Reconstructing past species assemblages reveals the changing patterns and drivers of extinction through time

Predicting future species extinctions from patterns of past extinctions or current threat status relies on the assumption that the taxonomic and biological selectivity of extinction is consistent through time. If the driving forces of extinction change through time, this assumption may be unrealistic. Testing the consistency of extinction patterns between the past and the present has been difficult, because the phylogenetically explicit methods used to model present-day extinction risk typically cannot be applied to the data from the fossil record. However, the detailed historical and fossil records of the New Zealand avifauna provide a unique opportunity to reconstruct a complete, large faunal assemblage for different periods in the past. Using the first complete phylogeny of all known native New Zealand bird species, both extant and extinct, we show how the taxonomic and phylogenetic selectivity of extinction, and biological correlates of extinction, change from the pre-human period through Polynesian and European occupation, to the present. These changes can be explained both by changes in primary threatening processes, and by the operation of extinction filter effects. The variable patterns of extinction through time may confound attempts to identify risk factors that apply across time periods, and to infer future species declines from past extinction patterns and current threat status.     

Quantifying the Extent of North American Mammal Extinction Relative to the Pre-Anthropogenic Baseline

Earth has experienced five major extinction events in the past 450 million years. Many scientists suggest we are now witnessing a sixth, driven by human impacts. However, it has been difficult to quantify the real extent of the current extinction episode, either for a given taxonomic group at the continental scale or for the worldwide biota, largely because comparisons of pre-anthropogenic and anthropogenic biodiversity baselines have been unavailable. Here, we compute those baselines for mammals of temperate North America, using a sampling-standardized rich fossil record to reconstruct species-area relationships for a series of time slices ranging from 30 million to 500 years ago. We show that shortly after humans first arrived in North America, mammalian diversity dropped to become at least 15%–42% too low compared to the “normal” diversity baseline that had existed for millions of years. While the Holocene reduction in North American mammal diversity has long been recognized qualitatively, our results provide a quantitative measure that clarifies how significant the diversity reduction actually was. If mass extinctions are defined as loss of at least 75% of species on a global scale, our data suggest that North American mammals had already progressed one-fifth to more than halfway (depending on biogeographic province) towards that benchmark, even before industrialized society began to affect them. Data currently are not available to make similar quantitative estimates for other continents, but qualitative declines in Holocene mammal diversity are also widely recognized in South America, Eurasia, and Australia. Extending our methodology to mammals in these areas, as well as to other taxa where possible, would provide a reasonable way to assess the magnitude of global extinction, the biodiversity impact of extinctions of currently threatened species, and the efficacy of conservation efforts into the future.     

Re-assessing current extinction rates

There is a widespread belief that we are experiencing a mass extinction event similar in severity to previous mass extinction events in the last 600 million years where up to 95% of species disappeared. This paper reviews evidence for current extinctions and different methods of assessing extinction rates including species–area relationships and loss of tropical forests, changing threat status of species, co-extinction rates and modelling the impact of climate change. For 30 years some have suggested that extinctions through tropical forest loss are occurring at a rate of up to 100 species a day and yet less than 1,200 extinctions have been recorded in the last 400 years. Reasons for low number of identified global extinctions are suggested here and include success in protecting many endangered species, poor monitoring of most of the rest of species and their level of threat, extinction debt where forests have been lost but species still survive, that regrowth forests may be important in retaining ‘old growth’ species, fewer co-extinctions of species than expected, and large differences in the vulnerability of different taxa to extinction threats. More recently, others have suggested similar rates of extinction to earlier estimates but with the key cause of extinction being climate change, and in particular rising temperatures, rather than deforestation alone. Here I suggest that climate change, rather than deforestation is likely to bring about such high levels of extinction since the impacts of climate change are local to global and that climate change is acting synergistically with a range of other threats to biodiversity including deforestation.     

How humans drive speciation as well as extinction

A central topic for conservation science is evaluating how human activities influence global species diversity. Humanity exacerbates extinction rates. But by what mechanisms does humanity drive the emergence of new species? We review human-mediated speciation, compare speciation and known extinctions, and discuss the challenges of using net species diversity as a conservation objective. Humans drive rapid evolution through relocation, domestication, hunting and novel ecosystem creation—and emerging technologies could eventually provide additional mechanisms. The number of species relocated, domesticated and hunted during the Holocene is of comparable magnitude to the number of observed extinctions. While instances of human-mediated speciation are known, the overall effect these mechanisms have upon speciation rates has not yet been quantified. We also explore the importance of anthropogenic influence upon divergence in microorganisms. Even if human activities resulted in no net loss of species diversity by balancing speciation and extinction rates, this would probably be deemed unacceptable. We discuss why, based upon ‘no net loss’ conservation literature—considering phylogenetic diversity and other metrics, risk aversion, taboo trade-offs and spatial heterogeneity. We conclude that evaluating speciation alongside extinction could result in more nuanced understanding of biosphere trends, clarifying what it is we actually value about biodiversity.     

