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Mutational meltdown in laboratory yeast populations.

In small or repeatedly bottlenecked populations, mutations are expected to accumulate by genetic drift, causing fitness declines. In mutational meltdown models, such fitness declines further reduce population size, thus accelerating additional mutation accumulation and leading to extinction. Because the rate of mutation accumulation is determined partly by the mutation rate, the risk and rate of meltdown are predicted to increase with increasing mutation rate. We established 12 replicate populations of Saccharomyces cerevisiae from each of two isogenic strains whose genomewide mutation rates differ by approximately two orders of magnitude. Each population was transferred daily by a fixed dilution that resulted in an effective population size near 250. Fitness declines that reduce growth rates were expected to reduce the numbers of cells transferred after dilution, thus reducing population size and leading to mutational meltdown. Through 175 daily transfers and approximately 2900 generations, two extinctions occurred, both in populations with elevated mutation rates. For one of these populations there is direct evidence that extinction resulted from mutational meltdown: Extinction immediately followed a major fitness decline, and it recurred consistently in replicate populations reestablished from a sample frozen after this fitness decline, but not in populations founded from a predecline sample. Wild-type populations showed no trend to decrease in size and, on average, they increased in fitness.

Biological Evolution↗

What it takes to fly: the structural and functional respiratory refinements in birds and bats.

In absolute terms, flight is a highly energetically expensive form of locomotion. However, with respect to its cost per unit distance covered, powered flight is a very efficient mode of transport. Birds and bats are the only extant vertebrate taxa that have achieved flight. Phylogenetically different, they independently accomplished this elite mode of locomotion by employing diverse adaptive schemes and strategies. Integration of functional and structural parameters, a transaction that resulted in certain trade-offs and compromises, was used to overcome exacting constraints. Unique morphological, physiological and biochemical properties were initiated and refined to enhance the uptake, transfer and utilization of oxygen for high aerobic capacities. In bats, exquisite pulmonary structural parameters were combined with optimal haematological ones: a thin blood-gas barrier, a large pulmonary capillary blood volume and a remarkably extensive alveolar surface area in certain species developed in a remarkably large lung. These factors were augmented by, for example, exceptionally high venous haematocrits and haemoglobin concentrations. In birds, a particularly large respiratory surface area and a remarkably thin blood-gas (tissue) barrier developed in a small, rigid lung; a highly efficient cross-current system was fabricated within the parabronchi. The development of flight in only four animal taxa (among all the animal groups that have ever evolved; i.e. insects, the now-extinct pterosaurs, birds and bats) provides evidence for the enormous biophysical and energetic constraints that have stymied volancy. Bats improved a fundamentally mammalian lung to procure the large amounts of oxygen needed for flight. The lung/air sac system of birds is not therefore a prescriptive morphology for flight: the essence of its design can be found in the evolution of the reptilian lung, the immediate progenitor stock from which birds arose. The attainment of flight is a classic paradigm of the remarkable adaptability inherent in organismal and organic biology for countering selective pressures by initiating elegant morphologies and physiologies.

Altitude↗

Allee effects, extinctions, and chaotic transients in simple population models.

Discrete time single species models with overcompensating density dependence and an Allee effect due to predator satiation and mating limitation are investigated. The models exhibit four behaviors: persistence for all initial population densities, bistability in which a population persists for intermediate initial densities and otherwise goes extinct, extinction for all initial densities, and essential extinction in which "almost every" initial density leads to extinction. For fast-growing populations, these models show populations can persist at high levels of predation even though lower levels of predation lead to essential extinction. Alternatively, increasing the predator's handling time, the population's carrying capacity, or the likelihood of mating success may lead to essential extinction. In each of these cases, the mechanism behind these disappearances are chaotic dynamics driving populations below a critical threshold determined by the Allee effect. These disappearances are proceeded by chaotic transients that are proven to be approximately exponentially distributed in length and highly sensitive to initial population densities.

