual facets. Here, we examine ecological and morphological traits of 12 633 individuals of two species of planktonic foraminifera with similar ecologies but contrasting evolutionary outcomes. Our results show that morphological and ecological changes are correlated to the interactions between multiple environmental factors. Models including interactions between climate variables explain at least twice as much variation in size, shape and abundance changes as models assuming that climate parameters operate independently. No dominant climatic driver can be identified: temperature alone explains remarkably little variation through our highly resolved temporal sequences, implying that a multivariate approach is required to understand evolutionary response to abiotic forcing. Our results caution against the use of a ‘silver bullet’ environmental parameter to represent global climate while studying evolutionary responses to abiotic change, and show that more comprehensive reconstruction of palaeobiological dynamics requires multiple biotic and abiotic dimensions.

Essential ocean variables for global sustained observations of biodiversity and ecosystem changes

Sustained observations of marine biodiversity and ecosystems focused on specific conservation and management problems are needed around the world to effectively mitigate or manage changes resulting from anthropogenic pressures. These observations, while complex and expensive, are required by the international scientific, governance and policy communities to provide baselines against which the effects of human pressures and climate change may be measured and reported, and resources allocated to implement solutions. To identify biological and ecological essential ocean variables (EOVs) for implementation within a global ocean observing system that is relevant for science, informs society, and technologically feasible, we used a driver-pressure-state-impact-response (DPSIR) model. We (1) examined relevant international agreements to identify societal drivers and pressures on marine resources and ecosystems, (2) evaluated the temporal and spatial scales of variables measured by 100+ observing programs, and (3) analysed the impact and scalability of these variables and how they contribute to address societal and scientific issues. EOVs were related to the status of ecosystem components (phytoplankton and zooplankton biomass and diversity, and abundance and distribution of fish, marine turtles, birds and mammals), and to the extent and health of ecosystems (cover and composition of hard coral, seagrass, mangrove and macroalgal canopy). Benthic invertebrate abundance and distribution and microbe diversity and biomass were identified as emerging EOVs to be developed based on emerging requirements and new technologies. The temporal scale at which any shifts in biological systems will be detected will vary across the EOVs, the properties being monitored and the length of the existing time-series. Global implementation to deliver useful products will require collaboration of the scientific and policy sectors and a significant commitment to improve human and infrastructure capacity across the globe, including the development of new, more automated observing technologies, and encouraging the application of international standards and best practices.

Mass extinction in tetraodontiform fishes linked to the Palaeocene-Eocene thermal maximum

Integrative evolutionary analyses based upon fossil and extant species provide a powerful approach for understanding past diversification events and for assessing the tempo of evolution across the Tree of Life. Herein, we demonstrate the importance of integrating fossil and extant species for inferring patterns of lineage diversification that would otherwise be masked in analyses that examine only one source of evidence. We infer the phylogeny and macroevolutionary history of the Tetraodontiformes (triggerfishes, pufferfishes and allies), a group with one of the most extensive fossil records among fishes. Our analyses combine molecular and morphological data, based on an expanded matrix that adds newly coded fossil species and character states. Beyond confidently resolving the relationships and divergence times of tetraodontiforms, our diversification analyses detect a major mass-extinction event during the Palaeocene-Eocene Thermal Maximum (PETM), followed by a marked increase in speciation rates. This pattern is consistently obtained when fossil and extant species are integrated, whereas examination of the fossil occurrences alone failed to detect major diversification changes during the PETM. When taking into account non-homogeneous models, our analyses also detect a rapid lineage diversification increase in one of the groups (tetraodontoids) during the middle Miocene, which is considered a key period in the evolution of reef fishes associated with trophic changes and ecological opportunity. In summary, our analyses show distinct diversification dynamics estimated from phylogenies and the fossil record, suggesting that different episodes shaped the evolution of tetraodontiforms during the Cenozoic.

