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PubMed1999

The position of Cetacea within mammalia: phylogenetic analysis of morphological data from extinct and extant taxa.

Knowledge of the phylogenetic position of the order Cetacea (whales, dolphins, and porpoises) within Mammalia is of central importance to evolutionary biologists studying the transformations of biological form and function that accompanied the shift from fully terrestrial to fully aquatic life in this clade. Phylogenies based on molecular data and those based on morphological data both place cetaceans among ungulates but are incongruent in other respects. Morphologists argue that cetaceans are most closely related to mesonychians, an extinct group of terrestrial ungulates. They have disagreed, however, as to whether Perissodactyla (odd-toed ungulates) or Artiodactyla (even-toed ungulates) is the extant clade most closely related to Cetacea, and have long maintained that each of these orders is monophyletic. The great majority of molecule-based phylogenies show, by contrast, not only that artiodactyls are the closest extant relatives of Cetacea, but also that Artiodactyla is paraphyletic unless cetaceans are nested within it, often as the sister group of hippopotamids. We tested morphological evidence for several hypotheses concerning the sister taxon relationships of Cetacea in a maximum parsimony analysis of 123 morphological characters from 10 extant and 30 extinct taxa. We advocate treating certain multistate characters as ordered because such a procedure incorporates information about hierarchical morphological transformation. In all most-parsimonious trees, whether multistate characters are ordered or unordered, Artiodactyla is the extant sister taxon of Cetacea. With certain multistate characters ordered, the extinct clade Mesonychia (Mesonychidae + Hapalodectidae) is the sister taxon of Cetacea, and Artiodactyla is monophyletic. When all fossils are removed from the analysis, Artiodactyla is paraphyletic with Cetacea nested inside, indicating that inclusion of mesonychians and other extinct stem taxa in a phylogenetic analysis of the ungulate clade is integral to the recovery of artiodactyl monophyly. Phylogenies derived from molecular data alone may risk recovering inconsistent branches because of an inability to sample extinct clades, which by a conservative estimate, amount to 89% of the ingroup. Addition of data from recently described astragali attributed to cetaceans does not overturn artiodactyl monophyly.

Animals↗
PubMed1981

Immunofluorescence analysis of the time-course of extinction, reexpression, and activation of albumin production in rat hepatoma-mouse fibroblast heterokaryons and hybrids.

We have used a combination of a sensitive immunocytochemical stain for intracellular albumin, and Hoechst 33258 dye for identification of parental nuclei to investigate the time-course of extinction, reexpression, and activation of albumin production in fusion products of 1s (hyperdiploid) or 2s (hypertetradiploid) rat hepatoma cells with mouse fibroblasts (L cells or embryonic cells). In all combinations, the initial event is extinction of albumin production. Extinction occurs immediately after fusion when the mouse fibroblast is a normal embryonic (senescent?) cell. In the case of an L cell, rat albumin is synthesized and secreted during the first 12 h after fusion; no production of mouse albumin occurs. Thereafter, albumin production ceases. 8-12 d after fusion, young hybrid colonies are found to resume the synthesis of rat albumin (reexpression), and several days later the production of mouse albumin begins (activation). The patterns of reexpression and activation indicate (a) that chromosome loss is not necessary for either event to occur and (b) that the cells active in the synthesis of mouse albumin are a subpopulation of those cells already engaged in the production of rat albumin. We conclude that (a) extinction is mediated by diffusible factor(s) from the L-cell parent that act in the hepatoma nucleus to prevent the formation of new albumin messenger RNA; (b) reexpression and activation are gene dosage-dependent but extinction is not; and (c) previously active genes are more rapidly expressed than previously silent ones.

Albumins↗
PubMed2002

Seed germination and reproductive features of Lysimachia minoricensis (Primulaceae), a wild-extinct plant.

