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PubMed2005

Paleogenomic record of the extinction of human endogenous retrovirus ERV9.

An outstanding question of genome evolution is what stops the invasion of a host genome by transposable elements (TEs). The human genome, harboring the remnants of many extinct TE families, offers an extraordinary opportunity to investigate this problem. ERV9 is an endogenous retrovirus repeatedly mobilized during primate evolution, 15 to 6 million years ago (MYA), which left a trace of over a hundred provirus-like copies and at least 4,000 solitary long terminal repeats (LTRs) in the human genome. Then, its proliferation ceased for unknown reasons, and the family went extinct. We have made a detailed reconstruction of its last active subfamily, ERV9_XII, by examining 115 solitary LTRs from it. These insertions were grouped into 11 sets according to shared nucleotide variants, which could be placed in a sequential order of 10 to 6 MYA. At least 75% of the subfamily was produced 8 to 6 MYA, during a stage of intense proliferation. With new analytical tools, we show that the youngest and most prolific sets may have been produced by effectively instantaneous expansions of corresponding single-sequence variants. The extinction of this family apparently was not a consequence of its slow gradual degeneration, but the outcome of the fixation of specific restrictive alleles in the human-chimpanzee ancestral population. Three species-specific insertions (two in humans and one in chimpanzees) were identified, further supporting that extinction took place when these two species were beginning to diverge. These are the only fixed differences of this kind so far observed between humans and chimpanzees, apart from those belonging to the human endogenous retrovirus K family.

Animals↗
PubMed2003

Survival and extinction in cyclic and neutral three-species systems.

We study the ABC model ( A + B mapsto 2 B, B + C mapsto 2 C, C + A mapsto 2 A), and its counterpart: the three-component neutral drift model ( A + B mapsto 2 A or 2 B, B + C mapsto 2 B or 2 C, C + A mapsto 2 C or 2 A.) In the former case, the mean-field approximation exhibits cyclic behaviour with an amplitude determined by the initial condition. When stochastic phenomena are taken into account the amplitude of oscillations will drift and eventually one and then two of the three species will become extinct. The second model remains stationary for all initial conditions in the mean-field approximation, and drifts when stochastic phenomena are considered. We analyzed the distribution of first extinction times of both models by simulations of the master equation, and from the point of view of the Fokker-Planck equation. Survival probability vs. time plots suggest an exponential decay. For the neutral model the extinction rate is inversely proportional to the system size, while the cyclic model exhibits anomalous behaviour for small system sizes. In the large system size limit the extinction times for both models will be the same. This result is compatible with the smallest eigenvalue obtained from the numerical solution of the Fokker-Planck equation. We also studied the behaviour of the probability distribution. The exponential decay is found to be robust against certain changes, such as the three reactions having different rates.

Journal Article↗
PubMed2004

Local extinction and recolonization, species effective population size, and modern human origins.

A primary objection from a population genetics perspective to a multiregional model of modern human origins is that the model posits a large census size, whereas genetic data suggest a small effective population size. The relationship between census size and effective size is complex, but arguments based on an island model of migration show that if the effective population size reflects the number of breeding individuals and the effects of population subdivision, then an effective population size of 10,000 is inconsistent with the census size of 500,000 to 1,000,000 that has been suggested by archeological evidence. However, these models have ignored the effects of population extinction and recolonization, which increase the expected variance among demes and reduce the inbreeding effective population size. Using models developed for population extinction and recolonization, we show that a large census size consistent with the multiregional model can be reconciled with an effective population size of 10,000, but genetic variation among demes must be high, reflecting low interdeme migration rates and a colonization process that involves a small number of colonists or kin-structured colonization. Ethnographic and archeological evidence is insufficient to determine whether such demographic conditions existed among Pleistocene human populations, and further work needs to be done. More realistic models that incorporate isolation by distance and heterogeneity in extinction rates and effective deme sizes also need to be developed. However, if true, a process of population extinction and recolonization has interesting implications for human demographic history.

Animals↗
PubMed2002

On the extinction of radiation by a homogeneous but spatially correlated random medium: comment.

Some extinction laws for radiation transmitted through inhomogeneous random media were discussed by Kostinski [J. Opt. Soc. Am. A 18, 1929 (2001)] by means of a complicated use of concepts of statistical theory of fluids. We show that these extinction laws are readily obtained in terms of classical probability theory. The validity of exponential extinction laws for large observation distances (as compared with the size of inhomogeneities of a medium) is proven and emphasized. It is shown that Kostinski's results turn out to be applicable to small observation distances only, for which the concept of extinction law is hardly applicable.

Comment↗
PubMed2006

Local extinction of a foundation species in a hypoxic estuary: integrating individuals to ecosystem.

