Extinction Threshold Research Articles

Survival of the scarcer in space

The dynamics leading to extinction or coexistence of competing species is of great interest in ecology and related fields. Recently a model of intra- and interspecific competition between two species was proposed by Gabel et al, in which the scarcer species (i.e., with smaller stationary population size) can be more resistant to extinction when it holds a competitive advantage; the latter study considered populations without spatial variation. Here we verify this phenomenon in populations distributed in space. We extend the model of Gabel et al to a d-dimensional lattice, and study its population dynamics both analytically and numerically. Survival of the scarcer in space is verified for situations in which the more competitive species is closer to the threshold for extinction than is the less competitive species, when considered in isolation. The conditions for survival of the scarcer species, as obtained applying renormalization group analysis and Monte Carlo simulation, differ in detail from those found in the spatially homogeneous case. Simulations highlight the speed of invasion waves in determining the survival times of the competing species.

Modeling Habitat Split: Landscape and Life History Traits Determine Amphibian Extinction Thresholds

Habitat split is a major force behind the worldwide decline of amphibian populations, causing community change in richness and species composition. In fragmented landscapes, natural remnants, the terrestrial habitat of the adults, are frequently separated from streams, the aquatic habitat of the larvae. An important question is how this landscape configuration affects population levels and if it can drive species to extinction locally. Here, we put forward the first theoretical model on habitat split which is particularly concerned on how split distance – the distance between the two required habitats – affects population size and persistence in isolated fragments. Our diffusive model shows that habitat split alone is able to generate extinction thresholds. Fragments occurring between the aquatic habitat and a given critical split distance are expected to hold viable populations, while fragments located farther away are expected to be unoccupied. Species with higher reproductive success and higher diffusion rate of post-metamorphic youngs are expected to have farther critical split distances. Furthermore, the model indicates that negative effects of habitat split are poorly compensated by positive effects of fragment size. The habitat split model improves our understanding about spatially structured populations and has relevant implications for landscape design for conservation. It puts on a firm theoretical basis the relation between habitat split and the decline of amphibian populations.

Does fragmentation increase extinction thresholds? A European‐wide test with seven forest birds

AbstractAimTheory predicts that fragmentation aggravates habitat loss, increasing the extinction threshold of habitat specialists. However, contradictory empirical results have fuelled claims that fragmentation has been overemphasized, and more attention should be given to habitat loss for preserving species. We assess variation in species sensitivity to forest amount and fragmentation and evaluate if fragmentation is related to extinction thresholds in seven forest bird species.LocationEurope.MethodsWe use the percentage of forest cover and the proportion of cover occurring in the largest patch to partition effects of forest amount versus fragmentation, and apply logistic regression to model the presence–absence of 17 forest bird species. For seven species showing robust models, we define two fragmentation scenarios, low and maximum, across the forest cover gradient and quantify species' sensitivity to forest contraction with no fragmentation, and to fragmentation under constant forest cover. Finally, we develop two tests of the extinction threshold hypothesis by comparing the occurrence probability of each species under the two fragmentation scenarios at different forest covers.ResultsAs expected, forest contraction had negative impacts on the occurrence probability of all seven species modelled, but – in line with theory – fragmentation also led to a higher extinction threshold for three (Western capercaillie, Hazel grouse and Eurasian pygmy‐owl). One species (Black woodpecker) exhibited the opposite pattern indicating that it probably benefits from fragmentation. Differences among species responses may reflect dispersal abilities, specializations in resources/habitat characteristics and/or sensitivity to potential modifications of interspecific interactions.Main conclusionsAlthough forest amount is of primary importance for the persistence of forest specialist birds, fragmentation is also relevant for some, and neglecting forest fragmentation would be a mistake for these species. Species‐specific traits can be helpful for interpreting species' reactions to fragmentation, and it should not be assumed that it always, or never, matters.