Alleles↗

Individual based modeling and parameter estimation for a Lotka-Volterra system.

Stochastic component, inevitable in biological systems, makes problematic the estimation of the model parameters from a single sequence of measurements, despite the complete knowledge of the system. We studied the problem of parameter estimation using individual-based computer simulations of a 'Lotka-Volterra world'. Two kinds (species) of particles--X (preys) and Y (predators)--moved on a sphere according to deterministic rules and at the collision (interaction) of X and Y the particle X was changed to a new particle Y. Birth of preys and death of predators were simulated by addition of X and removal of Y, respectively, according to exponential probability distributions. With this arrangement of the system, the numbers of particles of each kind might be described by the Lotka-Volterra equations. The simulations of the system with low (200-400 particles on average) number of individuals showed unstable oscillations of the population size. In some simulation runs one of the species became extinct. Nevertheless, the oscillations had some generic properties (e.g. mean, in one simulation run, oscillation period, mean ratio of the amplitudes of the consecutive maxima of X and Y numbers, etc.) characteristic for the solutions of the Lotka-Volterra equations. This observation made it possible to estimate the four parameters of the Lotka-Volterra model with high accuracy and good precision. The estimation was performed using the integral form of the Lotka-Volterra equations and two parameter linear regression for each oscillation cycle separately. We conclude that in spite of the irregular time course of the number of individuals in each population due to stochastic intraspecies component, the generic features of the simulated system evolution can provide enough information for quantitative estimation of the system parameters.

Animals↗

Wildlife conservation and reproductive cloning.

Reproductive cloning, or the production of offspring by nuclear transfer, is often regarded as having potential for conserving endangered species of wildlife. Currently, however, low success rates for reproductive cloning limit the practical application of this technique to experimental use and proof of principle investigations. In this review, we consider how cloning may contribute to wildlife conservation strategies. The cloning of endangered mammals presents practical problems, many of which stem from the paucity of knowledge about their basic reproductive biology. However, situations may arise where resources could be targeted at recovering lost or under-represented genetic lines; these could then contribute to the future fitness of the population. Approaches of this type would be preferable to the indiscriminate generation of large numbers of identical individuals. Applying cloning technology to non-mammalian vertebrates may be more practical than attempting to use conventional reproductive technologies. As the scientific background to cloning technology was pioneered using amphibians, it may be possible to breed imminently threatened amphibians, or even restore extinct amphibian species, by the use of cloning. In this respect species with external embryonic development may have an advantage over mammals as developmental abnormalities associated with inappropriate embryonic reprogramming would not be relevant.

Animals↗

Induced Pluripotent Stem Cells in Non-Model Species: Applications and Challenges.

Induced pluripotent stem cells have revolutionized biomedical research-yet the vast majority of life on Earth remains beyond their reach. Non-model species lack the annotated genomes, validated reagents, and species-specific culture infrastructure that make iPSC technology routine in humans and mice, and this infrastructure deficit, compounded by genuine biological differences in pluripotency network architecture across taxa, is what has kept the field narrow. The deep conservation of the core pluripotency network across vertebrates suggests that reprogramming may, in principle, be achievable across a far broader range of species than currently demonstrated-though the extent to which this holds across more divergent taxa remains to be established. This review consolidates current progress and future potential of iPSC technology across five domains: technical reprogramming challenges and advances; conservation applications including genetic rescue, in vitro gametogenesis, and de-extinction; medical applications within a one medicine framework; agricultural applications spanning disease resistance, climate resilience, and cultured meat; and species-specific iPSC-derived systems in ecotoxicology. Throughout, we distinguish what has been demonstrated from what remains aspirational and identify the priorities that will determine whether the iPSC revolution can be extended-rigorously and at scale-beyond model organism research.