Lysimachia minoricensis is one of the few Mediterranean endemic plants (Minorca, Balearic islands) that has gone extinct in the wild but which persists as extant germplasm or cultivated plants in several botanical gardens. Reproductive features (seed set, number of seeds per capsule, seed weight) and germination responses to constant temperatures, sea water and dry-heat pre-treatments were investigated to determine the extent to which they may have influenced the extinction of the species. Seed set in Lysimachia is not dependent on pollinators, suggesting a functional selfer breeding system. Most plants produced a large mean number of fruits (23.2) and seeds (466), and the mean production of seeds per individual was estimated to be almost 1,100. Overall, no highly specific requirements were observed for seed germination. Seed germination was not inhibited in the dark, and a high germinability (over 87% in all cases) was recorded in most experiments, with the exception of those performed at low temperatures (5 and 10 degrees C). These data suggest that fertility and seed viability were not the major causes of extinction. The high reproductive performance of L. minoricensis is in striking contrast to its status as a wild-extinct plant, suggesting that extrinsic factors were responsible for its extinction.

Conservation of Natural Resources↗
PubMed2004

Selection, subdivision and extinction and recolonization.

In a subdivided population, the interaction between natural selection and stochastic change in allele frequency is affected by the occurrence of local extinction and subsequent recolonization. The relative importance of selection can be diminished by this additional source of stochastic change in allele frequency. Results are presented for subdivided populations with extinction and recolonization where there is more than one founding allele after extinction, where these may tend to come from the same source deme, where the number of founding alleles is variable or the founders make unequal contributions, and where there is dominance for fitness or local frequency dependence. The behavior of a selected allele in a subdivided population is in all these situations approximately the same as that of an allele with different selection parameters in an unstructured population with a different size. The magnitude of the quantity N(e)s(e), which determines fixation probability in the case of genic selection, is always decreased by extinction and recolonization, so that deleterious alleles are more likely to fix and advantageous alleles less likely to do so. The importance of dominance or frequency dependence is also altered by extinction and recolonization. Computer simulations confirm that the theoretical predictions of both fixation probabilities and mean times to fixation are good approximations.

Biological Evolution↗
PubMed1999

Extinction of alpha1-antitrypsin expression in cell hybrids is independent of HNF1alpha and HNF4 and involves both promoter and internal DNA sequences.

In rat hepatoma x fibroblast somatic cell hybrids, extinction of rat alpha1-antitrypsin (alpha1AT) gene expression is accompanied by the loss of liver-enriched transcription factors hepatocyte nuclear factor 1 (HNF1alpha) and hepatocyte nuclear factor 4 (HNF4). Previous analysis showed that forced expression of functional HNF1alpha failed to prevent extinction of the rat alpha1AT locus in cell hybrids. Here I show that ectopic co-expression of HNF1alpha plus HNF4 fails to prevent extinction of either rat or human alpha1AT genes in cell hybrids. A 40 kb human alpha1AT minilocus integrated into the rat genome is fully silenced in cell hybrids in the presence of transacting factors. The integrated alpha1AT promoter, but not a viral or ubiquitously active promoter, is repressed 35-fold in the cell hybrids. In addition, position effects also contributed to extinction of many integrated transgenes in a cell type-dependent manner. Finally, internal DNA sequences within the human alpha1AT gene contributed dramatically to the extinction phenotype, resulting in a further 10- to 30-fold reduction in alpha1AT gene expression in cell hybrids. Thus, multiple mechanisms contribute to silencing of tissue-specific gene expression of the alpha1AT gene in cell hybrids.

Animals↗
PubMed2001

Long-lasting resistance to extinction of response reinstatement induced by ethanol-related stimuli: role of genetic ethanol preference.