Diversification Patterns of Lanternfishes Reveal Multiple Rate Shifts in a Critical Mesopelagic Clade Targeted for Human Exploitation

The mesopelagic (midwater) and deep-sea environments together comprise over 90% of the volume of the world ocean [1] and provide services that are only recently becoming recognized [2]. One of the most significant of these services relates to midwater fish biomass, recently estimated to be two orders of magnitude larger than the current worldwide fisheries catch [3, 4]. Calls to exploit midwater fish biomass have increased despite warnings about the unknown recovery potential of such organisms [2] and despite existing data suggesting that deep-sea fishes could be classified as endangered [5]. Here, to provide a null model for the respondability of midwater fishes, I use lanternfishes-which comprise the majority of worldwide midwater fish biomass [6]-to examine the diversification response of a critical midwater clade to oceanic changes over evolutionary timescales, including several extinction and turnover events. Using a time-calibrated molecular phylogeny based on seven autosomal protein-coding loci, with over 50% species sampling and three ingroup node calibrations, I show that lanternfishes exhibit a continuously increasing diversification rate, consistent with nonequilibrium speciation dynamics, and three major evolutionary rate shift locations with timing that is similar to those of marine clades in more well-known environments. These results suggest that lanternfish diversification patterns overlapped with major events in the physical partitioning of the ocean volume and that the clade has responded positively to a range of pre-Anthropocene extinction drivers [7]. However, lanternfish respondability to modern extinction drivers-habitat loss and overexploitation-is best addressed with populational and ecological data and remains largely unknown.

Contrasting responses of functional diversity to major losses in taxonomic diversity

Taxonomic diversity of benthic marine invertebrate shelf species declines at present by nearly an order of magnitude from the tropics to the poles in each hemisphere along the latitudinal diversity gradient (LDG), most steeply along the western Pacific where shallow-sea diversity is at its tropical maximum. In the Bivalvia, a model system for macroevolution and macroecology, this taxonomic trend is accompanied by a decline in the number of functional groups and an increase in the evenness of taxa distributed among those groups, with maximum functional evenness (FE) in polar waters of both hemispheres. In contrast, analyses of this model system across the two era-defining events of the Phanerozoic, the Permian-Triassic and Cretaceous-Paleogene mass extinctions, show only minor declines in functional richness despite high extinction intensities, resulting in a rise in FE owing to the persistence of functional groups. We hypothesize that the spatial decline of taxonomic diversity and increase in FE along the present-day LDG primarily reflect diversity-dependent factors, whereas retention of almost all functional groups through the two mass extinctions suggests the operation of diversity-independent factors. Comparative analyses of different aspects of biodiversity thus reveal strongly contrasting biological consequences of similarly severe declines in taxonomic diversity and can help predict the consequences for functional diversity among different drivers of past, present, and future biodiversity loss.

Critical factors for the recovery of marine mammals

{en} Over the past decades, much research has focused on understanding the critical factors for marine extinctions with the aim of preventing further species losses in the oceans. Although conservation and management strategies are enabling several species and populations to recover, others remain at low abundance levels or continue to decline. To understand these discrepancies, we used a published database on abundance trends of 137 populations of marine mammals worldwide and compiled data on 28 potentially critical factors for recovery. We then applied random forests and additive mixed models to determine which intrinsic and extrinsic factors are critical for the recovery of marine mammals. A mix of life-history characteristics, ecological traits, phylogenetic relatedness, population size, geographic range, human impacts, and management efforts explained why populations recovered or not. Consistently, species with lower age at maturity and intermediate habitat area were more likely to recover, which is consistent with life-history and ecological theory. Body size, trophic level, social interactions, dominant habitat, ocean basin, and habitat disturbance also explained some differences in recovery patterns. Overall, a variety of intrinsic and extrinsic factors were important for species' recovery, pointing to cumulative effects. Our results provide insight for improving conservation and management strategies to enhance recoveries in the future.

