			Home About us Contact

Effective Size (effective + size)

Distribution by Scientific Domains

Life Sciences	72%
Chemistry	5%
5 Other Domains	23%

Distribution within Life Sciences

Evolution	41%
Conservation Science	18%

Kinds of Effective Size

variance effective size

Selected Abstracts

Effective size of populations with unequal sex ratio and variation in mating success

JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 5 2002
T. Nomura
Summary To estimate the effective size (Ne) of populations with unequal sex ratio, a well-known formula, Ne=4NmNf/(Nm + Nf), has been frequently used, where Nm and Nf are the numbers of male and female parents, respectively. In this paper, the formula was examined under typical mating systems in animals. It was shown that the formula holds only when there are no variations in the numbers of mates (mating success) of parents of each sex. More appropriate equations were developed by accounting for the variation in mating success. It was found that for animal populations with harem mating system, an equation Ne=4NmNf/(2Nm+Nf) gives a more accurate estimate than the well-known formula. The effective population sizes of several wild, experimental and domestic animals are estimated by applying the derived equations to the published demographic and ecological data. Zusammenfassung Effektive Größe von Populationen mit ungleichem Geschlechterverhältnis und Variation im Anpaarungserfolg Zur Schätzung der effektiven Populationsgröße (Ne) mit ungleichem Geschlechterverhältnis, wurde häufig die allgemein bekannte Formel Ne=4NmNf/(Nm + Nf) verwendet, wobei Nm und Nf die Anzahl männlicher und weiblicher Eltern bezeichnen. In diesem Artikel wurde diese Formel unter verschiedenen Anpaarungssystemen überprüft. Es wurde gezeigt, daß die Formel nur zutrifft, wenn die Anzahl der angepaarten Tiere (Anpaarungserfolg) in jedem Geschlecht nicht variieren. Es wurden genauere Gleichungen entwickelt, die den Anpaarungserfolg mitberücksichtigen. Für Tierpopulationen mit Harempaarung wurde die Gleichung Ne=4NmNf/(2Nm + Nf) als genauerer Schätzer als die allgemein bekannte Formel gefunden. Die effektive Populationsgröße mehrerer Wild-, Versuchs- und Haustierpopulationen wurden mittels der abgeleiteten Gleichung und demographischen und ökologischen Daten geschätzt. [source]

Effective size of harvested ungulate populations

ANIMAL CONSERVATION, Issue 5 2009
B.-E. Sæther
Abstract The harvest of ungulate populations is often directed against certain sex or age classes to maximize the yield in terms of biomass, number of shot animals or number of trophies. Here we examine how such directional harvest affects the effective size of the population. We parameterize an age-specific model assumed to describe the dynamics of Fennoscandian moose. Based on expressions for the demographic variance for a small subpopulation of heterozygotes Aa bearing a rare neutral allele a, we use this model to calculate how different harvest strategies influence the effective size of the population, given that the population remains stable after harvest. We show that the annual genetic drift, determined by , increases with decreasing harvest rate of calves and increasing sex bias in the harvest towards bulls 1 year or older. The effective population size per generation decreased with reduced harvest of calves and increased harvest of bulls 1 year or older. The magnitude of these effects depends on the age-specific pattern of variation in reproductive success, which influences the demographic variance. This shows that the choice of harvest strategy strongly affects the genetic dynamics of harvested ungulate populations. [source]

