Long-term evolution of an ecosystem with spontaneous periodicity of mass extinctions

Twenty years ago, after analysing palaeontological data, Raup and Sepkoski suggested that mass extinctions on Earth appear cyclically in time with a period of approximately 26 million years (My). To explain the 26 My period, a number of proposals were made involving, e.g., astronomical effects, increased volcanic acitivity, or the Earth's magnetic field reversal, none of which, however, has been confirmed. Here we study a spatially extended discrete model of an ecosystem and show that the periodicity of mass extinctions might be a natural feature of the ecosystem's dynamics and not the result of a periodic external perturbation. In our model, periodic changes of the diversity of an ecosystem and some of its other characteristics are induced by the coevolution of species. In agreement with some palaeontological data, our results show that the longevity of a species depends on the evolutionary stage at which the species is created. Possible further tests of our model are also discussed.     

Improving nature conservancy strategies by ecological network theory

Over several decades nature conservancy research has gathered increasing evidence on the processes that drive species extinctions. Nevertheless, the world's ecosystems are currently exposed to a fast wave of species extinctions, and nature conservancy research has to face the challenge of predicting the consequences of extinctions. In the context of complex food webs that compose natural ecosystems, these primary extinctions affect the biomasses and growth rates of all co-existing species, which can eventually lead to secondary extinctions and extinction cascades of multiple species. Network theory provides a tool for predicting the consequences of extinctions for other species and ecosystem functions. In this sense, ecological network theory could become the next cornerstone of nature conservancy research.     

Predicting loss of evolutionary history: Where are we?

The Earth's evolutionary history is threatened by species loss in the current sixth mass extinction event in Earth's history. Such extinction events not only eliminate species but also their unique evolutionary histories. Here we review the expected loss of Earth's evolutionary history quantified by phylogenetic diversity (PD) and evolutionary distinctiveness (ED) at risk. Due to the general paucity of data, global evolutionary history losses have been predicted for only a few groups, such as mammals, birds, amphibians, plants, corals and fishes. Among these groups, there is now empirical support that extinction threats are clustered on the phylogeny; however this is not always a sufficient condition to cause higher loss of phylogenetic diversity in comparison to a scenario of random extinctions. Extinctions of the most evolutionarily distinct species and the shape of phylogenetic trees are additional factors that can elevate losses of evolutionary history. Consequently, impacts of species extinctions differ among groups and regions, and even if global losses are low within large groups, losses can be high among subgroups or within some regions. Further, we show that PD and ED are poorly protected by current conservation practices. While evolutionary history can be indirectly protected by current conservation schemes, optimizing its preservation requires integrating phylogenetic indices with those that capture rarity and extinction risk. Measures based on PD and ED could bring solutions to conservation issues, however they are still rarely used in practice, probably because the reasons to protect evolutionary history are not clear for practitioners or due to a lack of data. However, important advances have been made in the availability of phylogenetic trees and methods for their construction, as well as assessments of extinction risk. Some challenges remain, and looking forward, research should prioritize the assessment of expected PD and ED loss for more taxonomic groups and test the assumption that preserving ED and PD also protects rare species and ecosystem services. Such research will be useful to inform and guide the conservation of Earth's biodiversity and the services it provides.     

Late Holocene extinction of Puerto Rican native land mammals

West Indian land mammals have suffered the most severe extinctions of any Holocene mammal faunas. However, 'last-occurrence' dates based on radiometric or robust stratigraphic data remain unavailable for most West Indian species, making it impossible to identify factors responsible for these extinctions. Here, we present new radiometric dates from archaeological and palaeontological sites on Puerto Rico, the only Greater Antillean island to have lost all native land mammals. Although it has been suggested that these species died out earlier than other West Indian mammals, we demonstrate that Puerto Rican mammal last-occurrence dates are in close agreement with those from other Antillean islands, as several species in fact persisted for millennia following Amerindian arrival. Echimyid rodents and nesophontid 'island-shrews' were still present on Puerto Rico approximately 1000 years BP, and probably became extinct following European arrival. The large (13kg) heptaxodontid rodent Elasmodontomys obliquus also appears to have survived for over 2000 years after Amerindian colonization, suggesting that at least some large West Indian mammals became extinct in protracted pre-European 'sitzkrieg'-style events rather than 'blitzkrieg'-style overkill.     