Adding fossil occupancy trajectories to the assessment of modern extinction risk

Besides helping to identify species traits that are commonly linked to extinction risk, the fossil record may also be directly relevant for assessing the extinction risk of extant species. Standing geographical distribution or occupancy is a strong predictor of both recent and past extinction risk, but the role of changes in occupancy is less widely assessed. Here we demonstrate, based on the Cenozoic fossil record of marine species, that both occupancy and its temporal trajectory are significant determinants of risk. Based on extinct species we develop a model on the additive and interacting effects of occupancy and its temporal changes on extinction risk. We use this model to predict extinction risk of extant species. The predictions suggest a moderate risk for marine species on average. However, some species seem to be on a long-term decline and potentially at a latent extinction risk, which is not considered in current risk assessments.

Linking speciation to extinction: Diversification raises contemporary extinction risk in amphibians

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

Linking species habitat and past palaeoclimatic events to evolution of the teleost innate immune system

Host-intrinsic factors as well as environmental changes are known to be strong evolutionary drivers defining the genetic foundation of immunity. Using a novel set of teleost genomes and a time-calibrated phylogeny, we here investigate the family of Toll-like receptor (TLR) genes and address the underlying evolutionary processes shaping the diversity of the first-line defence. Our findings reveal remarkable flexibility within the evolutionary design of teleost innate immunity characterized by prominent TLR gene losses and expansions. In the order of Gadiformes, expansions correlate with the loss of major histocompatibility complex class II (MHCII) and diversifying selection analyses support that this has fostered new immunological innovations in TLRs within this lineage. In teleosts overall, TLRs expansions correlate with species latitudinal distributions and maximum depth. By contrast, lineage-specific gene losses overlap with well-described changes in palaeoclimate (global ocean anoxia) and past Atlantic Ocean geography. In conclusion, we suggest that the evolvability of the teleost immune system has most likely played a prominent role in the survival and successful radiation of this lineage.

Black-swan events in animal populations

Black swans are improbable events that nonetheless occur-often with profound consequences. Such events drive important transitions in social systems (e.g., banking collapses) and physical systems (e.g., earthquakes), and yet it remains unclear the extent to which ecological population numbers buffer or suffer from such extremes. Here, we estimate the prevalence and direction of black-swan events (heavy-tailed process noise) in 609 animal populations after accounting for population dynamics (productivity, density dependence, and typical stochasticity). We find strong evidence for black-swan events in [Formula: see text]4% of populations. These events occur most frequently for birds (7%), mammals (5%), and insects (3%) and are not explained by any life-history covariates but tend to be driven by external perturbations such as climate, severe winters, predators, parasites, or the combined effect of multiple factors. Black-swan events manifest primarily as population die-offs and crashes (86%) rather than unexpected increases, and ignoring heavy-tailed process noise leads to an underestimate in the magnitude of population crashes. We suggest modelers consider heavy-tailed, downward-skewed probability distributions, such as the skewed Student [Formula: see text] used here, when making forecasts of population abundance. Our results demonstrate the importance of both modeling heavy-tailed downward events in populations, and developing conservation strategies that are robust to ecological surprises.

Successive Losses of Central Immune Genes Characterize the Gadiformes' Alternate Immunity

Great genetic variability among teleost immunomes, with gene losses and expansions of central adaptive and innate components, has been discovered through genome sequencing over the last few years. Here, we demonstrate that the innate Myxovirus resistance gene (Mx) is lost from the ancestor of Gadiformes and the closely related Stylephorus chordatus, thus predating the loss of Major Histocompatibility Complex class II (MHCII) in Gadiformes. Although the functional implication of Mx loss is still unknown, we demonstrate that this loss is one of several ancient events appearing in successive order throughout the evolution of teleost immunity. In particular, we find that the loss of Toll-like receptor 5 predates the loss of Mx involving the entire Paracanthopterygii lineage. Using a time-calibrated phylogeny, we show that loss of MHCII and Mx overlap with major paleoclimatic and geological events indicating that these genetic changes were adaptive responses to the changing environment at the time.