Genetic Effects of Multiple Generations of Supportive Breeding

CONSERVATION BIOLOGY, Issue 6 2001
Jinliang Wang
This procedure is intended to increase population size without introducing exogenous genes into the managed population. Previous work examining the genetic effects of a single generation of supportive breeding has shown that although a successful program increases the census population size, it may reduce the genetically effective population size and thereby induce excessive inbreeding and loss of genetic variation. We expand and generalize previous analyses of supportive breeding and consider the effects of multiple generations of supportive breeding on rates of inbreeding and genetic drift. We derived recurrence equations for the inbreeding coefficient and coancestry, and thereby equations for inbreeding and variance effective sizes, under three models for selecting captive breeders: at random, preferentially among those born in captivity, and preferentially among those born in the wild. Numerical examples indicate that supportive breeding, when carried out successfully over multiple generations, may increase not only the census but also the effective size of the supported population as a whole. If supportive breeding does not result in a substantial and continuous increase of the census size of the breeding population, however, it might be genetically harmful because of elevated rates of inbreeding and genetic drift. Resumen: La práctica de apoyar poblaciones silvestres débiles mediante la captura de una fracción de los individuos silvestres, su cautiverio para la reproducción y la liberación a su descendencia en habitas naturales para que convivan con organismos silvestres se conoce como reproducción de apoyo y se ha empleado ampliamente en la biología de la conservación y en el manejo de pesca y vida silvestre. Este procedimiento tiene la intención de incrementar el tamaño de la población sin introducir genes exógenos en la población bajo manejo. Trabajos previos sobre los efectos genéticos de una sola generación de reproducción de apoyo muestran que, aunque un programa exitoso incrementa el tamaño poblacional, puede reducir la población genéticamente efectivae inducir así un exceso de consanguinidad y pérdida de variación genética. Expandimos y generalizamos análisis previos de la reproducción de apoyo y consideramos los efectos de múltiples generaciones de reproducción de soporte en las tasas de consanguinidad y de deriva génica. Derivamos ecuaciones de recurrencia para el coeficiente de consanguinidad y de coancestría, y por tanto ecuaciones de tamaños efectivos de consanguinidad y de varianza, para tres modelos de selección de reproductores en cautiverio : aleatoria, preferentemente entre los nacidos en cautiverio y preferentemente entre los nacidos en libertad. Los ejemplos numéricos indican que la reproducción de apoyo, cuando es exitosa en múltiples generaciones, puede ser favorable para el incremento no solo del tamaño, sino del tamaño efectivo de la población soportada en su conjunto. Sin embargo, si la reproducción de soporte no resulta en un incremento sustancial y continuo del tamaño de la población, puede ser genéticamente dañina debido a las altas tasas de consanguinidad y de deriva genética. [source]

DOES MATE LIMITATION IN SELF-INCOMPATIBLE SPECIES PROMOTE THE EVOLUTION OF SELFING?

EVOLUTION, Issue 6 2010
THE CASE OF LEAVENWORTHIA ALABAMICA
Genetic diversity at the S-locus controlling self-incompatibility (SI) is often high because of negative frequency-dependent selection. In species with highly patchy spatial distributions, genetic drift can overwhelm balancing selection and cause stochastic loss of S-alleles. Natural selection may favor the breakdown of SI in populations with few S-alleles because low S-allele diversity constrains the seed production of self-incompatible plants. We estimated S-allele diversity, effective population sizes, and migration rates in Leavenworthia alabamica, a self-incompatible mustard species restricted to discrete habitat patches in rocky glades. Patterns of polymorphism were investigated at the S-locus and 15 neutral microsatellites in three large and three small populations with 100-fold variation in glade size. Populations on larger glades maintained more S-alleles, but all populations were estimated to harbor at least 20 S-alleles, and mate availabilities typically exceeded 0.80, which is consistent with little mate limitation in nature. Estimates of the effective size (Ne) in each population ranged from 600 to 1600, and estimated rates of migration (m) ranged from 3 × 10,4 to nearly 1 × 10,3. According to theoretical models, there is limited opportunity for genetic drift to reduce S-allele diversity in populations with these attributes. Although pollinators or resources limit seed production in small glades, limited S-allele diversity does not appear to be a factor promoting the incipient breakdown of SI in populations of this species that were studied. [source]

EFFECTIVE POPULATION SIZES AND TEMPORAL STABILITY OF GENETIC STRUCTURE IN RANA PIPIENS, THE NORTHERN LEOPARD FROG

EVOLUTION, Issue 11 2004
Eric A. Hoffman
Abstract Although studies of population genetic structure are very common, whether genetic structure is stable over time has been assessed for very few taxa. The question of stability over time is particularly interesting for frogs because it is not clear to what extent frogs exist in dynamic metapopulations with frequent extinction and recolonization, or in stable patches at equilibrium between drift and gene flow. In this study we collected tissue samples from the same five populations of leopard frogs, Rana pipens, over a 22,30 year time interval (11,15 generations). Genetic structure among the populations was very stable, suggesting that these population were not undergoing frequent extinction and colonization. We also estimated the effective size of each population from the change in allele frequencies over time. There exist few estimates of effective size for frog populations, but the data available suggest that ranid frogs may have much larger ratios of effective size (Ne) to census size (Nc) that toads (bufonidae). Our results indicate that R. pipiens populations have effective sizes on the order of hundreds to at most a few thousand frogs, and Nee/Nc ratios in the range of 0.1,1.0. These estimates of Ne/Nc are consistent with those estimated for other Rana species. Finally, we compared the results of three temporal methods for estimating Ne. Moment and pseudolikelihood methods that assume a closed population gave the most similar point estimates, although the moment estimates were consistently two to four times larger. Wang and Whitlock's new method that jointly estimates Ne and the rate of immigration into a population (m) gave much smaller estimates of Ne and implausibly large estimates of m. This method requires knowing allele frequencies in the source of immigrants, but was thought to be insensitive to inexact estimates. In our case the method may have failed because we did not know the true source of immigrants for each population. The method may be more sensitive to choice of source frequencies than was previously appreciated, and so should be used with caution if the most likely source of immigrants cannot be identified clearly. [source]

