The stratigraphy of mass extinction

Patterns of last occurrences of fossil species are often used to infer the tempo and timing of mass extinction, even though last occurrences generally precede the time of extinction. Numerical simulations with constant extinction demonstrate that last occurrences are not randomly distributed, but tend to cluster at subaerial unconformities, surfaces of forced regression, flooding surfaces and intervals of stratigraphical condensation, all of which occur in predictable stratigraphical positions. This clustering arises not only from hiatuses and non‐deposition, but also from changes in water depth. Simulations with intervals of elevated extinction cause such clusters of last occurrences to be enhanced within and below the interval of extinction, suggesting that the timing and magnitude of extinctions in these instances could be misinterpreted. With the possible exception of the end‐Cretaceous, mass extinctions in the fossil record are characterized by clusters of last occurrences at these sequence stratigraphical horizons. Although these clusters of last occurrences may represent brief pulses of elevated extinction, they are equally likely to form by stratigraphical processes during a protracted period (more than several hundred thousand years) of elevated extinction rate. Geochemical proxies of extinction causes are also affected similarly, suggesting that many local expressions of mass extinction should be re‐evaluated for the timing of extinction and its relation to environmental change. We propose three tests for distinguishing pulses of extinction from clusters of last occurrences produced by stratigraphical processes.     

How does climate change cause extinction?

Anthropogenic climate change is predicted to be a major cause of species extinctions in the next 100 years. But what will actually cause these extinctions? For example, will it be limited physiological tolerance to high temperatures, changing biotic interactions or other factors? Here, we systematically review the proximate causes of climate-change related extinctions and their empirical support. We find 136 case studies of climatic impacts that are potentially relevant to this topic. However, only seven identified proximate causes of demonstrated local extinctions due to anthropogenic climate change. Among these seven studies, the proximate causes vary widely. Surprisingly, none show a straightforward relationship between local extinction and limited tolerances to high temperature. Instead, many studies implicate species interactions as an important proximate cause, especially decreases in food availability. We find very similar patterns in studies showing decreases in abundance associated with climate change, and in those studies showing impacts of climatic oscillations. Collectively, these results highlight our disturbingly limited knowledge of this crucial issue but also support the idea that changing species interactions are an important cause of documented population declines and extinctions related to climate change. Finally, we briefly outline general research strategies for identifying these proximate causes in future studies.     

When can the cause of a population decline be determined?

Inferring the factors responsible for declines in abundance is a prerequisite to preventing the extinction of wild populations. Many of the policies and programmes intended to prevent extinctions operate on the assumption that the factors driving the decline of a population can be determined. Exogenous factors that cause declines in abundance can be statistically confounded with endogenous factors such as density dependence. To demonstrate the potential for confounding, we used an experiment where replicated populations were driven to extinction by gradually manipulating habitat quality. In many of the replicated populations, habitat quality and density dependence were confounded, which obscured causal inference. Our results show that confounding is likely to occur when the exogenous factors that are driving the decline change gradually over time. Our study has direct implications for wild populations, because many factors that could drive a population to extinction change gradually through time.     

Extinction

A significant proportion of conservationists' work is directed towards efforts to save disappearing species. This relies upon the belief that species extinction is undesirable. When justifications are offered for this belief, they very often rest upon the assumption that extinction brought about by humans is different in kind from other forms of extinction. This paper examines this assumption and reveals that there is indeed good reason to suppose current anthropogenic extinctions to be different in kind from extinctions brought about at other times or by other factors. Having considered – and rejected – quantity and rate of extinction as useful distinguishing factors, four alternative arguments are offered, each identifying a way in which anthropogenic extinction is significantly different from other forms of extinction, even mass extinction: (1) Humans are a different kind of natural cause from other causes of extinction; (2) Extinctions brought about by humans are uniquely persistent; (3) Anthropogenic extinctions are effectively random whereas past mass extinctions are rule-bound; (4) The impact of the current anthropogenic extinction event differs from the impact of other extinction events of the past, such that future recovery may not follow past patterns. Together, these four arguments suggest that the present-day extinction event brought about by humans may be unprecedented and that we cannot clearly extrapolate from past to present recovery from extinctions. Although insufficient as justification for the claim that present-day extinctions are undesirable, the arguments provide some ammunition for conservationists' conviction that species extinction – in which humans play an accelerating role – ought to be prevented.     