Surviving rapid climate change in the deep sea during the Paleogene hyperthermals

Predicting the impact of ongoing anthropogenic CO2 emissions on calcifying marine organisms is complex, owing to the synergy between direct changes (acidification) and indirect changes through climate change (e.g., warming, changes in ocean circulation, and deoxygenation). Laboratory experiments, particularly on longer-lived organisms, tend to be too short to reveal the potential of organisms to acclimatize, adapt, or evolve and usually do not incorporate multiple stressors. We studied two examples of rapid carbon release in the geological record, Eocene Thermal Maximum 2 (∼53.2 Ma) and the Paleocene Eocene Thermal Maximum (PETM, ∼55.5 Ma), the best analogs over the last 65 Ma for future ocean acidification related to high atmospheric CO2 levels. We use benthic foraminifers, which suffered severe extinction during the PETM, as a model group. Using synchrotron radiation X-ray tomographic microscopy, we reconstruct the calcification response of survivor species and find, contrary to expectations, that calcification significantly increased during the PETM. In contrast, there was no significant response to the smaller Eocene Thermal Maximum 2, which was associated with a minor change in diversity only. These observations suggest that there is a response threshold for extinction and calcification response, while highlighting the utility of the geological record in helping constrain the sensitivity of biotic response to environmental change.

Robustness of empirical food webs with varying consumer's sensitivities to loss of resources

Food web responses to species loss have been mostly studied in binary food webs, thus without accounting for the amount of energy transferred in consumer–resource interactions.We introduce an energetic criterion, called extinction threshold, for which a species goes secondarily extinct when a certain fraction of its incoming energy is lost. We study the robustness to random node loss of 10 food webs based on empirically-derived weightings. We use different extinction scenarios (random removal and from most- to least-connected species), and we simulate 105 replicates for each extinction threshold to account for stochasticity of extinction dynamics.We quantified robustness on the basis of how many additional species (i.e. secondary extinctions) were lost after the direct removal of species (i.e. primary extinctions). For all food webs, the expected robustness linearly decreases with extinction threshold, although a large variance in robustness is observed. The sensitivity of robustness to variations in extinction threshold increases with food web species richness and quantitative unweighted link density, while we observed a nonlinear relationship when the predictor is food web connectance and no relationship with the proportion of autotrophs.

Ecosystem effects of shell aggregations and cycling in coastal waters: an example of Chesapeake Bay oyster reefs

Disease, overharvesting, and pollution have impaired the role of bivalves on coastal ecosystems, some to the point of functional extinction. An underappreciated function of many bivalves in these systems is shell formation. The ecological significance of bivalve shell has been recognized; geochemical effects are now more clearly being understood. A positive feedback exists between shell aggregations and healthy bivalve populations in temperate estuaries, thus linking population dynamics to shell budgets and alkalinity cycling. On oyster reefs a balanced shell budget requires healthy long‐lived bivalves to maximize shell input per mortality event thereby countering shell loss. Active and dense populations of filter‐feeding bivalves couple production of organic‐rich waste with precipitation of calcium carbonate minerals, creating conditions favorable for alkalinity regeneration. Although the dynamics of these processes are not well described, the balance between shell burial and metabolic acid production seems the key to the extent of alkalinity production vs. carbon burial as shell. We present an estimated alkalinity budget that highlights the significant role oyster reefs once played in the Chesapeake Bay inorganic‐carbon cycle. Sustainable coastal and estuarine bivalve populations require a comprehensive understanding of shell budgets and feedbacks among population dynamics, agents of shell destruction, and anthropogenic impacts on coastal carbonate chemistry.

Healing the Planet

Our planet is sick and perhaps on a tipping point of extinction. The causes are well known—global warming, the collapse of the world economy, human greed, and thermonuclear war—to name but a few agents at work in the contemporary world. America and China hold the world’s destiny in their grip. How they will interact is unknown. What is known is that both civilizations have in their traditions the ways and means to reverse this approaching apocalypse. Each country is now passing through cultural explosions. This article searches classical Chinese and American philosophy for concepts and social forms that can give shape to this era of upheaval. I have confidence in the genius of Confucius as well as that of certain great classical American philosophers. Read together they can help us come to deal with both the decay of established orders and the overwhelming novelty now sweeping through our consciousness.

Relations between deterministic and stochastic thresholds for disease extinction in continuous- and discrete-time infectious disease models

Thresholds for disease extinction provide essential information for control, eradication or management of diseases. Through relations between branching process theory and the corresponding deterministic model, it is shown that the deterministic and stochastic thresholds are in agreement for discrete-time and continuous-time infectious disease models with multiple infectious groups. Branching process theory can be applied in conjunction with the deterministic model to give additional information about disease extinction. These relations are illustrated, analytically and numerically, in two settings, a general stage-structured model and a vector-host model applied to West Nile virus in mosquitoes and birds.