HETEROZYGOTE EXCESS IN SMALL POPULATIONS AND THE HETEROZYGOTE-EXCESS EFFECTIVE POPULATION SIZE

EVOLUTION, Issue 9 2004
Franclois Balloux
Abstract It has been proposed that effective size could be estimated in small dioecious population by considering the heterozygote excess observed at neutral markers. When the number of breeders is small, allelic frequencies in males and females will slightly differ due to binomial sampling error. However, this excess of heterozygotes is not generated by dioecy but by the absence of individuals produced through selfing. Consequently, the approach can also be applied to self-incompatible monoecious species. Some inaccuracies in earlier equations expressing effective size as function of the heterozygote excess are also corrected in this paper. The approach is then extended to subdivided populations, where time of sampling becomes crucial. When adults are sampled, the effective size of the entire population can be estimated, whereas when juveniles are sampled, the average effective number of breeders per subpopulations can be estimated. The main limitation of the heterozygote excess method is that it will only perform satisfactorily for populations with a small number of reproducing individuals. While this situation is unlikely to happen frequently at the scale of the entire population, structured populations with small subpopulations are likely to be common. The estimation of the average number of breeders per subpopulations is thus expected to be applicable to many natural populations. The approach is straightforward to compute and independent of equilibrium assumptions. Applications to simulated data suggest the estimation of the number of breeders to be robust to mutation and migration rates, and to specificities of the mating system. [source]

GENETIC EVIDENCE ON THE DEMOGRAPHY OF SPECIATION IN ALLOPATRIC DOLPHIN SPECIES

EVOLUTION, Issue 4 2002
Matthew P. Hare
Abstract Under a neutral model, the stochastic lineage sorting that leads to gene monophyly proceeds slowly in large populations. Therefore, in many recent species with large population size, the genome will have mixed support for monophyly unless historical bottlenecks have accelerated coalescence. We use genealogical patterns in mitochondrial DNA and in introns of four nuclear loci to test for historical bottlenecks during the speciation and divergence of two temperate Lagenorhynchus dolphin species isolated by tropical Pacific waters (an antitropical distribution). Despite distinct morphologies, foraging behaviors, and mitochondrial DNAs, these dolphin species are polyphyletic at all four nuclear loci. The abundance of shared polymorphisms between these sister taxa is most consistent with the maintenance of large effective population sizes (5.09 × 104 to 10.9 × 104) during 0.74,1.05 million years of divergence. A variety of population size histories are possible, however. We used gene tree coalescent probabilities to explore the rejection region for historical bottlenecks of different intensity given best estimates of effective population size under a strict isolation model of divergence. In L. obliquidens the data are incompatible with a colonization propagule of an effective size of 10 or fewer individuals. Although the ability to reject less extreme historical bottlenecks will require data from additional loci, the intermixed genealogical patterns observed between these dolphin sister species are highly probable only under an extended history of large population size. If similar demographic histories are inferred for other marine antitropical taxa, a parsimonious model for the Pleistocene origin of these distributions would not involve rare breaches of a constant dispersal barrier by small colonization propagules. Instead, a history of large population size in L. obliquidens and L. obscurus contributes to growing biological and environmental evidence that the equatorial barrier became permeable during glacial/interglacial cycles, leading to vicariant isolation of antitropical populations. [source]

FIXATION OF NEW ALLELES AND THE EXTINCTION OF SMALL POPULATIONS: DRIFT LOAD, BENEFICIAL ALLELES, AND SEXUAL SELECTION

EVOLUTION, Issue 6 2000
Michael C. Whitlock
Abstract With a small effective population size, random genetic drift is more important than selection in determining the fate of new alleles. Small populations therefore accumulate deleterious mutations. Left unchecked, the effect of these fixed alleles is to reduce the reproductive capacity of a species, eventually to the point of extinction. New beneficial mutations, if fixed by selection, can restore some of this lost fitness. This paper derives the overall change in fitness due to fixation of new deleterious and beneficial alleles, as a function of the distribution of effects of new mutations and the effective population size. There is a critical effective size below which a population will on average decline in fitness, but above which beneficial mutations allow the population to persist. With reasonable estimates of the relevant parameters, this critical effective size is likely to be a few hundred. Furthermore, sexual selection can act to reduce the fixation probability of deleterious new mutations and increase the probability of fixing new beneficial mutations. Sexual selection can therefore reduce the risk of extinction of small populations. [source]