Contributions of mean temperature and temperature variation to population stability and community diversity

Future climate changes are predicted to not only increase global temperatures but also alter temporal variation in temperature. As thermal tolerances form an important component of a species’ niche, changes to the temperature regime have the capacity to negatively impact species, and therefore, the diversity of the communities they inhabit. In this study, we used protist microcosms to assess how mean temperature, as well as temporal variation in temperature, affected diversity. Communities consisted of seven species in a multitrophic food web. Each ecosystem was inoculated with the same abundances of each species at the start of the experiment, and species densities, Hill''s numbers (based on Shannon diversity), the number of extinctions, and the probability the microcosm contained predators were all calculated at the end of the experiment. To assess how mean temperature and temperature fluctuations affect stability, we also measured population densities through time. We found that increased temporal variation in temperature increased final densities, increased Hill''s numbers (at low mean temperatures), decreased rates of extinctions, and increased the probability that predators survived till the end of the experiment. Mean temperatures did not significantly affect either the number of extinctions or the probability of predators, but did reduce the positive effect of increased temporal variation in temperature on overall diversity. Our results indicate that climatic changes have the potential to impact the composition of ecological communities by altering multiple components of temperature regimes. However, given that some climate forecasts are predicting increased mean temperatures and reduced variability, our finding that increased mean temperature and reduced temporal variation are both generally associated with negative consequences is somewhat concerning.     

Species loss and the structure and functioning of multitrophic aquatic systems

Experiments and theory in single trophic level systems dominate biodiversity and ecosystem functioning research and recent debates. All natural ecosystems contain communities with multiple trophic levels, however, and this can have important effects on ecosystem structure and functioning. Furthermore, many experiments compare assembled communities, rather than examining loss of species directly. We identify three questions around which to organise an investigation of how species loss affects the structure and functioning of multitrophic systems. 1) What is the distribution of species richness among trophic levels; 2) from which trophic levels are species most often lost; and 3) does loss of species from different trophic levels influence ecosystem functioning differently? Our analyses show that: 1) Relatively few high‐quality data are available concerning the distribution of species richness among trophic levels. A new data‐set provides evidence of a decrease in species richness as trophic height increases. 2) Multiple lines of evidence indicate that species are lost from higher trophic levels more frequently than lower trophic levels. 3) A theoretical model suggests that both the structure of food webs (occurrence of omnivory and the distribution of species richness among trophic levels) and the trophic level from which species are lost determines the impact of species loss on ecosystem functioning, which can even vary in the sign of the effect. These results indicate that, at least for aquatic systems, models of single trophic level ecosystems are insufficient for understanding the functional consequences of extinctions. Knowledge is required of food web structure, which species are likely to be lost, and also whether cascading extinctions will occur.     

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 best sections method of studying mass extinctions

Phanerozoic mass extinctions have been studied primarily by analysing global diversity patterns compiled from the published literature. However, such compilations are beset by problems of incorrect correlation, imprecise age assignments and changing taxonomy. An alternative approach is to analyse mass extinctions by the ‘best sections’ method. This method identifies abundantly fossiliferous, well‐studied, stratigraphically dense and temporally extensive fossil records in strata that contain geochemical and other relevant non‐palaeontological data from a single depositional basin or geographically restricted outcrop area as the ‘best sections’ by which to analyse extinctions. A strength of the best sections method is that it allows the extinctions identified to be compared directly to changes in facies and other factors recorded in the best section. And, the hypothesis of a widespread extinction based on an extinction seen in a best section can be tested by its presence or absence in temporally equivalent sections. What we need are more field‐based studies of the best sections that encompass mass extinctions (real and hypothetical) and less of a reliance on literature‐based diversity compilations to produce a more reliable and comprehensive understanding of the history of extinctions.     