BACKGROUND: The conditioning of ethanol's reinforcing effects with specific environmental stimuli is thought to be a critical factor in long-lasting relapse risk associated with alcoholism. To study the significance of such learning factors in the addictive potential of ethanol, this experiment was designed (1) to characterize the effects of stimuli associated with alcohol availability on the reinstatement of responding at a previously ethanol-paired lever in rats with genetically determined ethanol preference versus nonpreference and (2) to examine the persistence of the motivating effects of these stimuli over time. METHODS: Male alcohol-preferring (P) and alcohol-nonpreferring (NP) rats were trained to operantly self-administer ethanol (10% w/v) or water on a fixed-ratio 1 schedule in a 30-min daily session. Ethanol and water sessions were scheduled in random sequence across training days. Ethanol availability was signaled by an olfactory discriminative stimulus (banana extract, S+), and each lever press was paired with brief presentation of the conditioning chamber's house light (CS+). The discriminative stimulus signaling water availability (i.e., nonreward) consisted of anise odor (S-), and lever-responses during water sessions were paired with a brief white noise generation (CS-). The rats then were placed on extinction conditions during which ethanol and water, as well as the corresponding stimuli, were withheld. The effects of noncontingent exposure to the S+ versus S- paired with response-contingent presentation of the CS+ versus CS- on responding at the previously active lever were then determined in 30-min reinstatement sessions. To study the resistance to extinction of the effects of the ethanol-associated stimuli, additional tests were conducted at 3-day intervals for a total of 50 days. RESULTS: The number of ethanol-reinforced responses during self-administration training was significantly greater in P than in NP rats (p < 0.01). After extinction, a significant recovery of responding was observed in both groups of rats under the stimulus conditions associated with ethanol (S+/CS+) but not those associated with water (S-/CS-). However, the response reinstatement was significantly greater in P than NP rats (p < 0.01). In addition, the results revealed a considerable resistance to extinction to the effects of the ethanol-associated stimuli. Throughout the 50-day test period, responding remained significantly above extinction levels in both P and NP rats (p < 0.01), but with an overall greater number of responses in P than NP rats (p < 0.05). CONCLUSIONS: The results support the hypothesis that conditioning factors contribute importantly to compulsive ethanol seeking and long-lasting vulnerability to relapse. In addition, the results suggest that genetic predisposition toward heightened ethanol intake extends to greater susceptibility to the motivating effects of ethanol-related environmental stimuli.

Alcoholism↗
PubMed2003

The cortical substrate of visual extinction.

Neuroimaging studies investigated the attentional systems of the human brain revealing two networks, one for voluntary allocation of attention and another for stimulus-driven attentional processes. Whereas lesions of the latter system were supposed to lead to spatial neglect, we show that such lesions rather are typical for the occurrence of visual extinction. Extinction describes the inability of brain-damaged patients to detect a contralesional target in the presence of a competing ipsilesional stimulus. In a sample of consecutively admitted patients with right hemisphere stroke, we found dissociable cortical substrates for spatial neglect and visual extinction. There was a surprising congruency between the typical lesion site in patients with extinction and the activation clusters found in previous neuroimaging studies of healthy subjects. The results show that the temporo-parietal junction (TPJ), considered to be a crucial part of the stimulus-driven attentional network, is the neural substrate of visual extinction.

Aged↗
PubMed2006

Human impacts and the global distribution of extinction risk.

Understanding the global geographical distribution of extinction risk is a key challenge in conservation biology. It remains controversial, however, to what extent areas become threat hotspots simply because of high human impacts or due to predisposing ecological conditions. Limits to the taxonomic and geographical extent, resolution and quality of previously available data have precluded a full global assessment of the relative roles of these factors. Here, we use a new global database on the geographical distributions of birds on continents and continental islands to show that, after controlling for species richness, the best predictors of the global pattern of extinction risk are measures of human impact. Ecological gradients are of secondary importance at a global scale. The converse is true for individual biogeographic realms, within which variation in human impact is reduced and its influence on extinction risk globally is therefore underestimated. These results underline the importance of a global perspective on the mechanisms driving spatial patterns of extinction risk, and the key role of anthropogenic factors in driving the current extinction crisis.

Animals↗
PubMed1989

Mass extinctions among tetrapods and the quality of the fossil record.