THE EFFECTS OF SUBDIVISION ON THE GENETIC DIVERGENCE OF POPULATIONS AND SPECIES

EVOLUTION, Issue 4 2000
John Wakeley
Abstract. An island model of migration is used to study the effects of subdivision within populations and species on sample genealogies and on between-population or between-species measures of genetic variation. The model assumes that the number of demes within each population or species is large. When populations (or species), connected either by gene flow or historical association, are themselves subdivided into demes, changes in the migration rate among demes alter both the structure of genealogies and the time scale of the coalescent process. The time scale of the coalescent is related to the effective size of the population, which depends on the migration rate among demes. When the migration rate among demes within populations is low, isolation (or speciation) events seem more recent and migration rates among populations seem higher because the effective size of each population is increased. This affects the probability of reciprocal monophyly of two samples, the chance that a gene tree of a sample matches the species tree, and relative likelihoods of different types of polymorphic sites. It can also have a profound effect on the estimation of divergence times. [source]

Characterization of strength properties of thin polycrystalline silicon films for MEMS applications

FATIGUE & FRACTURE OF ENGINEERING MATERIALS AND STRUCTURES, Issue 1 2007
R. Boroch
ABSTRACT The aim of this work is to characterize the strength properties of polycrystalline silicon (polysilicon) with the use of tensile and bending test specimens. The strength of thin polysilicon films with different geometry, size and stress concentrations has been measured and correlated with the effective size of the specimen and its stress distribution. The test results are evaluated using a probabilistic strength approach based on the weakest link theory with the use of STAU software. The use of statistic methods of strength prediction of polysilicon test structures with a complex geometry and loading based on test values for standard material tests specimen has been evaluated. [source]

Rethinking what constitutes suspended sediment

HYDROLOGICAL PROCESSES, Issue 9 2001
Ian G. Droppo
Abstract Although cohesive suspended sediment is now known to be transported primarily as flocculated material, there is still a misconception of what constitutes suspended sediment. Flocs represent a complex matrix of microbial communities, organic particles (e.g. detritus, extracellular polymers and cellular debris), inorganic particles (e.g. clays and silts) and substantial interfloc spaces (pores), which allow for the retention or flow through of water. Flocculation results in significant alteration of the hydrodynamics of the constituent particles (by modifying their effective size, shape, density and porosity), thereby affecting the transport of sediment and associated contaminants. The composition and structure of a floc is in a continuous state of change as the medium in which it is transported provides the floc with further building materials, energy, nutrients and chemicals for biological growth, chemical reactions and morphological development. As such, a floc's physical (e.g. transport), chemical (e.g. contaminant adsorption) and biological (community development and contaminant biotransformation) behaviour are also in a continuous state of change, with concomitant effects on their aquatic environment as a whole. Although it is recognized that floc form will influence floc behaviour, there is still a basic lack of knowledge of the complex links between the structural components of a floc and how their individual properties and behaviours in combination with others will influence a floc's physical, chemical and biological behaviour. This paper provides a comprehensive conceptual model that links the many interrelated structural components of typical flocs and their interrelated behavioural aspects, in order to enhance our understanding of what constitutes suspended sediment. Copyright © 2001 John Wiley & Sons, Ltd. [source]

Genealogical analyses in open populations: the case of three Arab-derived Spanish horse breeds

JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 5 2009
I. Cervantes
Summary This research assesses the genetic composition of three Arab-derived Spanish horse breeds as an example to highlight the major shortcomings related to genealogical analyses in open populations and to propose approaches useful to deal with this task. The studbooks of three Spanish Arab (SA)-derived horse breeds, Spanish Anglo-Arab (dAA), Hispano-Arab (dHA) and Spanish Sport Horse (dSSH) and those of their parental breeds SA, Spanish Purebred (SPB) and Thoroughbred (TB), totalling 211 754 individuals, were available. The genealogies of the dAA, dHA and dSSH were analysed not only using the corresponding studbook (breed exclusive dataset) but also including the genealogies of the founders from parental breeds (completed dataset). Coancestry analyses revealed that the present SA-derived populations share more genes with the Arab than with the other parental breeds. Effective population size was computed by accounting for migration rates to obtain an equivalent closed-population effective size (eqNe) of 39.2 for the dAA, 56.3 for dHA and 114.1 for dSSH. The essayed methodologies were useful for characterising populations involving migration. The consequences of the management of the analysed breeds are discussed. The results emphasize the need to include the complete genealogies of the individuals to attain reliable genealogical parameters. [source]

Using pedigree information to monitor genetic variability of endangered populations: the Xalda sheep breed of Asturias as an example

JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 2 2003
F. Goyache
Summary The aim of this work is to highlight the need of monitoring small populations to conserve their genetic variability by using a set of parameters to characterize both the structure of populations and management practices. As a representative example we analyse the pedigree information of the endangered Xalda sheep breed of Asturias. The herdbook of Xalda sheep included a total of 805 animals and 62 herds. The number of founders was 329. Nowadays, there are 562 live animals and 26 active herds. The breed is in risk of losing genetic diversity because of the abusive use of certain individuals as parents. The effective number of founder animals is 81.1. The effective number of founder herds is 9.9. The average value of inbreeding in the whole Xalda population was 1.5%. The average relatedness (AR) coefficient reached 1.8% in the whole pedigree. The genetic representation of the lines of founders is unbalanced. Inbreeding trends and effective size do not provide realistic information concerning the risk of loss of diversity as a result of the shallowness of the genealogical information. We suggest the monitoring of the breed using AR to unbalance the genetic contributions of specific individuals, equalizing the genetic representation of the founders and lines in the population. In addition, AR can suggest the introduction of new, under-represented animals in herds showing high average AR values relative to the population. Our results can be useful to improve the development of conservation initiatives involving open herdbooks to avoid the risk of loss of genetic diversity caused by incorrect management practices. Zusammenfassung Verwendung von Pedigree Informationen zur Konservierung genetischer Variabilität in gefährdeten Populationen: Das asturische Xalda Schaf als Beispiel Das Ziel dieser Arbeit ist es, die Notwendigkeit hervorzuheben, Pedigree Informationen in kleinen Populationen durch Verwendung bestimmter Parameter zu analysieren, um sowohl die Struktur der Populationen als auch Managementmaßnahmen zu charakterisieren. Als repräsentatives Beispiel analysieren wir Pedigree Informationen des gefährdeten Xalda Schafes in Asturien. Das Herdbuch des Xalda Schafes umfasst 805 Tiere in 62 Herden. Die Population ging aus 329 Tieren hervor. Zur Zeit beträgt die Population 562 lebende Tiere und 26 aktive Herden. Die Rasse ist aufgrund der starken Nutzung weniger Individuen als Elterntiere in Gefahr, genetische Variabilität zu verlieren. Die effektive Zahl an Gründertieren ist 81,1, die an Herden 9,9. Der durchschnittliche Inzuchtkoeffizient in der gesamten Xalda Population war 1,5%. Der durchschnittliche Verwandtschaftskoeffizient (AR) erreichte 1,8% im gesamten Pedigree. Die genetische Repräsentation der Ausgangslinien ist nicht ausgewogen. Der Inzuchtzuwachs und die effektive Größe bringen aufgrund unzureichender genealogischer Daten keine realistischen Informationen bezüglich Gefährdungsstatus. Wir empfehlen eine Untersuchung der Rasse unter Verwendung von AR, um die genetischen Anteile spezifischer Individuen auszugleichen und um die unausgewogene genetische Repräsentation der Gründer und Basislinien in der Population auszugleichen. Die Verwendung von AR legt die Nutzung neuer, unterrepräsentierter Tiere in den Herden nahe, die hohe durchschnittliche AR Werte im Vergleich zur Gesamtpopulation aufweisen. Unsere Ergebnisse können für die Weiterentwicklungen von Konservierungsmaßnahmen wie offene Herdbücher nützlich sein, um das Risiko eines Verlustes genetischer Diversität durch fehlerhafte Zuchtmaßnahmen zu vermeiden. [source]

Effective size of populations with unequal sex ratio and variation in mating success

Understanding the multiple meanings of ,inbreeding' and ,effective size' for genetic management of African rhinoceros populations

AFRICAN JOURNAL OF ECOLOGY, Issue 4 2009
Stanton Braude
Abstract Although some African rhinoceros populations are currently increasing, others are critically endangered. Even healthy populations are extensively managed in the wild and in captivity. While political and demographic considerations are of primary concern, many decisions are made in the name of genetic management. Such decisions should be informed by a full understanding of the multiple meanings of inbreeding and effective population size. In this essay, we examine inbreeding and effective size of wild and captive populations of African rhinoceroses. We conclude by showing how misunderstanding of effective size and Franklin's 50/500 rule can make a crucial difference in informing management decisions. Résumé Bien que certaines populations de rhinocéros africains soient actuellement en augmentation, d'autres sont en danger critique. Même les populations saines sont gérées très activement dans la nature et en captivité. Alors que les considérations politiques et démographiques soient les principaux motifs d'inquiétude, de nombreuses décisions sont prises au nom de la gestion génétique. Ces décisions devraient se faire en pleine connaissance des multiples implications de l'inbreeding et de ce qu'est une taille de population nécessaire. Dans cet essai, nous examinons l'inbreeding et la taille nécessaire des populations sauvages et captives de rhinocéros africains. Nous concluons en montrant comment une mauvaise compréhension de la taille nécessaire et de la règle 50/500 de Franklin peut entraîner une différence cruciale lorsqu'il s'agit de prendre, en connaissance de cause, les décisions opportunes. [source]