Predation selectively culls medium-sized species from island mammal faunas

Globally, elevated extinction risk in mammals is strongly associated with large body size. However, in regions where introduced predators exert strong top-down pressure on mammal populations, the selectivity of extinctions may be skewed towards species of intermediate body size, leading to a hump-shaped relationship between size and extinction risk. The existence of this kind of extinction pattern, and its link to predation, has been contentious and difficult to demonstrate. Here, we test the hypothesis of a hump-shaped body size–extinction relationship, using a database of 927 island mammal populations. We show that the size-selectivity of extinctions on many islands has exceeded that expected under null models. On islands with introduced predators, extinctions are biased towards intermediate body sizes, but this bias does not occur on islands without predators. Hence, on islands with a large-bodied mammal fauna, predators are selectively culling species from the lower end of the size distribution, and on islands with a small-bodied fauna they are culling species from the upper end. These findings suggest that it will be difficult to use predictable generalizations about extinction patterns, such as a positive body size–extinction risk association, to anticipate future species declines and plan conservation strategies accordingly.     

CLIMATE PREDICTORS OF LATE QUATERNARY EXTINCTIONS

Between 50,000 and 3,000 years before present (BP) 65% of mammal genera weighing over 44 kg went extinct, together with a lower proportion of small mammals. Why species went extinct in such large numbers is hotly debated. One of the arguments proposes that climate changes underlie Late Quaternary extinctions, but global quantitative evidence for this hypothesis is still lacking. We test the potential role of global climate change on the extinction of mammals during the Late Quaternary. Our results suggest that continents with the highest climate footprint values, in other words, with climate changes of greater magnitudes during the Late Quaternary, witnessed more extinctions than continents with lower climate footprint values, with the exception of South America. Our results are consistent across species with different body masses, reinforcing the view that past climate changes contributed to global extinctions. Our model outputs, the climate change footprint dataset, provide a new research venue to test hypotheses about biodiversity dynamics during the Late Quaternary from the genetic to the species richness level.     

The present, past and future of human-caused extinctions

This paper re-evaluates whether we are really at the start of a mass extinction caused by humans. I consider the present, past and future of human-caused extinctions. As regards the present, estimates of extinction rates based on Red Data Books underestimate real values by a large factor, because the books evaluate only those species that have attracted specific attention and searches. Especially in tropical areas with few resident biologists, many poorly known species go extinct without having been the object of specific attention, and others disappear even before being described. A 'green list' of species known to be secure is needed to complement 'red books' of species known to be extinct. As regards the past, it is now clear that the first arrival of humans at any oceanic island with no previous human inhabitants has always precipitated a mass extinction in the island biota. Well-known victims include New Zealand's moas, Madagascar's giant lemurs, and scores of bird species on Hawaii and other tropical Pacific islands. Late-Pleistocene or Holocene extinctions of large mammals after the first arrival of humans in North America, South America and Australia may also have been caused by humans. Hence human-caused mass extinction is not a hypothesis for the future but an event that has been underway for thousands of years. As regards the future, consideration of the main mechanisms of human-caused extinctions (overhunting, effects of introduced species, habitat destruction, and secondary ripple effects) indicates that the rate of extinction is accelerating.(ABSTRACT TRUNCATED AT 250 WORDS)     

Inconsistent detection of extinction debts using different methods

The extinction debt, delayed species extinctions following landscape degradation, is a widely discussed concept. But a consensus about the prevalence of extinctions debts is hindered by a multiplicity of methods and a lack of comparisons among habitats. We applied three contrasting species–area relationship methods to test for plant community extinction debts in three habitats which had different degradation histories over the last century: calcareous grassland, heathland and woodland. These methods differ in their data requirements, with the first two using information on past and current habitat area alongside current species richness, whilst the last method also requires data on past species richness. The most data‐intensive, and hence arguably most reliable method, identified extinction debts across all habitats for specialist species, whilst the other methods did not. All methods detected an extinction debt in calcareous grassland, which had undergone the most severe degradation. We conclude that some methods failed to detect an extinction debt, particularly in habitats that have undergone moderate degradation. Data on past species numbers are required for the most reliable method; as such data are rare, extinction debts may be under‐reported.     