Induced Pluripotent Stem Cells↗

Effects of habitat destruction in a prey-predator metapopulation model

A mean field, metapopulation model of a predator-prey interaction is developed in order to understand the consequences of habitate destruction at different trophic levels. Such a model allows is to explore different ecological scenarios (donor control vs. top-down control) by changing a single parameter. The response to habitat destruction is qualitatively the same for both predator and prey, although there are interesting differences linked to the trophic position. A similar decrease in the colonization rates affects the two species quite differently. Predators diminish faster than prey, and furthermore, the fraction of occupied sites decreases more sharply as colonization rates are lowered, i.e. there is a nonlinear relationship between regional abundance and colonization rate. There is a well-defined threshold in the colonization rate below which the predator becomes extinct. Thus, dispersal rate is critical for predicting the consequences of habitat destruction. Finally, these results are compared with the behavior of a spatially explicit simulation. The only difference between the analytical model and the simulation is that colonization is no longer a global phenomenon in the latter, but it is a local process, constrained to the nearest patches. The bulk of the results are similar to the mean field behavior, and we comment on some differences related with non-homogeneity and real space. Some general implications for conservation biology and biological control are outlined. Copyright 1998 Academic Press

Journal Article↗

The evolutionary life history of P transposons: from horizontal invaders to domesticated neogenes.

P elements, a family of DNA transposons, are known as aggressive intruders into the hitherto uninfected gene pool of Drosophila melanogaster. Invading through horizontal transmission from an external source they managed to spread rapidly through natural populations within a few decades. Owing to their propensity for rapid propagation within genomes as well as within populations, they are considered as the classic example of selfish DNA, causing havoc in a genomic environment permissive for transpositional activity. Tracing the fate of P transposons on an evolutionary scale we describe different stages in their evolutionary life history. Starting from horizontal transfer events, which now appear to be rather a common phenomenon, the initial transpositional burst in the new host is slowed down by the accumulation of defective copies as well as host-directed epigenetic silencing. This leads to the loss of mobility and, finally, to molecular erosion by random mutations. Possible escape routes from genomic extinction are the reactivation within the original host genome by recombination or suspension of the repressing regime, horizontal emigration to a virgin gene pool, or genomic integration and acquisition of a novel function as a domesticated host gene.

Animals↗

Current approaches to etiology and pathophysiology of specific phobia.

Specific phobia is a common, heterogeneous disorder whose central feature is persistent, unreasonable fear of a circumscribed object or situation. This article reviews current etiological theories and empirical data that seem likely to be important in investigating the pathophysiology of this disorder. These include conditioning, modified conditioning, and nonassociative models of phobia development, physiological response to the phobic stimulus, neuroimaging, primate, and biological challenge studies. Pathophysiological hypotheses suggested by recent research on the neurocircuitry of conditioned fear are also discussed. Though specific phobias have been of less public health and clinical interest than other anxiety disorders, their circumscribed nature and possible relationship to conditioned fear may make them a productive subject for research into basic pathophysiology.

Animals↗

Combined support for wholesale taxic atavism in gavialine crocodylians.

Morphological and molecular data sets favor robustly supported, contradictory interpretations of crocodylian phylogeny. A longstanding perception in the field of systematics is that such significantly conflicting data sets should be analyzed separately. Here we utilize a combined approach, simultaneous analyses of all relevant character data, to summarize common support and to reconcile discrepancies among data sets. By conjoining rather than separating incongruent classes of data, secondary phylogenetic signals emerge from both molecular and morphological character sets and provide solid evidence for a unified hypothesis of crocodylian phylogeny. Simultaneous analyses of four gene sequences and paleontological data suggest that putative adaptive convergences in the jaws of gavialines (gavials) and tomistomines (false gavials) offer character support for a grouping of these taxa, making Gavialinae an atavistic taxon. Simple new methods for measuring the influence of extinct taxa on topological support indicate that in this vertebrate order fossils generally stabilize relationships and accentuate hidden phylogenetic signals. Remaining inconsistencies in minimum length trees, including concentrated hierarchical patterns of homoplasy and extensive gaps in the fossil record, indicate where future work in crocodylian systematics should be directed.