Assessing Regional and Interspecific Variation in Threshold Responses of Forest Breeding Birds through Broad Scale Analyses

BackgroundIdentifying persistence and extinction thresholds in species-habitat relationships is a major focal point of ecological research and conservation. However, one major concern regarding the incorporation of threshold analyses in conservation is the lack of knowledge on the generality and transferability of results across species and regions. We present a multi-region, multi-species approach of modeling threshold responses, which we use to investigate whether threshold effects are similar across species and regions.Methodology/Principal FindingsWe modeled local persistence and extinction dynamics of 25 forest-associated breeding birds based on detection/non-detection data, which were derived from repeated breeding bird atlases for the state of Vermont. We did not find threshold responses to be particularly well-supported, with 9 species supporting extinction thresholds and 5 supporting persistence thresholds. This contrasts with a previous study based on breeding bird atlas data from adjacent New York State, which showed that most species support persistence and extinction threshold models (15 and 22 of 25 study species respectively). In addition, species that supported a threshold model in both states had associated average threshold estimates of 61.41% (SE = 6.11, persistence) and 66.45% (SE = 9.15, extinction) in New York, compared to 51.08% (SE = 10.60, persistence) and 73.67% (SE = 5.70, extinction) in Vermont. Across species, thresholds were found at 19.45–87.96% forest cover for persistence and 50.82–91.02% for extinction dynamics.Conclusions/SignificanceThrough an approach that allows for broad-scale comparisons of threshold responses, we show that species vary in their threshold responses with regard to habitat amount, and that differences between even nearby regions can be pronounced. We present both ecological and methodological factors that may contribute to the different model results, but propose that regardless of the reasons behind these differences, our results merit a warning that threshold values cannot simply be transferred across regions or interpreted as clear-cut targets for ecosystem management and conservation.

Assessing the robustness of networks of spatial genetic variation

Habitat transformation is one of the leading drivers of biodiversity loss. The ecological effects of this transformation have mainly been addressed at the demographic level, for example, finding extinction thresholds. However, interpopulation genetic variability and the subsequent potential for adaptation can be eroded before effects are noticed on species abundances. To what degree this is the case has been difficult to evaluate, partly because of the lack of both spatially extended genetic data and an appropriate framework to map and analyse such data. Here, we extend recent work on the analysis of networks of spatial genetic variation to address the robustness of these networks in the face of perturbations. We illustrate the potential of this framework using the case study of an amphibian metapopulation. Our results show that while the disappearance of some spatial sites barely changes the modular structure of the genetic network, other sites have a much stronger effect. Interestingly, these consequences can not be anticipated using topological, static measures. Mapping these networks of spatial genetic variation will allow identifying significant evolutionary units and how they vanish, merge and reorganise following perturbations.

Vertical profiles of aerosol optical properties over central Illinois and comparison with surface and satellite measurements