Atmospheric deposition of nutrients to the North Atlantic Basin

Atmospheric chemical models are used to estimate the deposition rate of various inorganic oxides of nitrogen (NO_y), reduced nitrogen species (NH_x) and mineral dust to the North Atlantic Ocean (NAO). The estimated deposition of NO_y to the NAO (excluding the coastal ocean) and the Caribbean is 360 × 10⁹ Moles-N m^–2 yr^–1 (5.0 Tg N); this is equivalent to about 13% of the estimated global emission rate (natural and anthropogenic) and a quarter of the emission rate from sources in North America and Europe. In the case of NH_x, 258 Moles-N m^–2 yr^–1 (3.6 Tg N) are deposited to the NAO and the Caribbean; this is about 6% of the global continental emissions. There is relatively little data on the deposition rate of organic nitrogen species; nonetheless, this evidence suggests that concentrations and deposition rates are comparable to those for inorganic nitrogen.Because of anthropogenic emissions, the present-day deposition rate of NO_y to the NAO is about five times greater than pre-industrial times largely due to emissions from energy production and biomass burning. The present-day emissions of NH_x from continental anthropogenic sources are about four-to-five times greater than natural sources, mostly due to the impact of emissions from animal wastes associated with food production. Indeed, present-day emissions of NH_x from animal waste are estimated to be about 10 times greater than the pre-human era. The deposition rate of mineral dust to the NAO is about 170 Tg yr^–1; deposited with the dust (assuming average crustal abundances) is about 6 Tg yr^–1 of Fe and 0.2 Tg yr^–1 of P. Dust deposition in the NAO is almost completely attributable to transport from North African sources; a substantial fraction of the dust over the NAO is probably mobilized as a consequence of land use practices in arid regions and, consequently, it should be regarded as a pollutant.     

Stepwise mass extinctions and impact events: Late Eocene to early Oligocene

Species ranges and relative abundances of dominant planktonic foraminifers of eight late Eocene to early Oligocene deep-sea sections are discussed to determine the nature and magnitude of extinctions and to investigate a possible cause-effect relationship between impact events and mass extinctions.Late Eocene extinctions are neither catastrophic nor mass extinctions, but occur stepwise over a period of about 1–2 million years. Four stepwise extinctions are identified at the middle/late Eocene boundary, the upperGlobigerapsis semiinvoluta zone, theG. semiinvoluta/Globorotalia cerroazulensis zone boundary and at the Eocene/Oligocene boundary. Each stepwise extinction event represents a time of accelerated faunal turnover characterized by generally less than 15% species extinct and in itself is not a significant extinction event. Relative species abundance changes at each stepwise extinction event, however, indicate a turnover involving > 60% of the population implying major environmental changes.There microtektite horizons are present in late Eocene sediments; one in the upperG. semiinvoluta zone (38.2 Ma) and two closely spaced layers only a few thousand years apart in the lower part of theGloborotalia cerroazulensis zone (37.2 Ma). Each of the three impact events appears to have had some effect on microplankton communities. However, the overriding factor that led to the stepwise mass extinctions may have been the result of multiple causes as there is no evidence of impacts associated with the step preceding, or the step following the deposition of the presently known microtektite horizons.     

Signatures of random and selective mass extinctions in phylogenetic tree balance

Current models of diversification with evolving speciation rates have trouble mimicking the extreme imbalance seen in estimated phylogenies. However, these models have not incorporated extinction. Here, we report on a simple simulation model that includes heritable and evolving speciation rates coupled with mass extinctions, Random (but not selective) mass extinctions, coupled with evolving among-lineage variation in speciation rates, increase imbalance of postrecovery clades. Thus, random mass extinctions are plausible contributors to the imbalance of modern clades. Paleontological evidence suggests that mass extinctions are often random with respect to ecological and morphological traits, consistent with our simulations. In contrast, evidence that the current anthropogenic mass extinction is phylogenetically selective suggests that the current extinction episode may be qualitatively different from past ones in the way it reshapes future biotas.     

Biogeography of Puerto Rican ants: a non-equilibrium case?