Environment,but not migration rate,influences extinction risk in experimental metapopulations

Ecological theory suggests that several demographic factors influence metapopulation extinction risk, including synchrony in population size between subpopulations, metapopulation size and the magnitude of fluctuations in population size. Theoretically, each of these is influenced by the rate of migration between subpopulations. Here we report on an experiment where we manipulated migration rate within metapopulations of the freshwater zooplankton Daphnia magna to examine how migration influenced each of these demographic variables, and subsequent effects on metapopulation extinction. In addition, our experimental procedures introduced unplanned but controlled differences between metapopulations in light intensity, enabling us to examine the relative influences of environmental and demographic factors. We found that increasing migration rate increased subpopulation synchrony. We failed to detect effects of migration on population size and fluctuations in population size at the metapopulation or subpopulation level, however. In contrast, light intensity did not influence synchrony, but was positively correlated with population size and negatively correlated with population fluctuation. Finally, synchrony did not influence time to extinction, while population size and the magnitude of fluctuations did. We conclude that environmental factors had a greater influence on extinction risk than demographic factors, and that metapopulation size and fluctuation were more important to extinction risk than metapopulation synchrony.     

Investigating age‐dependency of species extinction rates using dynamic survivorship analysis

Survivorship curves with taxon lifespans normalised to variations in the real‐time extinction rate (the ‘Corrected Survivorship Score’ technique) are plotted for various fossil groups. Of five groups tested at the ‘species level’ (strictly speaking, Linnean morphospecies), only the calcareous nannoplankton are found to have had a constant extinction probability with respect to morphospecies age. The planktonic foraminifer, trilobite, conodont and graptolite data all show a significant age‐dependent effect (convexity of survivorship curves), which reveals in each case a progressively increasing extinction probability as morphospecies became older. This effect is found to be much reduced for trilobite genera and absent for ammonoid families, suggesting that age‐dependency of extinction probability is primarily a characteristic of the species level in some, but not all groups. However, the pattern may be partly an artefact of taxonomic methodology. Morphospecies range data, which are gathered primarily for biostratigraphic purposes, are far from ideal for the purpose of survivorship analysis. Therefore, survivorship curves for a specially‐developed lineage phylogeny of Palaeogene planktonic foraminifera are also presented. These do not indicate a similar age‐dependency to the extinction probability with respect to either the terminal or non‐terminal lineages.     

The uncertain blitzkrieg of Pleistocene megafauna

We investigated, using meta‐analysis of empirical data and population modelling, plausible scenarios for the cause of late Pleistocene global mammal extinctions. We also considered the rate at which these extinctions may have occurred, providing a test of the so‐called ‘blitzkrieg’ hypothesis, which postulates a rapid, anthropogenically driven, extinction event. The empirical foundation for this work was a comprehensive data base of estimated body masses of mammals, comprising 198 extinct and 433 surviving species > 5 kg, which we compiled through an extensive literature search. We used mechanistic population modelling to simulate the role of human hunting efficiency, meat off‐take, relative naivety of prey to invading humans, variation in reproductive fitness of prey and deterioration of habitat quality (due to either anthropogenic landscape burning or climate change), and explored the capacity of different modelling scenarios to recover the observed empirical relationship between body mass and extinction proneness. For the best‐fitting scenarios, we calculated the rate at which the extinction event would have occurred. All of the modelling was based on sampling randomly from a plausible range of parameters (and their interactions), which affect human and animal population demographics. Our analyses of the empirical data base revealed that the relationship between body mass and extinction risk relationship increases continuously from small‐ to large‐sized animals, with no clear ‘megafaunal’ threshold. A logistic ancova model incorporating body mass and geography (continent) explains 92% of the variation in the observed extinctions. Population modelling demonstrates that there were many plausible mechanistic scenarios capable of reproducing the empirical body mass–extinction risk relationship, such as specific targeting of large animals by humans, or various combinations of habitat change and opportunistic hunting. Yet, given the current imperfect knowledge base, it is equally impossible to use modelling to isolate definitively any single scenario to explain the observed extinctions. However, one universal prediction, which applied in all scenarios in which the empirical distribution was correctly predicted, was for the extinctions to be rapid following human arrival and for surviving fauna to be suppressed below their pre‐‘blitzkrieg’ densities. In sum, human colonization in the late Pleistocene almost certainly triggered a ‘blitzkrieg’ of the ‘megafauna’, but the operational details remain elusive.     