The fossil record of tetrapods is very patchy because of the problems of preservation, in terrestrial sediments in particular, and because vertebrates are rarely very abundant. However, the fossil record of tetrapods has the advantages that it is easier to establish a phylogenetic taxonomy than for many invertebrate groups, and there is the potential for more detailed ecological analyses. The relative incompleteness of a fossil record may be assessed readily, and this can be used to test whether drops in overall diversity are related to mass extinctions or to gaps in our knowledge. Absolute incompleteness cannot be assessed directly, but a historical approach may offer clues to future improvements in our knowledge. One of the key problems facing palaeobiologists is paraphyly, the fact that many higher taxa in common use do not contain all of the descendants of the common ancestor. This may be overcome by cladistic analysis and the identification of monophyletic groups. The diversity of tetrapods increased from the Devonian to the Permian, remained roughly constant during the Mesozoic, and then began to increase in the late Cretaceous, and continued to do so during the Tertiary. The rapid radiation of 'modern' tetrapod groups--frogs, salamanders, lizards, snakes, turtles, crocodilians, birds and mammals--was hardly affected by the celebrated end-Cretaceous extinction event. Major mass extinctions among tetrapods took place in the early Permian, late Permian, early Triassic, late Triassic, late Cretaceous, early Oligocene and late Miocene. Many of these events appear to coincide with the major mass extinctions among marine invertebrates, but the tetrapod record is largely equivocal with regard to the theory of periodicity of mass extinctions.

Animals↗
PubMed1992

Extinction of alpha 1-antitrypsin gene expression in somatic cell hybrids: evidence for multiple controls.

Expression of the liver-specific alpha 1-antitrypsin (alpha 1AT) gene is extinguished in hepatoma/fibroblast hybrids. To define the mechanism of extinction, we identified DNA sequences involved in this process by transiently transfecting mutant alpha 1AT promoters into parental and hybrid cells. The wild-type alpha 1AT promoter (-554 to +44 bp) was highly expressed in rat hepatoma cells, but activity was 100-fold less in fibroblasts or cell hybrids. Mutations in this region failed to activate alpha 1AT expression in nonhepatic cells, but mutations in the binding site for liver factor B1 (LF-B1) reduced hepatic-specific expression greater than 100-fold. Furthermore, the hybrid cells failed to express LF-B1-binding activity and mRNA. This suggested that alpha 1AT extinction in hybrids might be an indirect, lack-of-activation phenotype mediated primarily through repression of LF-B1. To test this possibility, we stably transfected an LF-B1 expression cassette into parental and hybrid cells and monitored expression of transfected and endogenous alpha 1AT genes. Surprisingly, although constitutive LF-B1 expression could activate alpha 1AT-CAT transgenes in these cells, it neither prevented nor reversed extinction of the chromosomal alpha 1AT genes. We conclude that although extinction of the LF-B1 trans-activator accompanies alpha 1AT extinction in cell hybrids, it does not play a causal role in this process.

Animals↗
PubMed1999

Diversity and extinction in a lattice model of a population with fluctuating environment.

I study a lattice stochastic model of a mutating population sensitive to the influence of a fluctuating environment. The dynamics of the population stressed by linear and periodic disturbances is investigated. In agreement with previous studies of nonspatial models, I find a critical rate of change in the environmental variable beyond which the population becomes extinct, and I show explicitly that the presence of space in the model can affect the critical rate. Further, I study the diversity defined as the total number of different cell types present in the lattice as a function of intensity and frequency of the environmental disturbance. If the disturbance becomes fast and intense the population becomes extinct. Interestingly, I find that for moderate stresses the diversity increases with the intensity and frequency of disturbance. The transition between large diversity and extinction is sharp, implying that the populations with high diversity are generally the ones closest to the extinction threshold. When subjected to colored noise of increasing intensity the system grows in diversity but at the same time is more likely to become extinct.