Patterns, Causes, and Consequences of Anthropocene Defaunation

Anthropocene defaunation, the global extinction of faunal species and populations and the decline in abundance of individuals within populations, has been predominantly documented in terrestrial ecosystems, but indicators suggest defaunation has been more severe in freshwater ecosystems. Marine defaunation is in a more incipient stage, yet pronounced effects are already apparent and its rapid acceleration seems likely. Defaunation now impacts the planet's wildlife with profound cascading consequences, ranging from local to global coextinctions of interacting species to the loss of ecological services critical for humanity. Slowing defaunation will require aggressively reducing animal overexploitation and habitat destruction; mitigating climate disruption; and stabilizing the impacts of human population growth and uneven resource consumption. Given its omnipresence, defaunation should receive status of major global environmental change and should be addressed with the same urgency as deforestation, pollution, and climatic change. Global action is needed to prevent defaunation's current trajectory from catalyzing the planet's sixth major extinction.

The fossil record of the sixth extinction

Comparing the magnitude of the current biodiversity crisis with those in the fossil record is difficult without an understanding of differential preservation. Integrating data from palaeontological databases with information on IUCN status, ecology and life history characteristics of contemporary mammals, we demonstrate that only a small and biased fraction of threatened species (< 9%) have a fossil record, compared with 20% of non-threatened species. We find strong taphonomic biases related to body size and geographic range. Modern species with a fossil record tend to be large and widespread and were described in the 19(th) century. The expected magnitude of the current extinction based only on species with a fossil record is about half of that of one based on all modern species; values for genera are similar. The record of ancient extinctions may be similarly biased, with many species having originated and gone extinct without leaving a tangible record.

Eutrophication, microbial-sulfate reduction and mass extinctions

In post-Cambrian time, life on Earth experienced 5 major extinction events, likely instigated by adverse environmental conditions. Biodiversity loss among marine taxa, for at least 3 of these mass extinction events (Late Devonian, end-Permian and end-Triassic), has been connected with widespread oxygen-depleted and sulfide-bearing marine water. Furthermore, geochemical and sedimentary evidence suggest that these events correlate with rather abrupt climate warming and possibly increased terrestrial weathering. This suggests that biodiversity loss may be triggered by mechanisms intrinsic to the Earth system, notably, the biogeochemical sulfur and carbon cycle. This climate warming feedback produces large-scale eutrophication on the continental shelf, which, in turn, expands oxygen minimum zones by increased respiration, which can turn to a sulfidic state by increased microbial-sulfate reduction due to increased availability of organic matter. A plankton community turnover from a high-diversity eukaryote to high-biomass bacterial dominated food web is the catalyst proposed in this anoxia-extinction scenario and stands in stark contrast to the postulated productivity collapse suggested for the end-Cretaceous mass extinction. This cascade of events is relevant for the future ocean under predicted greenhouse driven climate change. The exacerbation of anoxic "dead" zones is already progressing in modern oceanic environments, and this is likely to increase due to climate induced continental weathering and resulting eutrophication of the oceans.

Marine extinction risk shaped by trait-environment interactions over 500 million years

Perhaps the most pressing issue in predicting biotic responses to present and future global change is understanding how environmental factors shape the relationship between ecological traits and extinction risk. The fossil record provides millions of years of insight into how extinction selectivity (i.e., differential extinction risk) is shaped by interactions between ecological traits and environmental conditions. Numerous paleontological studies have examined trait-based extinction selectivity; however, the extent to which these patterns are shaped by environmental conditions is poorly understood due to a lack of quantitative synthesis across studies. We conducted a meta-analysis of published studies on fossil marine bivalves and gastropods that span 458 million years to uncover how global environmental and geochemical changes covary with trait-based extinction selectivity. We focused on geographic range size and life habit (i.e., infaunal vs. epifaunal), two of the most important and commonly examined predictors of extinction selectivity. We used geochemical proxies related to global climate, as well as indicators of ocean acidification, to infer average global environmental conditions. Life-habit selectivity is weakly dependent on environmental conditions, with infaunal species relatively buffered from extinction during warmer climate states. In contrast, the odds of taxa with broad geographic ranges surviving an extinction (>2500 km for genera, >500 km for species) are on average three times greater than narrow-ranging taxa (estimate of odds ratio: 2.8, 95% confidence interval = 2.3-3.5), regardless of the prevailing global environmental conditions. The environmental independence of geographic range size extinction selectivity emphasizes the critical role of geographic range size in setting conservation priorities.