Importance of metapopulation dynamics to explain fish persistence in a river system

1. Habitat modification and fragmentation are key factors responsible for fish population decline worldwide. Previous assessments documented a total of 72 species extinctions for the sole class of Actinopterygii. However, global extinctions are difficult to monitor or study based on fossil records. By contrast, local extinctions occurring at the population level are easier to study. Given this context, an important question relates to whether extinction dynamics studied at the local scale can provide useful information to understand extinctions occurring at larger scales. This would be the case if local extinctions were not balanced by recolonisation as in a classic metapopulation. Our aim is thus to explain the observed regional (per basin) persistence of 252 fish populations by testing contribution of local extinction rates and more generally metapopulation dynamics components.
2. To address this aim, we used the annual extinction probability of 252 regional populations of up to 14 species inhabiting 18 coastal rivers, which became isolated c. 8,500 years ago. We specifically compared extinction probabilities obtained by seven theoretical models to investigate whether regional extinction rates (i.e. loss from a river system) were correlated to local extinction rates (i.e. loss from an occupied site) and the role of metapopulation dynamics to explain regional persistence.
3. Using empirical data, we showed the importance of variables related to metapopulation dynamics to explain extinction rates across the 18 river systems. As expected, the regional extinction rate decreased with the colonisation rate, area, metapopulation size, and percentage of occupied localities. By contrast, an inconsistent relationship emerged between regional and local extinction rates, as species with high local extinction rates were not particularly prone to regional extinction.
4. Our results provide strong support for the contribution of colonisation rates to explain persistence. Overall, our results show that the equilibrium number of occupied localities could be a good predictor of the long-term persistence of metapopulations in rivers. Finally, our results suggest the importance of connectivity to maintain sustainable populations within the river system.

     

Integration of palaeontological, historical, and geographical data on the extinction of koa-finches

Identifying the root causes of extinction or endangerment requires long chronological records that begin before a population started to decline and extend until its extinction or functional extinction. We present a case study of the koa‐finches, genus Rhodacanthis, an extinct group of Hawaiian honeycreepers that was specialized to feed on green pods and seeds of the koa tree or other leguminous plants. Six island populations of koa‐finches are known; four in the Holocene fossil record and two that survived until the 1890s. We document the palaeoecological context of the fossils and identify constraints on the age span of the specimen record for each population using stratigraphic contexts, associated radiometric determinations, and museum specimen data. We estimate the potential geographical range of koa‐finches at the time of human arrival using two methods: assessment of their historical and palaeo‐habitats, and geographical information system mapping of the pre‐human distribution of the koa plant (Acacia koa) and its sister species, the koai‘a plant (Acacia koaia). After integrating the foregoing data with chronological records and distributional maps of the potential forcing agents of extinction, we conclude that at least two extinctions of island populations were due to ecological change in the lowlands in the prehistorical and perhaps the early historical periods. In the same time frame, the koa‐finch populations on Hawai‘i Island became rare and restricted to upland refugia, making them vulnerable to the upland forest harvesting and degradation that was accelerating in the 1890s. Neither climatic variation nor mosquito‐vectored diseases are likely to have caused the observed extinctions. This study illustrates an approach that can be applied to many other extinct and endangered island species to better understand the causes of high extinction rates in the human era.     

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.     

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.     

