The causes of extinction

A species may go extinct either because it is unable to evolve rapidly enough to meet changing circumstances, or because its niche disappears and no capacity for rapid evolution could have saved it. Although recent extinctions can usually be interpreted as resulting from niche disappearance, the taxonomic distribution of parthenogens suggests that inability to evolve may also be important. A second distinction is between physical and biotic causes of extinction. Fossil evidence for constant taxonomic diversity, combined with species turnover, implies that biotic factors have been important. A similar conclusion emerges from studies of recent introductions of predators, competitors and parasites into new areas. The term 'species selection' should be confined to cases in which the outcome of selection is determined by properties of the population as a whole, rather than of individuals. The process has been of only trivial importance in producing complex adaptations, but of major importance in determining the distribution of different types of organisms. An adequate interpretation of the fossil record requires a theory of the coevolution of many interacting species. Such a theory is at present lacking, but various approaches to it are discussed.     

Historical bird and terrestrial mammal extinction rates and causes

Aim Conservation of species is an ongoing concern. Location Worldwide. Methods We examined historical extinction rates for birds and mammals and contrasted island and continental extinctions. Australia was included as an island because of its isolation. Results Only six continental birds and three continental mammals were recorded in standard databases as going extinct since 1500 compared to 123 bird species and 58 mammal species on islands. Of the extinctions, 95% were on islands. On a per unit area basis, the extinction rate on islands was 177 times higher for mammals and 187 times higher for birds than on continents. The continental mammal extinction rate was between 0.89 and 7.4 times the background rate, whereas the island mammal extinction rate was between 82 and 702 times background. The continental bird extinction rate was between 0.69 and 5.9 times the background rate, whereas for islands it was between 98 and 844 times the background rate. Undocumented prehistoric extinctions, particularly on islands, amplify these trends. Island extinction rates are much higher than continental rates largely because of introductions of alien predators (including man) and diseases. Main conclusions Our analysis suggests that conservation strategies for birds and mammals on continents should not be based on island extinction rates and that on islands the key factor to enhance conservation is to alleviate pressures from uncontrolled hunting and predation.     

Are human progestagens among the causes of amphibian extinction?

We hypothesised that massive elimination of human and animal progestagens through wastewater can be toxic for reproduction of amphibians. Several medical test using amphibian bioassays (i.e. Hogben test) have demonstrated that human chorionic gonadotropin is toxic for amphibians. Nowadays, a huge amount of sexual hormones from women, animal farms and aquaculture arrive to inland water systems and could be a cause of amphibians extinction.     

Relaxation of selective constraints causes independent selenoprotein extinction in insect genomes

Background

Selenoproteins are a diverse family of proteins notable for the presence of the 21st amino acid, selenocysteine. Until very recently, all metazoan genomes investigated encoded selenoproteins, and these proteins had therefore been believed to be essential for animal life. Challenging this assumption, recent comparative analyses of insect genomes have revealed that some insect genomes appear to have lost selenoprotein genes.

Methodology/Principal Findings

In this paper we investigate in detail the fate of selenoproteins, and that of selenoprotein factors, in all available arthropod genomes. We use a variety of in silico comparative genomics approaches to look for known selenoprotein genes and factors involved in selenoprotein biosynthesis. We have found that five insect species have completely lost the ability to encode selenoproteins and that selenoprotein loss in these species, although so far confined to the Endopterygota infraclass, cannot be attributed to a single evolutionary event, but rather to multiple, independent events. Loss of selenoproteins and selenoprotein factors is usually coupled to the deletion of the entire no-longer functional genomic region, rather than to sequence degradation and consequent pseudogenisation. Such dynamics of gene extinction are consistent with the high rate of genome rearrangements observed in Drosophila. We have also found that, while many selenoprotein factors are concomitantly lost with the selenoproteins, others are present and conserved in all investigated genomes, irrespective of whether they code for selenoproteins or not, suggesting that they are involved in additional, non-selenoprotein related functions.

Conclusions/Significance

Selenoproteins have been independently lost in several insect species, possibly as a consequence of the relaxation in insects of the selective constraints acting across metazoans to maintain selenoproteins. The dispensability of selenoproteins in insects may be related to the fundamental differences in antioxidant defense between these animals and other metazoans.     

Local extinction and the evolution of dispersal rates: causes and correlations

We present the results of individual-based simulation experiments on the evolution of dispersal rates of organisms living in metapopulations. We find conflicting results regarding the relationship between local extinction rate and evolutionarily stable (ES) dispersal rate depending on which principal mechanism causes extinction: if extinction is caused by environmental catastrophes eradicating local populations, we observe a positive correlation between extinction and ES dispersal rate; if extinction is a consequence of stochastic local dynamics and environmental fluctuations, the correlation becomes ambiguous; and in cases where extinction is caused by dispersal mortality, a negative correlation between local extinction rate and ES dispersal rate emerges. We conclude that extinction rate, which both affects and is affected by dispersal rates, is not an ideal predictor for optimal dispersal rates.     