Adaptation, Biological↗

Population genetic analysis identifies source-sink dynamics for two sympatric garter snake species (Thamnophis elegans and Thamnophis sirtalis).

Population genetic structure can be shaped by multiple ecological and evolutionary factors, but the genetic consequences of these factors for multiple species inhabiting the same environment remain unexplored. We used microsatellite markers to examine the population structures of two coexisting species of garter snake, Thamnophis elegans and Thamnophis sirtalis, to determine if shared landscape and biology imposed similar population genetic structures. These snakes inhabit a series of ponds, lakes and flooded meadows in northern California and tend to converge on prey type wherever they coexist. Both garter snakes had comparable effective population sizes and bidirectional migration rates (estimated using a maximum-likelihood method based on the coalescent) with low but significant levels of genetic differentiation (F(ST) = 0.024 for T. elegans and 0.035 for T. sirtalis). Asymmetrical gene flow revealed large source populations for both species as well as potential sinks, suggesting frequent extinction-recolonization and metapopulation dynamics. In addition, we found a significant correlation between their genetic structures based on both pairwise F(ST)s for shared populations (P = 0.009) and for bidirectional migration rates (P = 0.024). Possible ecological and evolutionary factors influencing similarities and differences in genetic structure for the two species are discussed. Genetic measures of effective population size and migration rates obtained in this study are also compared with estimates obtained from mark-recapture data.

Animal Migration↗

[Testing the activity of anti-foot-and-mouth disease vaccine in cattle: quantitative methods of antigenic extinction].

Two methods of evaluating the activity of the foot-and-mouth disease vaccine are compared, leading to the evaluation of the number of protective doses 50% or potency. These methods differ in sensitivity, precision and equivalence potency-percentage of protection. For the same vaccine the value of the PD50 is always larger than that of Pb. We chose the Pb method using a diluent containing no adjuvant. Standards based on the evaluation of average potency have not been taken into consideration; only those standards based on the evaluation of minimum potency ensure respect of OIE's recommendation. This recommendation: 70% minimum potency with 0.95 probability is not an easier alternative, since the average protection observed corresponds in fact to at least 90% taking into account the biological variability of bovines.

Animals↗

The effects of planting and harvesting on endangered species in discrete competitive systems.

The influence of planting the endangered species in a discretely reproducing ecosystem is studied. By applying constant rate and variable rate planting strategies we obtain that coexistence of species that would otherwise exclude each other with no planting occurs. We also show that with a high planting rate the endangered species not only recovers from the brink of extinction but it excludes the other competing species. A similar reversal of exclusion principles occurs if the dominant species is harvested with a sufficiently high harvesting constant while the endangered species is left undisturbed. In addition, we obtain mutual exclusion of species with harvesting where there is exclusion of only one species without harvesting.

Agriculture↗

Microbial predation in coupled chemostats: a global study of two coupled nonlinear oscillators.

Predator-prey systems in continuously operated chemostats exhibit sustained oscillations over a wide range of operating conditions. When two such chemostats interact through flow exchange, the interplay of the oscillation frequencies gives rise to a wealth of dynamic behavior patterns. Using numerical bifurcation techniques, we perform a detailed computational study of these patterns and the transitions between them as the coupling strength and relative frequencies of the two chemostats vary. We concentrate on certain strong resonance phenomena between the two frequencies as well as their mutual extinction and provide a representative sampling of possible phase portraits for our model system. Our observations corroborate recent mathematical results and case studies of coupled nonlinear chemical oscillators in which regions of mutual extinction as well as the Arnol'd structure for two-parameter families of maps of the plane have been observed. We highlight certain unexpected features of the operating diagram discovered through our computational study and discuss their implication for the dynamic response of the chemostat system.

Animals↗

Evolution of dispersal in metapopulations with local density dependence and demographic stochasticity.