Combining marine macroecology and palaeoecology in understanding biodiversity: microfossils as a model

There is growing interest in the integration of macroecology and palaeoecology towards a better understanding of past, present, and anticipated future biodiversity dynamics. However, the empirical basis for this integration has thus far been limited. Here we review prospects for a macroecology-palaeoecology integration in biodiversity analyses with a focus on marine microfossils [i.e. small (or small parts of) organisms with high fossilization potential, such as foraminifera, ostracodes, diatoms, radiolaria, coccolithophores, dinoflagellates, and ichthyoliths]. Marine microfossils represent a useful model system for such integrative research because of their high abundance, large spatiotemporal coverage, and good taxonomic and temporal resolution. The microfossil record allows for quantitative cross-scale research designs, which help in answering fundamental questions about marine biodiversity, including the causes behind similarities in patterns of latitudinal and longitudinal variation across taxa, the degree of constancy of observed gradients over time, and the relative importance of hypothesized drivers that may explain past or present biodiversity patterns. The inclusion of a deep-time perspective based on high-resolution microfossil records may be an important step for the further maturation of macroecology. An improved integration of macroecology and palaeoecology would aid in our understanding of the balance of ecological and evolutionary mechanisms that have shaped the biosphere we inhabit today and affect how it may change in the future.

Response of beta diversity to pulses of Ordovician-Silurian mass extinction

Ecologists are increasingly using the fossil record of mass extinction to build predictive models for the ongoing biodiversity crisis. During mass extinctions, major depletions in global (i.e., gamma) diversity may reflect decrease in alpha diversity (i.e., local assemblages support fewer taxa), and/or decrease in beta diversity (such that similar pools of taxa are common to a greater number of local areas). Contrasting the effects of extinction on alpha and beta diversity is therefore central to understanding how global richness becomes depleted over these critical events. Here we investigate the spatial effects of mass extinction by examining changes in alpha, beta, and gamma diversity in brachiopod communities over both pulses of Ordovician-Silurian extinction (-445.2 and -438.8 million years ago), which had dramatically different causal mechanisms. We furthermore reconstruct geographic range sizes for brachiopod genera to test competing models for drivers of beta diversity change. We find that: (1) alpha and beta diversity respond differently to extinction; (2) these responses differ between pulses of extinction; (3) changes in beta diversity associated with extinction are accompanied by changes in geographic range size; and (4) changes in global beta diversity were driven by the extinction of taxa with statistically small and large ranges, rather than range expansion/contraction in taxa that survive into the aftermath. A symptom of ongoing biotic crisis may therefore be the extinction of specific narrow- or wide-ranging taxa, rather than the global proliferation of opportunistic and "disaster" forms. In addition, our results illustrate that changes in beta diversity on these longer timescales may largely be dictated by emplacement and removal of barriers to dispersal. Lastly, this study reinforces the utility of the fossil record in addressing questions surrounding the role of global-scale processes (such as mass extinctions) in sculpting and assembling regional biotas.

Conservation archaeogenomics: ancient DNA and biodiversity in the Anthropocene

There is growing consensus that we have entered the Anthropocene, a geologic epoch characterized by human domination of the ecosystems of the Earth. With the future uncertain, we are faced with understanding how global biodiversity will respond to anthropogenic perturbations. The archaeological record provides perspective on human-environment relations through time and across space. Ancient DNA (aDNA) analyses of plant and animal remains from archaeological sites are particularly useful for understanding past human-environment interactions, which can help guide conservation decisions during the environmental changes of the Anthropocene. Here, we define the emerging field of conservation archaeogenomics, which integrates archaeological and genomic data to generate baselines or benchmarks for scientists, managers, and policy-makers by evaluating climatic and human impacts on past, present, and future biodiversity.