Indirect evidence from DNA sequence diversity for genetic degeneration of the Y-chromosome in dioecious species of the plant Silene: the SlY4/SlX4 and DD44-X/DD44-Y gene pairs

JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 2 2005
V. LAPORTE
Abstract The action of natural selection is expected to reduce the effective population size of a nonrecombining chromosome, and this is thought to be the chief factor leading to genetic degeneration of Y-chromosomes, which cease recombining during their evolution from ordinary chromosomes. Low effective population size of Y chromosomes can be tested by studying DNA sequence diversity of Y-linked genes. In the dioecious plant, Silene latifolia, which has sex chromosomes, one comparison (SlX1 vs. SlY1) indeed finds lower Y diversity compared with the homologous X-linked gene, and one Y-linked gene with no X-linked homologue has lower species-wide diversity than a homologous autosomal copy (SlAp3Y vs. SlAp3A). To test whether this is a general pattern for Y-linked genes, we studied two further recently described X and Y homologous gene pairs in samples from several populations of S. latifolia and S. dioica. Diversity is reduced for both Y-linked genes, compared with their X-linked homologues. Our new data are analysed to show that the low Y effective size cannot be explained by different levels of gene flow for the X vs. the Y chromosomes, either between populations or between these closely related species. Thus, all four Y-linked genes that have now been studied in these plants (the two studied here, and two previously studied genes, have low diversity). This supports other evidence for an ongoing degeneration process in these species. [source]

Rational design of shape selective separations and catalysis: Lattice relaxation and effective aperture size

AICHE JOURNAL, Issue 3 2010
Chrysanthos E. Gounaris
Abstract Gounaris et al. presented a computational method that can be used for the quick screening of zeolite structures and provide predictions regarding which of them have the potential to exhibit high selectivity among a set of molecules of interest. This article builds upon this earlier work and furthers our understanding of diffusion processes in zeolites and other microporous metal oxides. We first present an augmented formulation to account for the flexibility of the zeolitic portal and conduct an analysis to assess the effect of varying the parameters of the associated quadratic potential. We then introduce a methodology to map the energetic landscape, identify all locally optimal conformations, and probabilistically account for the multiplicity of conformers. Finally, we conduct sensitivity analysis on the effective size of the aperture, and show how the methodology can be fine,tuned through experimental observations. A comprehensive database of 290 molecules of industrial interest and a total of 123 different zeolite structures were used in this study. © 2009 American Institute of Chemical Engineers AIChE J, 2010 [source]

Beamline 10.3.2 at ALS: a hard X-ray microprobe for environmental and materials sciences

JOURNAL OF SYNCHROTRON RADIATION, Issue 3 2004
Matthew A. Marcus
Beamline 10.3.2 at the ALS is a bend-magnet line designed mostly for work on environmental problems involving heavy-metal speciation and location. It offers a unique combination of X-ray fluorescence mapping, X-ray microspectroscopy and micro-X-ray diffraction. The optics allow the user to trade spot size for flux in a size range of 5,17,µm in an energy range of 3,17,keV. The focusing uses a Kirkpatrick,Baez mirror pair to image a variable-size virtual source onto the sample. Thus, the user can reduce the effective size of the source, thereby reducing the spot size on the sample, at the cost of flux. This decoupling from the actual source also allows for some independence from source motion. The X-ray fluorescence mapping is performed with a continuously scanning stage which avoids the time overhead incurred by step-and-repeat mapping schemes. The special features of this beamline are described, and some scientific results shown. [source]

Genetic effective size, Ne, tracks density in a small freshwater cyprinid, Pecos bluntnose shiner (Notropis simus pecosensis)