In this paper, we predict the outcome of dispersal evolution in metapopulations based on the following assumptions: (i) population dynamics within patches are density-regulated by realistic growth functions; (ii) demographic stochasticity resulting from finite population sizes within patches is accounted for; and (iii) the transition of individuals between patches is explicitly modelled by a disperser pool. We show, first, that evolutionarily stable dispersal rates do not necessarily increase with rates for the local extinction of populations due to external disturbances in habitable patches. Second, we describe how demographic stochasticity affects the evolution of dispersal rates: evolutionarily stable dispersal rates remain high even when disturbance-related rates of local extinction are low, and a variety of qualitatively different responses of adapted dispersal rates to varied levels of disturbance become possible. This paper shows, for the first time, that evolution of dispersal rates may give rise to monotonically increasing or decreasing responses, as well as to intermediate maxima or minima.

Adaptation, Biological↗

Radiocarbon dates on bones of extinct birds from Hawaii.

Bones from a stratified sedimentary deposit in the Puu Naio Cave site on Maui, Hawaiian Islands, reveal the late Holocene extinction of 19 species of birds. The age of the sediment and associated fauna was determined by direct radiocarbon dating (tandem particle accelerator-mass spectrometer; TAMS) of amino acids extracted from bones weighing as little as 450 mg. The 14C dates indicate that sediment has been accumulating in the lava tube for at least the last 7750 years, a suitable time frame for testing the hypothesis that Holocene extinction on islands began after human colonization. Despite growing evidence that a worldwide wave of extinctions coincided with human colonization of oceanic islands, little radiometric data have been available to date the extinction of most small fossil vertebrates on islands. The TAMS technique of dating purified collagen from the bones of small vertebrates could lead to vastly improved chronologies of extinction for oceanic islands where catastrophic mid- to late-Holocene extinction is expected or known to have occurred. Chronologies derived from nonarcheological sites that show continuous sedimentation, such as the Puu Naio Cave deposit, may also yield key evidence on the timing of earliest human settlement of Oceania.

Animals↗

Determinism in a transient assemblage: the roles of dispersal and local competition.

Both dispersal and local competitive ability may determine the outcome of competition among species that cannot coexist locally. I develop a spatially implicit model of two-species competition at a small spatial scale. The model predicts the relative fitness of two competitors based on local reproductive rates and regional dispersal rates in the context of the number, size, and extinction probability of habitat patches in the landscape. I test the predictions of this model experimentally using two genotypes of the bacteriophagous soil nematode Caenorhabditis elegans in patchy microcosms. One genotype has higher fecundity while the other is a better disperser. With such a fecundity-dispersal trade-off between competitors, the model predicts that relative fitness will be affected most by local population size when patches do not go extinct and by the number of patches when there is a high probability of patch extinction. The microcosm experiments support the model predictions. Both approaches suggest that competitive dominance in a patchily distributed transient assemblage will depend upon the architecture and predictability of the environment. These mechanisms, operating at a small scale with high spatial admixture, may be embedded in a larger metacommunity process.

Animals↗

Space and the persistence of male-killing endosymbionts in insect populations.

Male-killing bacteria are bacteria that are transmitted vertically through the females of their insect hosts. They can distort the sex ratio of their hosts by killing infected male offspring. In nature, male-killing endosymbionts (male killers) often have a 100% efficient vertical transmission, and multiple male-killing bacteria infecting a single population are observed. We use different model formalisms to study these observations. In mean-field models a male killer with perfect transmission drives the host population to extinction, and coexistence between multiple male killers within one population is impossible; however, in spatially explicit models, both phenomena are readily observed. We show how the spatial pattern formation underlies these results. In the case of high transmission efficiencies, waves with a high density of male killers alternate with waves of mainly wild-type hosts. The male killers cause local extinction, but this creates an opportunity for uninfected hosts to re-invade these areas. Spatial pattern formation also creates an opportunity for two male killers to coexist within one population: different strains create spatial regions that are qualitatively different; these areas then serve as different niches, making coexistence possible.

Animals↗