The nature of extinction

The phenomenon of species extinction raises more and more concern among ecologists facing the actual crisis of biodiversity. Scientific investigations of the causes and effects of extinction must be completed by a philosophical analysis of the concept of extinction that aims to clarify the meanings of the term 'extinction' and to analyse modalities, criteria and degrees of extinction. We will focus our attention on the apparent paradox of the possible 'resurrection' of species in the near future with the help of genetic biotechnology and cloning techniques. The ontological background of the extinction concept is analysed in relation to the idea of species as classes. We will also show that there is no simple analogy between death and species extinction, and develop a conceptualist and dualistic system of supra-individual entities (species vs. population), supported by an instrumentalist approach to genetic manipulations which transform species into interactive kinds, which can go extinct and be recreated.     

Drivers of extinction: the case of Azorean beetles

Oceanic islands host a disproportionately high fraction of endangered or recently extinct endemic species. We report on species extinctions among endemic Azorean beetles following 97% habitat loss since AD 1440. We infer extinctions from historical and contemporary records and examine the influence of three predictors: geographical range, habitat specialization and body size. Of 55 endemic beetle species investigated (out of 63), seven can be considered extinct. Single-island endemics (SIEs) were more prone to extinction than multi-island endemics. Within SIEs restricted to native habitat, larger species were more extinction-prone. We thus show a hierarchical path to extinction in Azorean beetles: species with small geographical range face extinction first, with the larger bodied ones being the most threatened. Our study provides a clear warning of the impact of habitat loss on island endemic biotas.     

Martian channels and the search for extraterrestrial life

Summary The origin of the channels on Mars has been a subject of intense interest since they were first recognized on early Mariner 9 images (Driscoll, 1972; Masursky, 1973). Their presence on the planet, and their striking resemblance to terrestrial flood channels related to glacial outbursts or to dendritic river systems has suggested to most investigators (Baker, 1974, 1977; Nummedal, 1978; Carr, 1979; Masursky et al., 1977) that they were formed by running water. Because life as we know it is dependent on water, the discovery by the Mariner cameras, of watercut channels and volcanoes as a source for water, and water ice in the residual north polar cap by Viking, has reaffirmed the choice of Mars as the best target for the search for extraterrestrial life.     

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.     

The molar extinction of rhodopsin

The molar extinction of rhodopsin is 40,600 cm.² per mole equivalent of retinene; i.e., this is the extinction of a solution of rhodopsin which is produced by, or yields on bleaching, a molar solution of retinene. The molar extinctions of all-trans retinene and all-trans retinene oxime have also been determined in ethyl alcohol and aqueous digitonin solutions. On the assumption that each chromophoric group of rhodopsin is made from a single molecule of retinene, it is concluded that the primary photochemical conversion of rhodopsin to lumi-rhodopsin has a quantum efficiency of 1; though the over-all bleaching of rhodopsin in solution to retinene and opsin may have a quantum efficiency as low as one-half. On bleaching cattle rhodopsin, about two sulfhydryl groups appear for each molecule of retinene liberated. In frog rhodopsin the —SH:retinene ratio appears to be higher, 5:2 or perhaps even 3:1. Some of this sulfhydryl appears to have been engaged in binding retinene to opsin; some may have been exposed as the result of changes in opsin which accompany bleaching, comparable with protein denaturation.     

The mechanism of background extinction

Following publication of On the Origin of Species, biologists concentrated on and resolved the mechanisms of adaptation and speciation, but largely ignored extinction. Thus, extinction remained essentially a discipline of palaeontology. Adequate language is not available to describe extinction phenomena because they must be discussed in the passive voice, wherein populations simply ‘go extinct’ without reference to process, specifics, effects, or causality. Extinction is also described typically in terms of its dynamics (including rate or risk), and although correlative variables enhance our ability to predict extinction, they do not necessarily enable an understanding of process. Yet background extinction, like evolution, is a process requiring a functional explanation, without which it is impossible to formulate mechanisms. We define the mechanism of background extinction as a typically long‐term, multi‐generational loss of reproductive fitness. This simple concept has received little credence because of a perception that excess generation of progeny ensures population sustainability, and perhaps the misconception that the loss of reproductive fitness somehow constitutes selection against reproduction itself. During environmental shifts, reproductive fitness is compromised when biotic or abiotic extremes consistently exceed existing norms of reaction. Subsequent selection will now favour individual survival over reproductive fitness, initiating long‐term negative selection pressure and population decline. Background extinction consists typically of two intergrading phases: habitat attenuation and habitat dissolution. These processes generate the relict populations that characterize many species undergoing background extinction. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 255–268.     