Deciphering the evolution of birdwing butterflies 150 years after Alfred Russel Wallace

One hundred and fifty years after Alfred Wallace studied the geographical variation and species diversity of butterflies in the Indomalayan-Australasian Archipelago, the processes responsible for their biogeographical pattern remain equivocal. We analysed the macroevolutionary mechanisms accounting for the temporal and geographical diversification of the charismatic birdwing butterflies (Papilionidae), a major focus of Wallace's pioneering work. Bayesian phylogenetics and dating analyses of the birdwings were conducted using mitochondrial and nuclear genes. The combination of maximum likelihood analyses to estimate biogeographical history and diversification rates reveals that diversity-dependence processes drove the radiation of birdwings, and that speciation was often associated with founder-events colonizing new islands, especially in Wallacea. Palaeo-environment diversification models also suggest that high extinction rates occurred during periods of elevated sea level and global warming. We demonstrated a pattern of spatio-temporal habitat dynamics that continuously created or erased habitats suitable for birdwing biodiversity. Since birdwings were extinction-prone during the Miocene (warmer temperatures and elevated sea levels), the cooling period after the mid-Miocene climatic optimum fostered birdwing diversification due to the release of extinction. This also suggests that current global changes may represent a serious conservation threat to this flagship group.

Biology in the Anthropocene: Challenges and insights from young fossil records

With overwhelming evidence of change in habitats, biologists today must assume that few, if any, study areas are natural and that biological variability is superimposed on trends rather than stationary means. Paleobiological data from the youngest sedimentary record, including death assemblages actively accumulating on modern land surfaces and seabeds, provide unique information on the status of present-day species, communities, and biomes over the last few decades to millennia and on their responses to natural and anthropogenic environmental change. Key advances have established the accuracy and resolving power of paleobiological information derived from naturally preserved remains and of proxy evidence for environmental conditions and sample age so that fossil data can both implicate and exonerate human stressors as the drivers of biotic change and permit the effects of multiple stressors to be disentangled. Legacy effects from Industrial and even pre-Industrial anthropogenic extirpations, introductions, (de)nutrification, and habitat conversion commonly emerge as the primary factors underlying the present-day status of populations and communities; within the last 2 million years, climate change has rarely been sufficient to drive major extinction pulses absent other human pressures, which are now manifold. Young fossil records also provide rigorous access to the baseline composition and dynamics of modern-day biota under pre-Industrial conditions, where insights include the millennial-scale persistence of community structures, the dominant role of physical environmental conditions rather than biotic interactions in determining community composition and disassembly, and the existence of naturally alternating states.

Fossils, phylogenies, and the challenge of preserving evolutionary history in the face of anthropogenic extinctions

Anthropogenic impacts are endangering many long-lived species and lineages, possibly leading to a disproportionate loss of existing evolutionary history (EH) in the future. However, surprisingly little is known about the loss of EH during major extinctions in the geological past, and thus we do not know whether human impacts are pruning the tree of life in a manner that is unique in the history of life. A major impediment to comparing the loss of EH during past and current extinctions is the conceptual difference in how ages are estimated from paleontological data versus molecular phylogenies. In the former case the age of a taxon is its entire stratigraphic range, regardless of how many daughter taxa it may have produced; for the latter it is the time to the most recent common ancestor shared with another extant taxon. To explore this issue, we use simulations to understand how the loss of EH is manifested in the two data types. We also present empirical analyses of the marine bivalve clade Pectinidae (scallops) during a major Plio-Pleistocene extinction in California that involved a preferential loss of younger species. Overall, our results show that the conceptual difference in how ages are estimated from the stratigraphic record versus molecular phylogenies does not preclude comparisons of age selectivities of past and present extinctions. Such comparisons not only provide fundamental insights into the nature of the extinction process but should also help improve evolutionarily informed models of conservation prioritization.