MOLECULAR ECOLOGY, Issue 14 2010
MEGAN J. OSBORNE
Abstract Genetic monitoring tracks changes in measures of diversity including allelic richness, heterozygosity and genetic effective size over time, and has emerged as an important tool for understanding evolutionary consequences of population management. One proposed application of genetic monitoring has been to estimate abundance and its trajectory through time. Here, genetic monitoring was conducted across five consecutive year for the Pecos bluntnose shiner, a federally threatened minnow. Temporal changes in allele frequencies at seven microsatellite DNA loci were used to estimate variance effective size (NeV) across adjacent years in the time series. Likewise, effective size was computed using the linkage disequilibrium method (NeD) for each sample. Estimates of Ne were then compared to estimates of adult fish density obtained from traditional demographic monitoring. For Pecos bluntnose shiner, density (catch-per-unit-effort), NeV and NeD were positively associated across this time series. Results for Pecos bluntnose shiner were compared to a related and ecologically similar species, the Rio Grande silvery minnow. In this species, density and NeV were negatively associated, which suggested decoupling of abundance and effective size trajectories. Conversely, density and NeD were positively associated. For Rio Grande silvery minnow, discrepancies among estimates of Ne and their relationships with adult fish density could be related to effects of high variance in reproductive success in the wild and/or effects of supplementation of the wild population with captive-bred and reared fish. The efficacy of Ne as a predictor of density and abundance may depend on intrinsic population dynamics of the species and how these dynamics are influenced by the landscape features, management protocols and other factors. [source]

Genetic diversity, population structure, effective population size and demographic history of the Finnish wolf population

MOLECULAR ECOLOGY, Issue 6 2006
J. ASPI
Abstract The Finnish wolf population (Canis lupus) was sampled during three different periods (1996,1998, 1999,2001 and 2002,2004), and 118 individuals were genotyped with 10 microsatellite markers. Large genetic variation was found in the population despite a recent demographic bottleneck. No spatial population subdivision was found even though a significant negative relationship between genetic relatedness and geographic distance suggested isolation by distance. Very few individuals did not belong to the local wolf population as determined by assignment analyses, suggesting a low level of immigration in the population. We used the temporal approach and several statistical methods to estimate the variance effective size of the population. All methods gave similar estimates of effective population size, approximately 40 wolves. These estimates were slightly larger than the estimated census size of breeding individuals. A Bayesian model based on Markov chain Monte Carlo simulations indicated strong evidence for a long-term population decline. These results suggest that the contemporary wolf population size is roughly 8% of its historical size, and that the population decline dates back to late 19th century or early 20th century. Despite an increase of over 50% in the census size of the population during the whole study period, there was only weak evidence that the effective population size during the last period was higher than during the first. This may be caused by increased inbreeding, diminished dispersal within the population, and decreased immigration to the population during the last study period. [source]

Small effective population sizes in a widespread selfing species, Lymnaea truncatula (Gastropoda: Pulmonata)

MOLECULAR ECOLOGY, Issue 9 2004
C. MEUNIER
Abstract We present here a spatial and temporal population genetic survey of a common freshwater snail, also a predominantly selfing species, Lymnaea truncatula. The rate of genetic diversity loss was quantified by estimating the effective size (Ne) of the snail populations, using two different methods. A temporal survey allowed estimation of a variance effective size of the populations, and a spatial survey allowed the estimation of an inbreeding effective size, from two-locus identity disequilibria estimates. Both methods were consistent and provided low Ne values. Drift due to (i) high amounts of selfing and (ii) fluctuations in population sizes because of temporary habitats, and also selection coupled to genome-wide linkage disequilibria, could explain such reductions in Ne. The loss of genetic diversity appears to be counterbalanced only very partially by low apparent rates of gene flow. [source]

Population genetic structure of male black grouse (Tetrao tetrix L.) in fragmented vs. continuous landscapes

MOLECULAR ECOLOGY, Issue 9 2003
Alain Caizergues
Abstract We investigated the association of habitat fragmentation with genetic structure of male black grouse Tetrao tetrix. Using 14 microsatellites, we compared the genetic differentiation of males among nine localities in continuous lowland habitats in Finland to the genetic differentiation among 14 localities in fragmented habitats in the Alps (France, Switzerland and Italy). In both areas, we found significant genetic differentiation. However, the average differentiation, measured as ,, was more than three times higher in the Alps than in Finland. The greater differentiation found in the Alps is probably due to the presence of mountain ridges rising above natural habitats of the species, which form barriers to gene flow, and to a higher influence of genetic drift resulting from lower effective sizes in highly fragmented habitats. The detection of isolation by distance in the Alps suggests that gene flow among populations does occur. The genetic variability measured as gene diversity HE and allelic richness A was lower in the Alps than in Finland. This could result from the higher fragmentation and/or from the fact that populations in the Alps are isolated from the main species range and have a lower effective size than in Finland. This study suggests that habitat fragmentation can affect genetic structure of avian species with relatively high dispersal propensities. [source]

estim 1.0: a computer program to infer population parameters from one- and two-locus gene identity probabilities

MOLECULAR ECOLOGY RESOURCES, Issue 4 2001
R. Vitalis
Abstract Estimating effective population size is an important issue in population and conservation genetics. Recently, we proposed a new method to infer effective size and migration rate from one- and two-locus identity probability measures. We now announce the release of a user-friendly Microsoft® Windows program that uses this method to provide joint estimates of local effective population size and immigration rate for each subpopulation in a population genetics data set. [source]