The extinction of the dinosaurs

Non‐avian dinosaurs went extinct 66 million years ago, geologically coincident with the impact of a large bolide (comet or asteroid) during an interval of massive volcanic eruptions and changes in temperature and sea level. There has long been fervent debate about how these events affected dinosaurs. We review a wealth of new data accumulated over the past two decades, provide updated and novel analyses of long‐term dinosaur diversity trends during the latest Cretaceous, and discuss an emerging consensus on the extinction's tempo and causes. Little support exists for a global, long‐term decline across non‐avian dinosaur diversity prior to their extinction at the end of the Cretaceous. However, restructuring of latest Cretaceous dinosaur faunas in North America led to reduced diversity of large‐bodied herbivores, perhaps making communities more susceptible to cascading extinctions. The abruptness of the dinosaur extinction suggests a key role for the bolide impact, although the coarseness of the fossil record makes testing the effects of Deccan volcanism difficult.     

Selecting for extinction: nonrandom disease-associated extinction homogenizes amphibian biotas

Studying the patterns in which local extinctions occur is critical to understanding how extinctions affect biodiversity at local, regional and global spatial scales. To understand the importance of patterns of extinction at a regional spatial scale, we use data from extirpations associated with a widespread pathogenic agent of amphibian decline, Batrachochytrium dendrobatidis ( Bd ) as a model system. We apply novel null model analyses to these data to determine whether recent extirpations associated with Bd have resulted in selective extinction and homogenization of diverse tropical American amphibian biotas. We find that Bd -associated extinctions in this region were nonrandom and disproportionately, but not exclusively, affected low-occupancy and endemic species, resulting in homogenization of the remnant amphibian fauna. The pattern of extirpations also resulted in phylogenetic homogenization at the family level and ecological homogenization of reproductive mode and habitat association. Additionally, many more species were extirpated from the region than would be expected if extirpations occurred randomly. Our results indicate that amphibian declines in this region are an extinction filter, reducing regional amphibian biodiversity to highly similar relict assemblages and ultimately causing amplified biodiversity loss at regional and global scales.     

The extinction context enables extinction performance after a change in context

One experiment with human participants determined the extent to which recovery of extinguished responding with a context switch was due to a failure to retrieve contextually controlled learning, or some other process such as participants learning that context changes signal reversals in the meaning of stimulus-outcome relationships. In a video game, participants learned to suppress mouse clicking in the presence of a stimulus that predicted an attack. Then, that stimulus underwent extinction in a different context (environment within the game). Following extinction, suppression was recovered and then extinguished again during testing in the conditioning context. In a final test, participants that were tested in the context where extinction first took place showed less of a recovery than those tested in a neutral context, but they showed a recovery of suppression nevertheless. A change in context tended to cause a change in the meaning of the stimulus, leading to recovery in both the neutral and extinction contexts. The extinction context attenuated that recovery, perhaps by enabling retrieval of the learning that took place in extinction. Recovery outside an extinction context is due to a failure of the context to enable the learning acquired during extinction, but only in part.     

The time to extinction for a stochastic SIS-household-epidemic model

We analyse a Markovian SIS epidemic amongst a finite population partitioned into households. Since the population is finite, the epidemic will eventually go extinct, i.e., have no more infectives in the population. We study the effects of population size and within household transmission upon the time to extinction. This is done through two approximations. The first approximation is suitable for all levels of within household transmission and is based upon an Ornstein-Uhlenbeck process approximation for the diseases fluctuations about an endemic level relying on a large population. The second approximation is suitable for high levels of within household transmission and approximates the number of infectious households by a simple homogeneously mixing SIS model with the households replaced by individuals. The analysis, supported by a simulation study, shows that the mean time to extinction is minimized by moderate levels of within household transmission.     

The currency and tempo of extinction

This study examines estimates of extinction rates for the current purported biotic crisis and from the fossil record. Studies that compare current and geological extinctions sometimes use metrics that confound different sources of error and reflect different features of extinction processes. The per taxon extinction rate is a standard measure in paleontology that avoids some of the pitfalls of alternative approaches. Extinction rates reported in the conservation literature are rarely accompanied by measures of uncertainty, despite many elements of the calculations being subject to considerable error. We quantify some of the most important sources of uncertainty and carry them through the arithmetic of extinction rate calculations using fuzzy numbers. The results emphasize that estimates of current and future rates rely heavily on assumptions about the tempo of extinction and on extrapolations among taxa. Available data are unlikely to be useful in measuring magnitudes or trends in current extinction rates.