Convergence, divergence, and parallelism in marine biodiversity trends: Integrating present-day and fossil data

Paleontological data provide essential insights into the processes shaping the spatial distribution of present-day biodiversity. Here, we combine biogeographic data with the fossil record to investigate the roles of parallelism (similar diversities reached via changes from similar starting points), convergence (similar diversities reached from different starting points), and divergence in shaping the present-day latitudinal diversity gradients of marine bivalves along the two North American coasts. Although both faunas show the expected overall poleward decline in species richness, the trends differ between the coasts, and the discrepancies are not explained simply by present-day temperature differences. Instead, the fossil record indicates that both coasts have declined in overall diversity over the past 3 My, but the western Atlantic fauna suffered more severe Pliocene-Pleistocene extinction than did the eastern Pacific. Tropical western Atlantic diversity remains lower than the eastern Pacific, but warm temperate western Atlantic diversity recovered to exceed that of the temperate eastern Pacific, either through immigration or in situ origination. At the clade level, bivalve families shared by the two coasts followed a variety of paths toward today's diversities. The drivers of these lineage-level differences remain unclear, but species with broad geographic ranges during the Pliocene were more likely than geographically restricted species to persist in the temperate zone, suggesting that past differences in geographic range sizes among clades may underlie between-coast contrasts. More detailed comparative work on regional extinction intensities and selectivities, and subsequent recoveries (by in situ speciation or immigration), is needed to better understand present-day diversity patterns and model future changes.

Extinctions. Paleontological baselines for evaluating extinction risk in the modern oceans

Marine taxa are threatened by anthropogenic impacts, but knowledge of their extinction vulnerabilities is limited. The fossil record provides rich information on past extinctions that can help predict biotic responses. We show that over 23 million years, taxonomic membership and geographic range size consistently explain a large proportion of extinction risk variation in six major taxonomic groups. We assess intrinsic risk-extinction risk predicted by paleontologically calibrated models-for modern genera in these groups. Mapping the geographic distribution of these genera identifies coastal biogeographic provinces where fauna with high intrinsic risk are strongly affected by human activity or climate change. Such regions are disproportionately in the tropics, raising the possibility that these ecosystems may be particularly vulnerable to future extinctions. Intrinsic risk provides a prehuman baseline for considering current threats to marine biodiversity.

Phytoplankton adapt to changing ocean environments

Model projections indicate that climate change may dramatically restructure phytoplankton communities, with cascading consequences for marine food webs. It is currently not known whether evolutionary change is likely to be able to keep pace with the rate of climate change. For simplicity, and in the absence of evidence to the contrary, most model projections assume species have fixed environmental preferences and will not adapt to changing environmental conditions on the century scale. Using 15 y of observations from Station CARIACO (Carbon Retention in a Colored Ocean), we show that most of the dominant species from a marine phytoplankton community were able to adapt their realized niches to track average increases in water temperature and irradiance, but the majority of species exhibited a fixed niche for nitrate. We do not know the extent of this adaptive capacity, so we cannot conclude that phytoplankton will be able to adapt to the changes anticipated over the next century, but community ecosystem models can no longer assume that phytoplankton cannot adapt.

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.

Evolutionary and biogeographical patterns of barnacles from deep-sea hydrothermal vents

The characterization of evolutionary and biogeographical patterns is of fundamental importance to identify factors driving biodiversity. Due to their widespread but discontinuous distribution, deep-sea hydrothermal vent barnacles represent an excellent model for testing biogeographical hypotheses regarding the origin, dispersal and diversity of modern vent fauna. Here, we characterize the global genetic diversity of vent barnacles to infer their time of radiation, place of origin, mode of dispersal and diversification. Our approach was to target a suite of multiple loci in samples representing seven of the eight described genera. We also performed restriction-site associated DNA sequencing on individuals from each species. Phylogenetic inferences and topology hypothesis tests indicate that vent barnacles have colonized deep-sea hydrothermal vents at least twice in history. Consistent with preliminary estimates, we find a likely radiation of barnacles in vent ecosystems during the Cenozoic. Our analyses suggest that the western Pacific was the place of origin of the major vent barnacle lineage, followed by circumglobal colonization eastwards through the Southern Hemisphere during the Neogene. The inferred time of radiation rejects the classic hypotheses of antiquity of vent taxa. The timing and the mode of origin, radiation and dispersal are consistent with recent inferences made for other deep-sea taxa, including nonvent species, and are correlated with the occurrence of major geological events and mass extinctions. Thus, we suggest that the geological processes and dispersal mechanisms discussed here can explain the current distribution patterns of many other marine taxa and have played an important role shaping deep-sea faunal diversity. These results also constitute the critical baseline data with which to assess potential effects of anthropogenic disturbances on deep-sea ecosystems.