Biophysical Phenomena↗
PubMed2001

Extinctions in the random replicator model.

The statistical properties of an ecosystem composed of species interacting via pairwise, random interactions and deterministic, concentration limiting self-interactions are studied analytically with tools of equilibrium statistical mechanics of disordered systems. Emphasis is given to the effects of externally induced extinction of a fixed fraction of species at the outset of the evolutionary process. The manner the ecosystem copes with the initial extinction event depends on the degree of competition among the species as well as on the strength of that event. For instance, in the regime of high competition the ecosystem diversity, given by the fraction of surviving species, is practically insensitive to the strength of the initial extinction provided it is not too large, while in the less competitive regime the diversity decreases linearly with the size of the event. In the case of large extinction events we find that no further biotic extinctions take place and, furthermore, that rare species become very unlikely to be found in the ecosystem at equilibrium. In addition, we show that the reciprocal of the Edwards-Anderson order parameter yields a good measure of the diversity of the model ecosystem.

Animals↗
PubMed1995

Hexamethylenetetramine: extinction and thermal vibrations from neutron diffraction at six temperatures.

Neutron diffraction data have been collected for hexamethylenetetramine (HMT) at 15, 50, 80, 120, 160 and 200K using a single crystal (mass 8.1 mg). The structure refinement at each temperature included two extinction parameters and third-order thermal parameters for the H nuclei. Extinction effects are very severe with extinction factors as small as 0.2Fkin2 for three reflections (800, 110 and 440). Application of the Sabine extinction theory indicates that the crystal domain size decreases from 115 microns at 200 K to 85 microns at 15 K. The half-width in the mosaic spread (7" of arc) is almost independent of temperature. An extinction model without phase correlations between mosaic blocks gives a slightly better fit to the diffraction data. The nuclear mean square thermal displacements have been analysed assuming no coupling between the external (rigid body) and internal vibrations. This gives mean square displacements for rigid-body vibration in which zero-point vibrational effects are apparent. The methylene H nuclei have internal vibrations approximately independent of temperature. At 200 K, the H nuclear vibrations have a small anharmonic component, but at temperatures below 160 K this becomes insignificant in terms of the experimental error.

Crystallization↗
PubMed2006

Using population viability analysis to predict the effects of climate change on the extinction risk of an endangered limestone endemic shrub, Arizona cliffrose.

The threat of global warming to rare species is a growing concern, yet few studies have predicted its effects on rare populations. Using demographic data gathered in both drought and nondrought years between 1996-2003 in central Arizona upper Sonoran Desert, we modeled population viability for the federally endangered Purshia subintegra (Kearney) Henrickson (Arizona cliffrose). We used deterministic matrix projection models and stochastic models simulating weather conditions during our study, given historical weather variation and under scenarios of increased aridity. Our models suggest that the P. subintegra population in Verde Valley is slowly declining and will be at greater risk of extinction with increased aridity. Across patches at a fine spatial scale, demographic performance was associated with environmental factors. Moist sites (patches with the highest soil moisture, lowest sand content, and most northern aspects) had the highest densities, highest seedling recruitment, and highest risk of extinction over the shortest time span. Extinction risk in moist sites was exacerbated by higher variance in recruitment and mortality. Dry sites had higher cumulative adult survival and lower extinction risk but negative growth rates. Steps necessary for the conservation of the species include introductions at more northern latitudes and in situ manipulations to enhance seedling recruitment and plant survival. We demonstrate that fine spatial-scale modeling is necessary to predict where patches with highest extinction risk or potential refugia for rare species may occur Because current climate projections for the 21st century imply range shifts at rates of 300 to 500 km/century, which are beyond even exceptional examples of shifts in the fossil record of 100-150 km, it is likely that preservation of many rare species will require human intervention and a long-term commitment. Global warming conditions are likely to reduce the carrying capacity of many rare species' habitats.

Arizona↗
PubMed2006

Global warming and extinctions of endemic species from biodiversity hotspots.