Ants were studied on Puerto Rico and 44 islands surrounding Puerto Rico. Habitat diversity was the best predictor of the number of species per island and the distributions of species followed a nested subset pattern. The number of extinctions per island was low, approximately 1–2 extinctions per island in a period of 18 years, and the rates of colonization seem to be greater than the extinction rates. Ant dynamics on these islands do not seem to support the basic MacArthur and Wilson model of island biogeography. The MacArthur and Wilson equilibrium is based on the notion that species are interchangeable, but some extinctions and colonizations can change the composition and number of species drastically.     

The form of direct interspecific competition modifies secondary extinction patterns in multi‐trophic food webs

Forcibly removing species from ecosystems has important consequences for the remaining assemblage, leading to changes in community structure, ecosystem functioning and secondary (cascading) extinctions. One key question that has arisen from single‐ and multi‐trophic ecosystem models is whether the secondary extinctions that occur within competitive communities (guilds) are also important in multi‐trophic ecosystems? The loss of consumer–resource links obviously causes secondary extinction of specialist consumers (topological extinctions), but the importance of secondary extinctions in multi‐trophic food webs driven by direct competitive exclusion remains unknown. Here I disentangle the effects of extinctions driven by basal competitive exclusion from those caused by trophic interactions in a multi‐trophic ecosystem (basal producers, intermediate and top consumers). I compared food webs where basal species either show diffuse (all species compete with each other identically: no within guild extinctions following primary extinction) or asymmetric competition (unequal interspecific competition: within guild extinctions are possible). Basal competitive exclusion drives extra extinction cascades across all trophic levels, with the effect amplified in larger ecosystems, though varying connectance has little impact on results. Secondary extinction patterns based on the relative abundance of the species lost in the primary extinction differ qualitatively between diffuse and asymmetric competition. Removing asymmetric basal species with low (high) abundance triggers fewer (more) secondary extinctions throughout the whole food web than removing diffuse basal species. Rare asymmetric competitors experience less pressure from consumers compared to rare diffuse competitors. Simulations revealed that diffuse basal species are never involved in extinction cascades, regardless of the trophic level of a primary extinction, while asymmetric competitors were. This work highlights important qualitative differences in extinction patterns that arise when different assumptions are made about the form of direct competition in multi‐trophic food webs.     

The shrinking ark: patterns of large mammal extinctions in India

Mammal extinctions are widespread globally, with South Asian species being most threatened. We examine local extinctions of 25 mammals in India. We use historical records to obtain a set of locations at which each species was known to have been present at some time in the last 200 years. We then use occupancy estimation models to draw inferences about current presence at these same locations based on field observations of local experts. We examine predictions about the influence of key factors such as protected areas, forest cover, elevation, human population density and cultural tolerance on species extinction. For all 25 species, estimated local extinction probabilities (referenced to a 100 year time frame) range between 0.14 and 0.96. Time elapsed since the historical occurrence record was an important determinant of extinction probability for 14 species. Protected areas are positively associated with lower extinction of 18 species, although many species occur outside them. We find evidence that higher proportion of forest cover is associated with lower extinction probabilities for seven species. However, for species that prefer open habitats (which have experienced intensive land-use change), forest cover alone appears insufficient to ensure persistence (the complement of extinction). We find that higher altitude is positively associated with lower extinction for eight species. Human population density is positively associated with extinction of 13 species. We find that ‘culturally tolerated’ species do exhibit higher persistence. Overall, large-bodied, rare and habitat specialist mammals tend to have higher extinction probabilities.     

The future of evolutionary diversity in reef corals

One-third of the world''s reef-building corals are facing heightened extinction risk from climate change and other anthropogenic impacts. Previous studies have shown that such threats are not distributed randomly across the coral tree of life, and future extinctions have the potential to disproportionately reduce the phylogenetic diversity of this group on a global scale. However, the impact of such losses on a regional scale remains poorly known. In this study, we use phylogenetic metrics in conjunction with geographical distributions of living reef coral species to model how extinctions are likely to affect evolutionary diversity across different ecoregions. Based on two measures—phylogenetic diversity and phylogenetic species variability—we highlight regions with the largest losses of evolutionary diversity and hence of potential conservation interest. Notably, the projected loss of evolutionary diversity is relatively low in the most species-rich areas such as the Coral Triangle, while many regions with fewer species stand to lose much larger shares of their diversity. We also suggest that for complex ecosystems like coral reefs it is important to consider changes in phylogenetic species variability; areas with disproportionate declines in this measure should be of concern even if phylogenetic diversity is not as impacted. These findings underscore the importance of integrating evolutionary history into conservation planning for safeguarding the future diversity of coral reefs.     