K-Pg events facilitated lineage transitions between terrestrial and aquatic ecosystems

We use dated phylogenetic trees for tetrapod vertebrates to identify lineages that shifted between terrestrial and aquatic ecosystems in terms of feeding or development, and to assess the timing of such events. Both stem and crown lineage ages indicate a peak in transition events in correspondence with the K-Pg mass extinction. This meets the prediction that changes in competitive pressure and resource availability following mass extinction events should facilitate such transitions.

Out of sight, out of mind: threats to the marine biodiversity of the Canary Islands (NE Atlantic Ocean)

Lack of knowledge of the marine realm may bias our perception of the current status and threats to marine biodiversity. Less than 10% of all ecological literature is related to the ocean, and the information we have on marine species that are threatened or on the verge of extinction is scarce. This lack of information is particularly critical for isolated areas such as oceanic archipelagos. Here we review published and grey literature on the current status of marine organisms in the Canary Islands as a case description of the consequences that current out-of-sight out-of-mind attitudes may have on this unique environment. Global change, as represented by coastal development, pollution, exotic species and climate change, are currently affecting the distribution and abundance of Canarian marine organisms, and pose multiple threats to local species and communities. Environmental risks are significant at community and species levels, particularly for threatened species. Failure to address these trends will result in shifts in local biodiversity with important ecological, social, and economic consequences. Scientists, policy makers, educators, and relevant societal groups need to collaborate to reverse deleterious coastal biodiversity trends.

The impact of 850,000 years of climate changes on the structure and dynamics of mammal food webs

Most evidence of climate change impacts on food webs comes from modern studies and little is known about how ancient food webs have responded to climate changes in the past. Here, we integrate fossil evidence from 71 fossil sites, body-size relationships and actualism to reconstruct food webs for six large mammal communities that inhabited the Iberian Peninsula at different times during the Quaternary. We quantify the long-term dynamics of these food webs and study how their structure changed across the Quaternary, a period for which fossil data and climate changes are well known. Extinction, immigration and turnover rates were correlated with climate changes in the last 850 kyr. Yet, we find differences in the dynamics and structural properties of Pleistocene versus Holocene mammal communities that are not associated with glacial-interglacial cycles. Although all Quaternary mammal food webs were highly nested and robust to secondary extinctions, general food web properties changed in the Holocene. These results highlight the ability of communities to re-organize with the arrival of phylogenetically similar species without major structural changes, and the impact of climate change and super-generalist species (humans) on Iberian Holocene mammal communities.

Climate-change impacts on sandy-beach biota: crossing a line in the sand

Sandy ocean beaches are iconic assets that provide irreplaceable ecosystem services to society. Despite their great socioeconomic importance, beaches as ecosystems are severely under-represented in the literature on climate-change ecology. Here, we redress this imbalance by examining whether beach biota have been observed to respond to recent climate change in ways that are consistent with expectations under climate change. We base our assessments on evidence coming from case studies on beach invertebrates in South America and on sea turtles globally. Surprisingly, we find that observational evidence for climate-change responses in beach biota is more convincing for invertebrates than for highly charismatic turtles. This asymmetry is paradoxical given the better theoretical understanding of the mechanisms by which turtles are likely to respond to changes in climate. Regardless of this disparity, knowledge of the unique attributes of beach systems can complement our detection of climate-change impacts on sandy-shore invertebrates to add rigor to studies of climate-change ecology for sandy beaches. To this end, we combine theory from beach ecology and climate-change ecology to put forward a suite of predictive hypotheses regarding climate impacts on beaches and to suggest ways that these can be tested. Addressing these hypotheses could significantly advance both beach and climate-change ecology, thereby progressing understanding of how future climate change will impact coastal ecosystems more generally.