Megafauna extinction,tree species range reduction,and carbon storage in Amazonian forests

During the Late Pleistocene and early Holocene 59 species of South American megafauna went extinct. Their extinction potentially triggered population declines of large‐seeded tree species dispersed by the large‐bodied frugivores with which they co‐evolved, a theory first proposed by Janzen and Martin (1982). We tested this hypothesis using species range maps for 257 South American tree species, comparing 63 species thought to be primarily distributed by megafauna with 194 distributed by other animals. We found a highly significant (p < 0.001) decreased mean range size of 26% for the megafauna dispersed fruit (n = 63 species) versus fruit dispersed by other animals (n = 194), results which support the hypothesis. We then developed a mathematical model of seed dispersal to estimate the theoretical impact of megafauna extinction on tree species range and found the estimated dispersal capacity (Φ_seed) of a 2 g seed decreases by > 95% following disperser extinction. A numerical gap dynamic simulations suggests that over a 10 000 yr period following the disperser extinctions, the average convex hull range size of large‐seeded tree species decreased by ～ 31%, while the estimated decrease in population size was ～ 54%, indicating a likely greater decrease in species population size than indicated by the empirical range patterns. Finally, we found a positive correlation between seed size and wood density of animal‐dispersed tree species implying that the Late Pleistocene and early Holocene megafaunal extinctions reduced carbon content in the Amazon by ～ 1.5 ± 0.7%. In conclusion, we 1) provide some empirical evidence that megafauna distributed fruit species have a smaller mean range size than wind, water or other animal‐dispersed species, 2) demonstrate mathematically that such range reductions are expected from megafauna extinctions ca 12 000 yr ago, and 3) illustrate that these extinctions may have reduced the Amazon's carbon storage capacity.     

More losers than winners: investigating Anthropocene defaunation through the diversity of population trends

The global-scale decline of animal biodiversity (‘defaunation’) represents one of the most alarming consequences of human impacts on the planet. The quantification of this extinction crisis has traditionally relied on the use of IUCN Red List conservation categories assigned to each assessed species. This approach reveals that a quarter of the world's animal species are currently threatened with extinction, and ~1% have been declared extinct. However, extinctions are preceded by progressive population declines through time that leave demographic ‘footprints’ that can alert us about the trajectories of species towards extinction. Therefore, an exclusive focus on IUCN conservation categories, without consideration of dynamic population trends, may underestimate the true extent of the processes of ongoing extinctions across nature. In fact, emerging evidence (e.g. the Living Planet Report), reveals a widespread tendency for sustained demographic declines (an average 69% decline in population abundances) of species globally. Yet, animal species are not only declining. Many species worldwide exhibit stable populations, while others are even thriving. Here, using population trend data for >71,000 animal species spanning all five groups of vertebrates (mammals, birds, reptiles, amphibians and fishes) and insects, we provide a comprehensive global-scale assessment of the diversity of population trends across species undergoing not only declines, but also population stability and increases. We show a widespread global erosion of species, with 48% undergoing declines, while 49% and 3% of species currently remain stable or are increasing, respectively. Geographically, we reveal an intriguing pattern similar to that of threatened species, whereby declines tend to concentrate around tropical regions, whereas stability and increases show a tendency to expand towards temperate climates. Importantly, we find that for species currently classed by the IUCN Red List as ‘non-threatened’, 33% are declining. Critically, in contrast with previous mass extinction events, our assessment shows that the Anthropocene extinction crisis is undergoing a rapid biodiversity imbalance, with levels of declines (a symptom of extinction) greatly exceeding levels of increases (a symptom of ecological expansion and potentially of evolution) for all groups. Our study contributes a further signal indicating that global biodiversity is entering a mass extinction, with ecosystem heterogeneity and functioning, biodiversity persistence, and human well-being under increasing threat.     