Abstract. Between June 2006 and September 2009, an instrumented light aircraft measured over 400 vertical profiles of aerosol and trace gas properties over eastern and central Illinois. The primary objectives of this program were to (1) measure the in situ aerosol properties and determine their vertical and temporal variability and (2) relate these aircraft measurements to concurrent surface and satellite measurements. The primary profile location was within 15 km of the NOAA/ESRL surface aerosol monitoring station near Bondville, Illinois. Identical instruments at the surface and on the aircraft ensured that the data from both platforms would be directly comparable and permitted a determination of how representative surface aerosol properties were of the lower column. Aircraft profiles were also conducted occasionally at two other nearby locations to increase the frequency of A-Train satellite underflights for the purpose of comparing in situ and satellite-retrieved aerosol data. Measurements of aerosol properties conducted at low relative humidity over the Bondville site compare well with the analogous surface aerosol data and do not indicate any major sampling issues or that the aerosol is radically different at the surface compared with the lowest flyby altitude of ~ 240 m above ground level. Statistical analyses of the in situ vertical profile data indicate that aerosol light scattering and absorption (related to aerosol amount) decreases substantially with increasing altitude. Parameters related to the nature of the aerosol (e.g., single-scattering albedo, Ångström exponent, etc.), however, are relatively constant throughout the mixed layer, and do not vary as much as the aerosol amount throughout the profile. While individual profiles often showed more variability, the median in situ single-scattering albedo was 0.93–0.95 for all sampled altitudes. Several parameters (e.g., submicrometer scattering fraction, hemispheric backscattering fraction, and scattering Ångström exponent) suggest that the fraction of smaller particles in the aerosol is larger near the surface than at high altitudes. The observed dependence of scattering on size, wavelength, angular integration range, and relative humidity, together with the spectral dependence of absorption, show that the aerosol at higher altitudes is larger, less hygroscopic, and more strongly absorbing at shorter wavelengths, suggesting an increased contribution from dust or organic aerosols. The aerosol profiles show significant differences among seasons. The largest amounts of aerosol (as determined by median light extinction profile measurements) throughout most of the sampled column were observed during summer, with the lowest amounts in the winter and intermediate values in the spring and fall. The highest three profile levels (3.1, 3.7, 4.6 km), however, showed larger median extinction values in the spring, which could reflect long-range transport of dust or smoke aerosols. The aerosols in the mixed layer were darkest (i.e., lowest single-scattering albedo) in the fall, in agreement with surface measurements at Bondville and other continental sites in the US. In situ profiles of aerosol radiative forcing efficiency showed little seasonal or vertical variability. Underflights of the CALIPSO satellite show reasonable agreement in a majority of retrieved profiles between aircraft-measured extinction at 532 nm (adjusted to ambient relative humidity) and CALIPSO-retrieved extinction, and suggest that routine aircraft profiling programs can be used to better understand and validate satellite retrieval algorithms. CALIPSO tended to overestimate the aerosol extinction at this location in some boundary layer flight segments when scattered or broken clouds were present, which could be related to problems with CALIPSO cloud screening methods. The in situ aircraft-collected aerosol data suggest extinction thresholds for the likelihood of aerosol layers being detected by the CALIOP lidar. In this study, aerosol layers with light extinction (532 nm) values > 50 Mm−1 were detected by CALIPSO ~ 95% of the time, while aerosol layers with extinction values lower than 10 Mm−1 had a detection efficiency of < 2%. For all collocated comparison cases, a 50% probability of detection falls at an in situ extinction level of 20–25 Mm−1. These statistical data offer guidance as to the likelihood of CALIPSO's ability to retrieve aerosol extinction at various locations around the globe.

Ecological and genetic effects of introduced species on their native competitors

Species introductions to new habitats can cause a decline in the population size of competing native species and consequently also in their genetic diversity. We are interested in why these adverse effects are weak in some cases whereas in others the native species declines to the point of extinction. While the introduction rate and the growth rate of the introduced species in the new environment clearly have a positive relationship with invasion success and impact, the influence of competition is poorly understood. Here, we investigate how the intensity of interspecific competition influences the persistence time of a native species in the face of repeated and ongoing introductions of the nonnative species. We analyze two stochastic models: a model for the population dynamics of both species and a model that additionally includes the population genetics of the native species at a locus involved in its adaptation to a changing environment. Counterintuitively, both models predict that the persistence time of the native species is lowest for an intermediate intensity of competition. This phenomenon results from the opposing effects of competition at different stages of the invasion process: With increasing competition intensity more introduction events are needed until a new species can establish, but increasing competition also speeds up the exclusion of the native species by an established nonnative competitor. By comparing the ecological and the eco-genetic model, we detect and quantify a synergistic feedback between ecological and genetic effects.

Economics and Enviromental Resources: Review

We review the component elements of environmental resources in order to provide insights into their economic characteristics and properties. Environmental resources are the goods and services provided by the natural environment and are constituted into three categories: atmosphere; water; and land and soil. The economic literature emphasizes two points in regard to the economic characteristics of environmental resources. First, many environmental goods are renewable resources and have features of public goods-accessible to all in the community at no charge, so that excluding unwanted users is difficult, which lends them to over-exploitation to the point of extinction in many instances. Second, environmental resources constitute a kind of capital and so makes measurable contribution to output similar to the role played by physical and human capital, and so should be accounted for, invested in, and exploited efficiently.