Global warming is a key threat to biodiversity, but few researchers have assessed the magnitude of this threat at the global scale. We used major vegetation types (biomes) as proxies for natural habitats and, based on projected future biome distributions under doubled-CO2 climates, calculated changes in habitat areas and associated extinctions of endemic plant and vertebrate species in biodiversity hotspots. Because of numerous uncertainties in this approach, we undertook a sensitivity analysis of multiple factors that included (1) two global vegetation models, (2) different numbers of biome classes in our biome classification schemes, (3) different assumptions about whether species distributions were biome specific or not, and (4) different migration capabilities. Extinctions were calculated using both species-area and endemic-area relationships. In addition, average required migration rates were calculated for each hotspot assuming a doubled-CO2 climate in 100 years. Projected percent extinctions ranged from <1 to 43% of the endemic biota (average 11.6%), with biome specificity having the greatest influence on the estimates, followed by the global vegetation model and then by migration and biome classification assumptions. Bootstrap comparisons indicated that effects on hotpots as a group were not significantly different from effects on random same-biome collections of grid cells with respect to biome change or migration rates; in some scenarios, however, botspots exhibited relatively high biome change and low migration rates. Especially vulnerable hotspots were the Cape Floristic Region, Caribbean, Indo-Burma, Mediterranean Basin, Southwest Australia, and Tropical Andes, where plant extinctions per hotspot sometimes exceeded 2000 species. Under the assumption that projected habitat changes were attained in 100 years, estimated global-warming-induced rates of species extinctions in tropical hotspots in some cases exceeded those due to deforestation, supporting suggestions that global warming is one of the most serious threats to the planet's biodiversity.

Biodiversity↗
PubMed2006

Ecological determinants of distribution decline and risk of extinction in moths.

For successful conservation of species it is important to identify traits that predispose species to the risk of extinction. By identifying such traits conservation efforts can be directed toward species that are most at risk of becoming threatened. We used data derived from the literature to determine ecological traits that affect distribution, distribution change, and the risk of extinction in Finnish noctuid moths (Lepidoptera, Noctuidae). The ecological traits we examined included body size, larval specificity, length of the flight period, and overwintering stage. In addition, in monophagous species we examined the effects of resource distribution. Larval specificity, length of the flight period, and the overwintering stage each had an independent effect on the risk of extinction when the effects of other traits were controlled by entering all traits into the same regression model. Not a single trait predicted the risk of extinction when analysis was conducted without controlling for the other traits. This discrepancy among the results suggests that a single trait may not be enough to allow prediction of the risk of extinction. Instead, it seems that for successful, predictive conservation science data on several ecological characteristics are needed.

Animals↗
PubMed2004

Comparative losses of British butterflies, birds, and plants and the global extinction crisis.

There is growing concern about increased population, regional, and global extinctions of species. A key question is whether extinction rates for one group of organisms are representative of other taxa. We present a comparison at the national scale of population and regional extinctions of birds, butterflies, and vascular plants from Britain in recent decades. Butterflies experienced the greatest net losses, disappearing on average from 13% of their previously occupied 10-kilometer squares. If insects elsewhere in the world are similarly sensitive, the known global extinction rates of vertebrate and plant species have an unrecorded parallel among the invertebrates, strengthening the hypothesis that the natural world is experiencing the sixth major extinction event in its history.

Animals↗
PubMed1987

Environmental trends in extinction during the Paleozoic.

Extinction intensities calculated from 505 Paleozoic marine assemblages divided among six environmental zones and 40 stratigraphic intervals indicate that whole communities exhibit increasing extinction offshore but that genera within individual taxonomic classes tend to have their highest extinction onshore. The offshore trend at the community level results from a concentration of genera in classes with low characteristic extinction rates in nearshore environments. This finding is consistent with the ecologic expectation that organisms inhabiting unpredictably fluctuating environments should suffer more extinction than counterparts living under more predictably equitable conditions.

Animals↗