We integrated across individual, population, community, and ecosystem levels to understand the impact of environmental stress by tracking the foundation species Mytilus edulis in the hypoxic estuary Narragansett Bay, Rhode Island, USA. Our initial surveys revealed that the mussels occurred in nine extensive (2-28 ha) dense (814-9943 individuals/m2) subtidal reefs that attracted a diverse suite of predators (sea stars, crabs, gastropods). Hypoxia occurred in the summer of 2001, and a mussel transplant experiment revealed overall reduced growth rates of individuals, and higher mortality rates among larger mussels. At the population level, large decreases in densities and cover of mussels were correlated with dissolved oxygen concentrations, leading to extinction at one site and reductions of over an order of magnitude at others. Within one year, seven of the eight remaining populations were edged to extinction, and the previously extinct population was recolonized. At the community level, a predator exclusion experiment indicated that predation was an unimportant source of mussel mortality during the hypoxic period, in part due to the emigration of sea stars, as predicted by the Consumer Stress Model. However, mussels were too intolerant to hypoxia to have a net benefit from the predation refuge. The seasonal (summer) occurrence of hypoxia allowed sea stars to return following a lag, as predicted by a stress return time model, and the resumption of predation contributed to the subsequent extinction of mussel populations. At the ecosystem level, the initial filtration rate of the mussel reefs was estimated at 134.6 x 10(6) m3/d, equivalent to filtering the volume of the bay 1.3 times during the 26-d average residence time. That function was reduced by >75% following hypoxia. The effect of hypoxia on each level of organization had consequences at others. For example, size-specific mortality and decreased growth of individuals, and reduced filtration capacity of reefs, indicated a loss of the ability of mussels to entrain planktonic productivity and potential to control future eutrophication and hypoxia. Our study quantified patterns of loss and identified pathways within an integrative framework of feedbacks, summarized in a conceptual model that is applicable to similar foundation species subjected to environmental stress.

Animals↗
PubMed1966

Extinction-induced aggression.

Pigeons were conditioned to peck a response key under a procedure that alternated periods of food reinforcement with periods of extinction. The pigeons attacked a nearby pigeon at the onset of extinction. Some also attacked a stuffed model of a pigeon. The duration of attack was an inverse function of the time since the last food reinforcement and a direct function of the number of reinforcements. The pigeons attacked after the last food delivery whether or not the conditioned pecking response was required and whether or not the extinction period was signaled. The food had to be eaten; the mere sight and sound of food being delivered did not produce attack. Prior satiation reduced attack. The phenomenon was not attributable to a past history of competition between pigeons since socially deprived pigeons also attacked. Superstitious reinforcement of attack was not found to be a factor. The results indicated that the transition from food reinforcement to extinction was an aversive event that produced aggression.

Journal Article↗
PubMed1969

Extinction of a discriminative operant following discrimination learning with and without errors.

Different groups of pigeons were trained to respond to red and not to green with and without errors (responses to green) under a free operant procedure, in which responding to red was intermittently reinforced, and under a trial procedure in which all responses to red were reinforced. The response to red was then extinguished under a procedure in which the discriminative stimuli were successively alternated as during discrimination training. The performances of those birds that learned the discrimination without errors under the trial procedure were seriously disrupted during extinction; the birds persistently responded to green for the first time. The performances of those subjects that learned the discrimination without errors under the free operant procedure were not disrupted during extinction. In a second experiment, the same discrimination was trained without errors under a trial procedure in which the response to red was intermittently reinforced. Extinction did not disrupt discrimination performance. Thus, errorless discrimination performance was shown to remain intact during extinction so long as the response to red was intermittently reinforced during discrimination training.

Journal Article↗
PubMed1970

Instructional control of human operant responding during extinction following fixed-ratio conditioning.

When given pre-conditioning instructions correctly indicating the maximum number of reinforcements obtainable, subjects made few responses during extinction following FR 10 conditioning. More extinction responses occurred when the maximum-reinforcement instructions suggested that reinforcements were obtainable during extinction. The highest rates of responding during extinction were produced by subjects who had no maximum-reinforcement instructions.

Journal Article↗
PubMed1973

Response decrements produced by extinction and by response-independent reinforcement.

The effects of extinction and of response-independent (free) reinforcement in decreasing rates of key pecking by pigeons were compared in single schedule (Phase 1) and multiple (Phase 2) conditions. In both phases, response rates decreased more rapidly with extinction than with free reinforcement conditions. Behavioral contrast was obtained from subjects trained in a multiple schedule involving extinction in Phase 2, whereas subjects trained in a multiple schedule involving free reinforcement showed a slight negative induction effect. Whether subjects experienced extinction or free reinforcement under single stimulus conditions did not affect subsequent performance in the discrimination situation of the second phase. Disinhibition testing was carried out at the end of both phases, but there was no evidence for disinhibitory effects under any condition.