Unraveling the drivers of community dissimilarity and species extinction in fragmented landscapes

Communities in fragmented landscapes are often assumed to be structured by species extinction due to habitat loss, which has led to extensive use of the species-area relationship (SAR) in fragmentation studies. However, the use of the SAR presupposes that habitat loss leads species to extinction but does not allow for extinction to be offset by colonization of disturbed-habitat specialists. Moreover, the use of SAR assumes that species richness is a good proxy of community changes in fragmented landscapes. Here, we assessed how communities dwelling in fragmented landscapes are influenced by habitat loss at multiple scales; then we estimated the ability of models ruled by SAR and by species turnover in successfully predicting changes in community composition, and asked whether species richness is indeed an informative community metric. To address these issues, we used a data set consisting of 140 bird species sampled in 65 patches, from six landscapes with different proportions of forest cover in the Atlantic Forest of Brazil. We compared empirical patterns against simulations of over 8 million communities structured by different magnitudes of the power-law SAR and with species-specific rules to assign species to sites. Empirical results showed that, while bird community composition was strongly influenced by habitat loss at the patch and landscape scale, species richness remained largely unaffected. Modeling results revealed that the compositional changes observed in the Atlantic Forest bird metacommunity were only matched by models with either unrealistic magnitudes of the SAR or by models ruled by species turnover, akin to what would be observed along natural gradients. We show that, in the presence of such compositional turnover, species richness is poorly correlated with species extinction, and z values of the SAR strongly underestimate the effects of habitat loss. We suggest that the observed compositional changes are driven by each species reaching its individual extinction threshold: either a threshold of forest cover for species that disappear with habitat loss, or of matrix cover for species that benefit from habitat loss.

Interrelationship between HIV-1 Fitness and Mutation Rate

Differences in replication fidelity, as well as mutator and antimutator strains, suggest that virus mutation rates are heritable and prone to natural selection. Human immunodeficiency virus type 1 (HIV-1) has many distinct advantages for the study of mutation rate optimization given the wealth of structural and biochemical data on HIV-1 reverse transcriptase (RT) and mutants. In this study, we conducted parallel analyses of mutation rate and viral fitness. In particular, a panel of 10 RT mutants-most having drug resistance phenotypes-was analyzed for their effects on viral fidelity and fitness. Fidelity differences were measured using single-cycle vector assays, while fitness differences were identified using ex vivo head-to-head competition assays. As anticipated, virus mutants possessing either higher or lower fidelity had a corresponding loss in fitness. While the virus panel was not chosen randomly, it is interesting that it included more viruses possessing a mutator phenotype rather than viruses possessing an antimutator phenotype. These observations provide the first description of an interrelationship between HIV-1 fitness and mutation rate and support the conclusion that mutator and antimutator phenotypes correlate with reduced viral fitness. In addition, the findings here help support a model in which fidelity comes at a cost of replication kinetics and may help explain why retroviruses like HIV-1 and RNA viruses maintain replication fidelity near the extinction threshold.

Neglecting uncertainty behind Allee effect estimation may generate false predictions of population extinction risk

Estimation of extinction thresholds arising from Allee effects (Allee thresholds) and related probabilities of population extinction is notoriously difficult. One way is to analyze adequately parameterized population models. Traditionally, a point estimate is substituted for the Allee effect strength in such models. However, each point estimate entails an underlying uncertainty. We explore how accounting for this uncertainty affects the probability of population extinction, and show that this probability decreases sigmoidally with increasing population density, even in the absence of any stochasticity. Deviations from when only a point estimate of the Allee effect strength is used can be significant, unless stochasticity is added and the stochastic noise intensity is high. Significant deviations from when only a point estimate is used also occur when the Allee threshold and the environmental carrying capacity of the species are close enough one to another. We also show that the impact of the uncertainty in the Allee effect strength estimate increases as the Allee effect strength itself increases and decreases as the species recovery potential increases. This is not a good news, since we would like to preferentially and efficiently manage slowly recovering populations prone to strong Allee effects. Still, there is a way to come up with relatively good Allee threshold estimates. Besides an obvious option of collecting as many data as possible, the impact of the uncertainty can be mitigated by diversifying Allee effect experiments such that we put more emphasis on larger size groups. This is somewhat surprising, given that frequent complaints on the (im)possibility of detecting Allee effects concern difficulties in locating, observing and experimenting on rare populations. Our results extend current theory surrounding Allee effects and have broad ramifications for applied ecology.