Effects of local extinction of the plains vizcacha (Lagostomus maximus) on vegetation patterns in semi-arid scrub

We studied spatial and temporal effects of local extinction of the plains vizcacha (Lagostomus maximus) on plant communities following widespread, natural extinctions of vizcachas in semi-arid scrub of Argentina. Spatial patterns in vegetation were examined along transects extending outward from active and extinct vizcacha burrow systems. Responses of vegetation to removal of vizcachas were assessed experimentally with exclosures and by documenting vegetation dynamics for 6 years following extinctions. Transect data demonstrated clear spatial patterns in plant cover, particularly an increase in perennial grasses, outward from active vizcacha burrows. These patterns were consistent with predictions based on foraging theory and studies that document grasses as the preferred food of vizcachas. Removal of vizcachas, experimentally and with extinctions, resulted in an immediate increase in perennial and annual forbs indicating that intense herbivory can depress forb cover, as well as grasses. After a 1-year lag following cessation of herbivory, cover of grasses increased. Forbs declined as grasses increased. The long-term effect of extinction of vizcachas was a conversion of colony sites from open patches dominated by forbs to dense bunch grass characteristic of the matrix. Major changes in vegetation occurred within 2–3 years after extinction, resulting in a large pulse of landscape change. However, some species of grasses were uncommon until 5–6 years after the vizcacha extinction. With extinction and colonization, vizcachas generate a dynamic mosaic of patches on the landscape and create temporal, as well as spatial, heterogeneity in semi-arid scrub.     

Lessons from a kill

During their colonization by Polynesians and later by Europeans, the Hawaiian islands suffered a massive loss of species. All the extinctions are indirectly attributable to human impact. Nonetheless, it has proved extremely difficult to specify which of several possible mechanisms caused each particular extinction. This seems to admit defeat in the battle to understand past extinctions. Such understanding could guide our efforts to protect species that are now threatened with extinction. Will it be easier to understand the causes of future extinctions? Surveys of future extinctions stress habitat destruction as the simple and dominant mechanism. This contrasts to its secondary (and generally confused) role in past extinctions. I argue that this contrast between the complexity of the past and the apparent simplicity of the future arises because extinction mechanisms are inherently synergistic. Once extensive species losses begin, it may be impossible to separate the mechanisms and thus manage an individual species as if its decline had a single cause.     

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

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

Anthropogenic stressors and riverine fish extinctions

Human activities are often implicated in the contemporary extinction of contemporary species. Concerning riverine fishes, the major biotic and abiotic threats widely cited include introduction of non-native species, habitat fragmentation and homogenization in stream flow dynamics due to the damming of rivers, dumping of organic loadings, degradation of the riverine habitat by agricultural practices and water abstraction for human and agricultural consumption. However, few studies have evaluated the role of each of these threats on fish extinction at large spatial scales. Focusing on Western Europe and the USA, two of the most heavily impacted regions on Earth, we quantify fish species loss per river basin and evaluate for the first time to what extent, if any, these threats have been promoting fish extinctions. We show that mean fish extinction rates during the last 110 years in both continents is ∼112 times higher than calculated natural extinction rates. However, we identified only weak effects of our selected anthropogenic stressors on fish extinctions. Only river fragmentation by dams and percentage of non-native species seem to be significant, although weak, drivers of fish species extinction. In our opinion, the most probable explanation for the weak effects found here comes from limitations of both biological and threats datasets currently available. Obtaining realistic estimates on both extinctions and anthropogenic threats in individual river basins is thus urgently needed.     

Extinction rates of the Meade Basin rodents: application to current biodiversity losses

Extinction rates for terrestrial rodent species from palaeontological sites in the Meade Basin of southwestern Kansas and an archaeological site in New Mexico are compared with extinction rates for modern rodents from locations affected by anthropogenic activities. Background extinction rates are defined as global extinctions occurring over proscribed intervals in the absence of significant environmental perturbations. Background rates for the Meade Basin are estimated at 0–~1.0 E/MSY (extinctions per million species years). Elevated rates from 1.4 to 6.25 E/MSY are associated with volcanic events and Late Pleistocene environmental change. These rates are considerably less than those for rodent extinction rates promoted by human activities during the Holocene, the latter ranging from 42.3 to 50,000 E/MSY.