Extinction,survivorship and evolution of planktic foraminifera across the Cretaceous/Tertiary boundary at El Kef,Tunisia

An expanded sediment record at El Kef shows that the K/T boundary extinctions of planktic foraminifera extend over an interval from 25 cm below the geochemical boundary (Ir anomaly) to 7 cm above. Species extinctions appear sequential with complex, large, ornate forms disappearing first and smaller, less ornate, forms surviving longer. The 14 species extinctions below the boundary appear unrelated to an impact event.Cretaceous species survivorship is greater than previously assumed. About 10 species survive (22%) into Subzone P1a (Globigerina eugubina). All Cretaceous survivors are small primitive forms which are generally smaller than their ancestors in Cretaceous sediments.Species evolution after the K/T event occurs in two pulses. The first new Paleocene species evolve in the basal black clay (Zone PO) immediately after the major Cretaceous extinctions. Evolving species are small and primitive similar to Cretaceous survivors. The second pulse in species evolution occurs in the lower part of Subzone P1b with the appearance of larger more diverse species. The first major increase in carbonate sedimentation and productivity occurs at this time and signals the recoveyr of the ecosystem nearly 300,000 years after the K/T event. The species extinctions prior to the generally assumed impact event implied by the Ir anomaly, and the long recovery period of the ecosystem thereafter cannot be explained by a single impact, but suggest that multiple causes may be responsible such as climatic changes, volcanism, a sea level drop, production of warm saline bottom water and the chemical consequences associated with increased salinity.     

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.     

Cascading extinctions, functional complementarity, and selection in two-trophic-level model communities: A trait-based mechanistic approach

The influence of diversity on ecosystem functioning and ecosystem services is now well established. Yet predictive mechanistic models that link species traits and community-level processes remain scarce, particularly for multitrophic systems. Here we revisit MacArthur's classical consumer resource model and develop a trait-based approach to predict the effects of consumer diversity on cascading extinctions and aggregated ecosystem processes in a two-trophic-level system. We show that functionally redundant efficient consumers generate top-down cascading extinctions. This counterintuitive result reveals the limits of the functional redundancy concept to predict the consequences of species deletion. Our model also predicts that the biodiversity-ecosystem functioning relationship is different for different ecosystem processes and depends on the range of variation of consumer traits in the regional species pool, which determines the sign of selection effects. Lastly, competition among resources and consumer generalism both weaken complementarity effects, which suggests that selection effects may prevail at higher trophic levels. Our work emphasizes the potential of trait-based approaches for transforming biodiversity and ecosystem functioning research into a more predictive science.     

Global warming and amphibian extinctions in eastern Australia

Abstract Pounds et al. recently argued that the dramatic, fungal pathogen‐linked extinctions of numerous harlequin frogs (Atelopus spp.) in upland rainforests of South America mostly occurred immediately following exceptionally warm years, implicating global warming as a likely trigger for these extinctions. I tested this hypothesis using temperature data for eastern Australia, where at least 14 upland‐rainforest frog species have also experienced extinctions or striking population declines attributed to the same fungal pathogen, and where temperatures have also risen significantly in recent decades. My analyses provide little direct support for the warm‐year hypothesis of Pounds et al., although my statistical power to detect effects of small (0.5°C) temperature increases was limited. However, I found stronger support for a modified version of the warm‐year hypothesis, whereby frog declines were likely to occur following three consecutive years of unusually warm weather. This trend was apparent only at tropical latitudes, where rising minimum temperatures were greatest. Although much remains uncertain, my findings appear consistent with the notion that global warming could predispose some upland amphibian populations to virulent pathogens.     