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 change effects on animal and plant phylogenetic diversity in southern Africa

Much attention has been paid to the effects of climate change on species' range reductions and extinctions. There is however surprisingly little information on how climate change driven threat may impact the tree of life and result in loss of phylogenetic diversity (PD). Some plant families and mammalian orders reveal nonrandom extinction patterns, but many other plant families do not. Do these discrepancies reflect different speciation histories and does climate induced extinction result in the same discrepancies among different groups? Answers to these questions require representative taxon sampling. Here, we combine phylogenetic analyses, species distribution modeling, and climate change projections on two of the largest plant families in the Cape Floristic Region (Proteaceae and Restionaceae), as well as the second most diverse mammalian order in Southern Africa (Chiroptera), and an herbivorous insect genus (Platypleura) in the family Cicadidae to answer this question. We model current and future species distributions to assess species threat levels over the next 70 years, and then compare projected with random PD survival. Results for these animal and plant clades reveal congruence. PD losses are not significantly higher under predicted extinction than under random extinction simulations. So far the evidence suggests that focusing resources on climate threatened species alone may not result in disproportionate benefits for the preservation of evolutionary history.     

种群统计随机性和环境随机性对种群绝灭的影响

影响种群绝灭的随机干扰可分为种群统计随机性、环境随机性和随机灾害三大类。在相对稳定的环境条件下和相对较短的时间内,以前两类随机干扰对种群绝灭的影响为生态学家关注的焦点。但是,由于自然种群动态及其影响因子的复杂特征,进一步深入研究随机干扰对种群绝灭的作用在理论上和实践上都必须发展新的技术手段。本文回顾了种群统计随机性与环境随机性的概念起源与发展,系统阐述了其分析方法。归纳了两类随机性在种群绝灭研究中的应用范围、作用方式和特点的异同和区别方法。各类随机作用与种群动态之间关系的理论研究与对种群绝灭机理的实践研究紧密相关。根据理论模型模拟和自然种群实际分析两方面的研究现状,作者提出了进一步深入研究随机作用与种群非线性动态方法的策略。指出了随机干扰影响种群绝灭过程的研究的方向：更多的研究将从单纯的定性分析随机干扰对种群动力学简单性质的作用,转向结合特定的种群非线性动态特征和各类随机力作用特点具体分析绝灭极端动态的成因,以期做出精确的预测。     

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.     

Environmental change drove macroevolution in cupuladriid bryozoans

Most macroevolutionary events are correlated with changes in the environment, but more rigorous evidence of cause and effect has been elusive. We compiled a 10 Myr record of origination and extinction, changes in mode of reproduction, morphologies and abundances of cupuladriid bryozoan species, spanning the time when primary productivity collapsed in the southwestern Caribbean as the Isthmus of Panama closed. The dominant mode of reproduction shifted dramatically from clonal to aclonal, due in part to a pulse of origination followed by extinction that was strongly selective in favour of aclonal species. Modern-day studies predict reduced clonality in increasingly oligotrophic conditions, thereby providing a mechanistic explanation supporting the hypothesis that the collapse in primary productivity was the cause of turnover. However, whereas originations were synchronous with changing environments, extinctions lagged 1–2 Myr. Extinct species failed to become more robust and reduce their rate of cloning when the new environmental conditions arose, and subsequently saw progressive reductions in abundance towards their delayed demise. Environmental change is therefore established as the root cause of macroevolutionary turnover despite the lag between origination and extinction.     

Effects of habitat quality and size on extinction in experimental populations

Stochastic population theory makes clear predictions about the effects of reproductive potential and carrying capacity on characteristic time-scales of extinction. At the same time, the effects of habitat size and quality on reproduction and regulation have been hotly debated. To trace the causal relationships among these factors, we looked at the effects of habitat size and quality on extinction time in experimental populations of Daphnia magna. Replicate model systems representative of a broad-spectrum consumer foraging on a continuously supplied resource were established under crossed treatments of habitat size (two levels) and habitat quality (three levels) and monitored until eventual extinction of all populations. Using statistically derived estimates of key parameters, we related experimental treatments to persistence time through their effect on carrying capacity and the population growth rate. We found that carrying capacity and the intrinsic rate of increase were each influenced similarly by habitat size and quality, and that carrying capacity and the intrinsic rate of increase were in turn both correlated with time to population extinction. We expected habitat quality to have a greater influence on extinction. However, owing to an unexpected effect of habitat size on reproductive potential, habitat size and quality were similarly important for population persistence. These results support the idea that improving the population growth rate or carrying capacity will reduce extinction risk and demonstrate that both are possible by improving habitat quality or increasing habitat size.     