Effective size of harvested ungulate populations

Development of a microsatellite multiplex genotyping tool for the fish Gilthead seabream (Sparus aurata): applicability in population genetics and pedigree analysis

AQUACULTURE RESEARCH, Issue 10 2010
Javier Porta
Abstract In spite of the numerous studies performed in the aquacultured fish gilthead seabream, the overall structure of wild and cultivated stocks is rather confusing. In this study, we developed a 10 microsatellite genotyping tool SaGT(6+4), conformed by two polymerase chain reaction-multiplex reactions (SaGT6 and SaGT4), which can be simultaneously combined in automatic sequencers. The utility of this tool was proven through the following applications: (i) characterization and differentiation of wild and cultivated populations; (ii) pedigree reconstruction and estimation of the effective size in a cultivated stock; (iii) ability for pedigree reconstruction under different simulated situations; and (iv) determination of genetic relationships in the absence of data from parents. Based on our results, some recommendations have been provided on the management of the screened stocks. Our results also support the use of this tool in a standardized way, to understand the actual status of gilthead seabream from both wild and cultivated populations. [source]

Allozyme diversity and history of distribution expansion in the maritime perennial plant Hedyotis strigulosa (Rubiaceae), distributed over the wide latitudes in the Japanese Archipelago

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2008
MASAYUKI MAKI
Allozyme diversity was examined in 30 populations of the maritime perennial plant Hedyotis strigulosa var. parviflora, which is distributed from subtropical islands to the central mainland of Japan. Genetic diversity within populations tended to be larger in southern island populations than in northern mainland populations. In the southern part of the distribution, the population size is generally large and populations are distributed more continuously than in the northern area, resulting in the larger effective size of southern populations as a whole. These factors play a major role in maintaining greater genetic diversity in the southern populations. By contrast, genetic diversity in the northern populations is very low, probably resulting from bottlenecks of population establishments during recolonization from refugial area to the northern areas. Geographically close populations were located near each other in the multidimensional scaling and the phenogram based on genetic distances, suggesting that gene flow among remote populations is rather limited. The pattern of genetic diversity in H. strigulosa var. parviflora is likely caused by the distribution expansion of the species; in the last glacier era, the species was restricted to the southern area; its advance to the northern area is relatively recent. Another variety endemic only to the Daito Islands, H. strigulosa var. luxurians, has lower genetic diversity than H. strigulosa var. parviflora and has genetically diverged from H. strigulosa var. parviflora. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 93, 679,688. [source]

Understanding the multiple meanings of ,inbreeding' and ,effective size' for genetic management of African rhinoceros populations

Genetic Effects of Multiple Generations of Supportive Breeding

MINIMAL SELFING, FEW CLONES, AND NO AMONG-HOST GENETIC STRUCTURE IN A HERMAPHRODITIC PARASITE WITH ASEXUAL LARVAL PROPAGATION

EVOLUTION, Issue 3 2006
Charles D. Criscione
Abstract Little is known about actual mating systems in natural populations of parasites or about what constitutes the limits of a parasite deme. These parameters are interesting because they affect levels of genetic diversity, opportunities for local adaptation, and other evolutionary processes. We expect that transmission dynamics and the distribution of parasites among hosts should have a large effect on mating systems and demic structure, but currently we have mostly speculation and very few data. For example, infrapopulations (all the parasites in a single host) should behave as demes if parasite offspring are transmitted as a clump from host to host over several generations. However, if offspring are well mixed, then the parasite component population (all the parasites among a host population) would function as the deme. Similarly, low mean intensities or a high proportion of worms in single infections should increase the selfing rate. For species having an asexual amplification stage, transmission between intermediate and definitive (final) hosts will control the variance in clonal reproductive success, which in turn could have a large influence on effective sizes and rates of inbreeding. We examined demic structure, selfing rates, and the variance in clonal reproductive success in natural populations of Plagioporus shawi, a hermaphroditic trematode that parasitizes salmon. Overall levels of genetic diversity were very high. An a posteriori inference of population structure overwhelmingly supports the component population as the deme, rather than individual infrapopulations. Only a single pair of 597 adult individuals was identified as clones. Thus, the variance in clonal reproductive success was almost zero. Despite being hermaphroditic, P. shawi appears to be almost entirely outcrossing. Genetic estimates of selfing (<5%) were in accordance with the proportion of parasites from single infections. Thus, it appears that individual flukes outcross whenever possible and only resort to selfing when alone. Finally, our data support the hypothesis that aquatic transmission and the use of several intermediate hosts promotes high genetic diversity and well-mixed infrapopulations. [source]