Cascading extinctions and ecosystem functioning: contrasting effects of diversity depending on food web structure

The consequences of species loss on cascading extinctions in food webs have been the focus of several recent theoretical studies, with differing results. Changes in ecosystem properties consecutive to cascading extinctions have received far less attention even though such dramatic events might strongly alter ecosystem functioning. Here we use various food web models to investigate the effects of species loss and diversity on both secondary extinctions and their associated changes in ecosystem properties. Our analysis shows that diversity has contrasting effects depending on the presence of self-limiting terms at consumer levels and, to a lower extent, on connectance and interspecific competition. Ecosystems that lose a high proportion of species through cascading extinctions exhibit the most important changes in ecosystem properties. Linking studies on cascading extinctions in food webs with studies that investigate the effects of biodiversity on ecosystem functioning appears crucial for a better understanding of the consequences of species extinctions.     

Dynamics of extinction and the selection of nature reserves

Familiar quantitative reserve-selection techniques are tailored to simple decision problems, where the representation of species is sought at minimum cost. However, conservationists have begun to ask whether representing species in reserve networks is sufficient to avoid local extinctions within selected areas. An attractive, but previously untested idea is to model current species' probabilities of occurrence as an estimate of local persistence in the near future. Using distribution data for passerine birds in Great Britain, we show that (i) species' probabilities of occurrence are negatively related to local probabilities of extinction, at least when a particular 20-year period is considered, and (ii) local extinctions can be reduced if areas are selected to maximize current species' probabilities of occurrence We suggest that more extinctions could be avoided if even a simple treatment of persistence were to be incorporated within reserve selection methods.     

Cyclism revisited: extinction and ‘Achilles’ Heels' keep diversification in check on macroevolutionary time scales

Mass extinctions of varying magnitude prune the continuous diversification predicted by Darwinian evolutionary processes. They are caused by events that are too rare to become adaptatively accommodated. Their effects depend not only on the nature and magnitude of the triggering event but also on the state of the biosphere at the particular time. This is most clearly shown by the existence of Golden Ages preceding all Phanerozoic mass extinctions. These coincide with greenhouse periods, in which doomed clades gave rise to heteromorphs, deviating in strange ways from established bauplans. When critically examined, the seemingly ‘decadent’ morphologies of Schindewolf's ‘typolytic stages’ turn out to have been highly functional. The paradoxical link between adaptive peaks and evolutionary failure can now be explained. Specialisation tends to increase vulnerability (1) by narrowing niches and (2) by the retention of clade-specific conservative features that happen to become fatal Achilles’ Heels for entire clades in the face of a particular perturbation. Following extinctions, the availability of open niches favoured relatively rapid diversification of more innovative clades and their rise to ecological dominance (Schindewolf's ‘typogenetic stage’). Although the long-term changes can be observed only in the fossil record, Golden Biotopes in the present biosphere show that the Darwinian process may also be promoted by ecological isolation. As a result, clade histories do resemble individual biographies, but for ecological rather than orthogenetic reasons. This insight may help us to deal with the present mass extinction caused by our own species.     

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

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

Global versus local extinction in a network model of plant–pollinator communities

The loss of a species from an ecological community can trigger a cascade of additional extinctions; the complex interactions that comprise ecological communities make the dynamics and impacts of such a cascade challenging to predict. Previous studies have typically considered global extinctions, where a species cannot re-enter a community once it is lost. However, in some cases a species only becomes locally extinct, and may be able to reinvade from surrounding communities. Here, we use a dynamic, Boolean network model of plant–pollinator community assembly to analyze the differences between global and local extinction events in mutualistic communities. As expected, we find that compared to global extinctions, communities respond to local extinctions with lower biodiversity loss, and less variation in topological network properties. We demonstrate that in the face of global extinctions, larger communities suffer greater biodiversity loss than smaller communities when similar proportions of species are lost. Conversely, smaller communities suffer greater loss in the face of local extinctions. We show that targeting species with the most interacting partners causes more biodiversity loss than random extinctions in the case of global, but not local, extinctions. These results extend our understanding of how mutualistic communities respond to species loss, with implications for community management and conservation efforts.     

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.