Effects of extinction on food web structures on an evolutionary time scale

Extinction affected food web structure in paleoecosystems. Recent theoretical studies that examined the effects of extinction intensity on food web structure on ecological time scales have considered extinction to involve episodic events, with pre-extinction food webs becoming established without dynamics. However, in terms of the paleontological time scale, food web structures are generated from feedback with repeated extinctions, because extinction frequency is affected by food web structure, and food web structure itself is a product of previous extinctions. We constructed a simulation model of changes in tri-trophic-level food webs to examine how continual extinction events affect food webs on an evolutionary time scale. We showed that under high extinction intensity (1) species diversity, especially that of consumer species, decreased; (2) the total population density at each trophic level decreased, while the densities of individual species increased; and (3) the trophic link density of the food web increased. In contrast to previous models, our results were based on an assumption of long-term food web development and are able to explain overall trends posited by empirical investigations based on fossil records.     

The role of infectious diseases in biological conservation

Recent increases in the magnitude and rate of environmental change, including habitat loss, climate change and overexploitation, have been directly linked to the global loss of biodiversity. Wildlife extinction rates are estimated to be 100–1000 times greater than the historical norm, and up to 50% of higher taxonomic groups are critically endangered. While many types of environmental changes threaten the survival of species all over the planet, infectious disease has rarely been cited as the primary cause of global species extinctions. There is substantial evidence, however, that diseases can greatly impact local species populations by causing temporary or permanent declines in abundance. More importantly, pathogens can interact with other driving factors, such as habitat loss, climate change, overexploitation, invasive species and environmental pollution to contribute to local and global extinctions. Regrettably, our current lack of knowledge about the diversity and abundance of pathogens in natural systems has made it difficult to establish the relative importance of disease as a significant driver of species extinction, and the context when this is most likely to occur. Here, we review the role of infectious diseases in biological conservation. We summarize existing knowledge of disease-induced extinction at global and local scales and review the ecological and evolutionary forces that may facilitate disease-mediated extinction risk. We suggest that while disease alone may currently threaten few species, pathogens may be a significant threat to already-endangered species, especially when disease interacts with other drivers. We identify control strategies that may help reduce the negative effects of disease on wildlife and discuss the most critical challenges and future directions for the study of infectious diseases in the conservation sciences.     

Organism activity levels predict marine invertebrate survival during ancient global change extinctions

Multistressor global change, the combined influence of ocean warming, acidification, and deoxygenation, poses a serious threat to marine organisms. Experimental studies imply that organisms with higher levels of activity should be more resilient, but testing this prediction and understanding organism vulnerability at a global scale, over evolutionary timescales, and in natural ecosystems remain challenging. The fossil record, which contains multiple extinctions triggered by multistressor global change, is ideally suited for testing hypotheses at broad geographic, taxonomic, and temporal scales. Here, I assess the importance of activity level for survival of well‐skeletonized benthic marine invertebrates over a 100‐million‐year‐long interval (Permian to Jurassic periods) containing four global change extinctions, including the end‐Permian and end‐Triassic mass extinctions. More active organisms, based on a semiquantitative score incorporating feeding and motility, were significantly more likely to survive during three of the four extinction events (Guadalupian, end‐Permian, and end‐Triassic). In contrast, activity was not an important control on survival during nonextinction intervals. Both the end‐Permian and end‐Triassic mass extinctions also triggered abrupt shifts to increased dominance by more active organisms. Although mean activity gradually returned toward pre‐extinction values, the net result was a permanent ratcheting of ecosystem‐wide activity to higher levels. Selectivity patterns during ancient global change extinctions confirm the hypothesis that higher activity, a proxy for respiratory physiology, is a fundamental control on survival, although the roles of specific physiological traits (such as extracellular pCO₂ or aerobic scope) cannot be distinguished. Modern marine ecosystems are dominated by more active organisms, in part because of selectivity ratcheting during these ancient extinctions, so on average may be less vulnerable to global change stressors than ancient counterparts. However, ancient extinctions demonstrate that even active organisms can suffer major extinction when the intensity of environmental disruption is intense.