Modelling plankton ecosystems and the Library of Lotka

Predicting how change will impact ecosystems requires the development of complex models. The complexity of ecosystem models often defies the power of analytical mathematical techniques so they are commonly solved using computers. A problem with this approach is the difficulty in assessing the credibility of model simulation results.We apply ecological axioms to the construction of complex model ecologies. The axioms ensure realistic ecological properties and internal consistency of a broad class of models that encompass many theoretical and applied models. A key new analytical result for our dynamical systems in ecospace is that extinctions can be studied without knowledge of either interior equilibrium points or their stability. By looking only at boundary extinction points we can immediately comment on the extinction behaviour without solving for any of the dynamics. This is a striking simplification, and even holds when the dynamics are chaotic.We demonstrate the approach by constructing three plankton ecosystem models that we designed to have specific properties and show that the effect of change on plankton blooms and/or extinctions depends on the properties of the model chosen for the simulation.

Swimming Upstream

Once found in schools of millions off much of the eastern seaboard, river herring have been overfished in many areas to the point of virtual extinction. As small, minnow-like forage fish, river herring play a crucial role in the marine ecosystem by providing food for striped bass, bluefish, and other commercially important species.

Spitsbergen’s endangered bowhead whales sing through the polar night

Bowhead whales Balaena mysticetus are long-lived cetaceans, uniquely adapted among the baleen whales to live year-round in the Arctic. All bowhead whale populations were greatly reduced by commercial whaling from the 1600s through the 1800s, with the largest, the Spitsber- gen population in the North Atlantic, depleted to the point of extinction. Recent sightings of bow- head whales west of Svalbard precipitated an effort to listen for their vocalizations via 2 re - corders deployed in 2008 on oceanographic moor- ings spaced 95 km apart at 78.8° N latitude in the Fram Strait. Year-round acoustic records were examined for the occurrence of bowhead whale sounds. Simple calls, call sequences, and complex songs were recorded. Repeated call sequences or bowhead whale songs were detected nearly every hour from early November 2008 through late April 2009 on the western Fram Strait recorder. More than 60 unique songs were recorded from October 2008 to April 2009. In contrast, simple calls and call sequences were the most common signals recorded on the central Fram Strait instrument. Peak levels of song production coincided with the period of lowest water temperature, dense ice con- centration, and almost complete darkness. Given the diversity, loudness, and period over which songs were recorded, western Fram Strait appears to be a wintering ground — and potentially a mat- ing area — for this Critically Endangered popula- tion of bowhead whales.

Nucleoside Analogue Mutagenesis of a Single-Stranded DNA Virus: Evolution and Resistance

It has been well established that chemical mutagenesis has adverse fitness effects in RNA viruses, often leading to population extinction. This is mainly a consequence of the high RNA virus spontaneous mutation rates, which situate them close to the extinction threshold. Single-stranded DNA viruses are the fastest-mutating DNA-based systems, with per-nucleotide mutation rates close to those of some RNA viruses, but chemical mutagenesis has been much less studied in this type of viruses. Here, we serially passaged bacteriophage X174 in the presence of the nucleoside analogue 5-fluorouracil (5-FU). We found that 5-FU was unable to trigger population extinction for the range of concentrations tested, but it negatively affected viral adaptability. The phage evolved partial drug resistance, and parallel nucleotide substitutions appearing in independently evolved lines were identified as candidate resistance mutations. Using site-directed mutagenesis, two single-nucleotide substitutions in the lysis protein E (T572C and A781G) were shown to be selectively advantageous in the presence of 5-FU. In RNA viruses, base analogue resistance is often mediated by changes in the viral polymerase, but this mechanism is not possible for X174 and other single-stranded DNA viruses because they do not encode their own polymerase. In addition to increasing mutation rates, 5-FU produces a wide variety of cytotoxic effects at the levels of replication, transcription, and translation. We found that substitutions T572C and A781G lost their ability to confer 5-FU resistance after cells were supplemented with deoxythymidine, suggesting that their mechanism of action is at the DNA level. We hypothesize that regulation of lysis time may allow the virus to optimize progeny size in cells showing defects in DNA synthesis.