Journal Article↗
PubMed1973

Extinction-induced aggression during errorless discrimination learning.

Pigeons were trained to discriminate without errors between a green light and a dark key. The key-pecking response was reinforced in the presence of green, and extinction was in effect in the presence of the dark key. The duration of the dark key was gradually increased during the first few sessions of conditioning. The opportunity to attack a restrained target pigeon was also present. During discrimination training, the rate of attack in the presence of the dark key was higher for each animal than the operant level, even though most of the animals acquired the discrimination without errors. Furthermore, the rate of attack did not decrease during 45 sessions of discrimination training. Attack also occurred in the presence of the green stimulus, although to a lesser extent than during extinction. Reinforcement during green is a determinant of attack during extinction because removal of reinforcement virtually eliminated attack during extinction.

Journal Article↗
PubMed1975

The control of switching into blackout during extinction.

During the extinction component of a multiple variable-interval extinction schedule, four pigeons learned to peck a second key that switched off the keylights. Two experiments attempted to isolate the events that control this behavior. In the first experiment, switching into blackout was equally maintained when switches were restricted to the first minute as when they were restricted to the last minute of the extinction component. When switches could be emitted in the first and last minutes, they occurred more frequently in the first. Restricting switching to the first minute of each component and eliminating the blackout between components had no effect on switching. In the second experiment, when the stimulus correlated with extinction was omitted, switching decreased slightly. Omission of both multiple schedule stimuli decreased the switching rate, but switching was still maintained. Food reinforcement was then omitted and switching by two birds increased. Switching ceased when blackout was no longer the consequence of pecking the switching key. It was concluded that switching was not controlled by the similarity of the blackouts produced by the switching key and those that occurred between components; nor was it maintained by the temporal proximity of switching responses to the onset of the reinforced component. Finally, switching did not appear to be controlled by the main-key stimuli correlated with the components of the multiple schedule.

Journal Article↗
PubMed1976

Alternative response training, differential reinforcement of other behavior, and extinction in squirrel monkeys (Saimiri sciureus).

In Experiment I, (a) extinction, (b) extinction plus reinforcement of a discrete alternative response, and (c) differential reinforcement of other behavior were each correlated with a different stimulus in a three-component multiple schedule. The alternative-response procedure more rapidly and completely suppressed behavior than did differential reinforcement of other behavior. Differential reinforcement of other behavior was slightly more effective than extinction alone. In Experiment II, reinforcement of specific alternative behavior during extinction and differential reinforcement of other behavior were used in two components, while one component continued to provide reinforcement for the original response. Once again, the alternative-response procedure was most effective in reducing responding as long as it remained in effect. However, the responding partially recovered when reinforcement for competing behavior was discontinued. In general, responding was less readily reduced by differential reinforcement of other behavior than by the specific alternative-response procedure.

Journal Article↗
PubMed1986

An assessment of the role of handling cues in "spontaneous recovery" after extinction.

Three experiments examined the assertion that presession handling cues that accompany training with reinforcement might account for spontaneous recovery when they reoccur following extinction. In Experiment 1, after extensive training on a variable-interval schedule, key pecking in pigeons was extinguished following either normal or distinctively different handling and transportational cues. Those cues resulted in enhanced spontaneous recovery 24 hr later when normal cues were reinstated. In Experiment 2, however, subjects tested following the normal handling cues showed no more spontaneous recovery than did subjects that spent the entire extinction-test interval in the experimental chambers and thus were tested without handling cues altogether. In Experiment 3, a group whose test for recovery began 10 min after being placed in the chambers yielded as much spontaneous recovery as did a group tested normally. Furthermore, a group for which extinction began at mid-session and for which handling therefore could not be a discriminative cue for extinction showed no more spontaneous recovery than did the other two groups. Handling cues thus contributed to spontaneous recovery only after explicit discrimination training, as provided in Experiment 1.

Journal Article↗
PubMed1994

The transfer of respondent eliciting and extinction functions through stimulus equivalence classes.

Two studies investigated the transfer of respondent elicitation through equivalence classes. In Experiment 1, match-to-sample procedures were used to teach 8 subjects two four-member equivalence classes. One member of one class was then paired with electric shock, and one member of the other class was presented without shock. All remaining stimuli were then presented. Using skin conductance as the measure of conditioning, transfer of conditioning was demonstrated in 6 of the 8 subjects. In Experiment 2, similar procedures were used to replicate the results of Experiment 1 and investigate the transfer of extinction. Following equivalence training and conditioning to all members of one class, one member was then presented in extinction. When the remaining stimuli from this class were then presented, they failed to elicit skin conductance. In the final phase of the experiment, the stimulus that was previously presented in extinction was reconditioned. Test trials with other members of the class revealed that they regained elicitation function. These results demonstrate that both respondent elicitation and extinction can transfer through stimulus classes. The clinical and applied significance of the results is discussed.

Journal Article↗
PubMed2004

Role of the hippocampus and amygdala in the extinction of fear-motivated learning.

Fear-motivated learning is at the root of phobias, panic, generalized anxiety and the posttraumatic stress disorder. This makes the inhibition of fear-motivated behavior a therapeutic desideratum in these diseases. The simplest way to accomplish this is by extinction, a procedure by which a given association between a conditioned stimulus or context (CS) and a fearsome event is replaced by a new association between the CS and the lack of the fearsome stimulus. This is a new learning for the subject and, in rats, it requires gene expression and protein synthesis both in the hippocampus and the basolateral amygdala, alongside with the activation of various metabolic signaling pathways. These requirements are similar to, but not identical with those for consolidation of the original memory. In addition, some systems uninvolved in original consolidation appear to be involved in extinction, namely, the endocannabinoid system. Extinction can be enhanced by prolonging the exposure to the lack of fearsome stimulation; e.g., in rats, by increasing the time of permanence in the compartment where the animals no longer receive a footshock. Further research into the possibilities of enhancing extinction at the expense of the original fearsome learning is desirable.

Amygdala↗
PubMed1989

Contralateral and ipsilateral tactile extinction in patients with right and left focal brain damage.

Heilman has suggested that right hemisphere lesions produce neglect both in the spaces contralateral and ipsilateral to the damaged hemisphere. To test this hypothesis, we studied the incidence of contralateral and ipsilateral tactile extinctions in 44 right and 59 left brain-damaged patients, by means of a standard test of a double tactile simultaneous stimulation of symmetrical and asymmetrical parts of the two sides of the body and of ipsilateral body parts. Results did not confirm Heilman's hypothesis; while contralateral tactile extinction was more frequent and severe in right than in left brain-damaged patients, no hemispheric difference was found when the number of ipsilateral extinctions was taken into account. Furthermore, ipsilateral tactile extinction was significantly related to aspecific factors (such as age, severity of sensorimotor impairment and widespread mental deterioration), irrespective of the hemispheric side of lesion.

Brain Diseases↗
PubMed2001

[Biological crisis at the end of the Cretaceous and the extinction of the dinosaurs. Validity of the cosmic hypothesis].

The history of life, which appeared more than 500 million years ago, has been characterized by a constant faunal and floral turnover. On five occasions, the background extinctions has become a mass extinction (ME), i.e. a major biotic crisis collapsing the upward curve of the biodiversity. The mass extinction of the end of the Permian is the most murderous but the end-Cretaceous one, which experiences dinosaur's death, is the most well-known. In fact, these land-dwelling reptiles with upright limbs, as well as the pterosaurs, the mosasaurs and numerous invertebrates die as far as the last. There exists a lot of hypotheses tending to explain their death but they are often extravagant and/or impossible to be verified. The last one, referring to a collapse between the earth and a heavenly large bolide has given rise, since more than 20 years, to heated debates between catastrophists and gradualists, even if the reality of the impact seems no more doubtful (discovery of Chicxulub impact crater, iridium anomaly, tektite glass, shocked quartz, spinels with high nickel concentrations). It is now the extent of the deleterious effects (regional or worldwide repercussion) which is debating. By referring to the obtained data in oceanic environment and, if necessary, in terrestrial environment where fossil record is too often incomplete, it can be noticed an important fact corresponding to a selective character of extinctions, the event of the C/T boundary killing off some taxa while others are preserved. This remark does not really correspond to the hypothesis of a sudden planetary catastrophe of large magnitude. Consequently, it seems to be reasonable to make arise intrinsic factors associated to the dynamics of the globe (volcanic eruptions, marine regression, fall of temperature) over a long period. The collapse with the Chicxulub asteroid should then come up, especially in Western North-America, as a "coup de grâce" in a weakened ecosystem.

Animals↗
PubMedDate not supplied

Conditions of visual verbal extinction: does the ipsilesional stimulus have to be identified?

Six left-neglect patients were presented with four-letter words in the left and/or right hemifield, in different contextual conditions: unilateral, bilateral-x in which one word appears on one side and a string of "x" appears on the other side (the side of "x'' was not predictable), and bilateral-word (presentation of one word in each hemifield). In Experiment 1, left extinction occurred even if the right stimulus was an easily discriminable string of "x." Experiment 2 showed that increasing the size of the left stimuli reduced extinction when a string of "x" was presented on the right hemifield. However, extinction was stronger with bilateral-word presentation. These results indicate the presence of an early component in the extinction phenomenon, i.e., a "magnetic" attraction toward the ipsilesional hemifield, but are also in favor of some additional deficit, at a later stage of information processing.

Brain↗