Relation of population changes to the distribution of genetic factors

Abstract

During the 1800's, the population of Ireland underwent a rapid increase and subsequent decrease in population size. The effects of this change upon population structure were assessed using a simulation of the isolation by distance model and comparing the results to those obtained assuming constant population size. These results indicate that changes in within‐group genetic similarity (kinship) brought about by a rapid increase in population size are cancelled by the effects of a rapid decrease in population size. Parameters of the isolation by distance model are hardly affected by population size changes. These results suggest that violation of the assumption of constant population size for population structure models may not be that serious when population size changes rapidly and in both directions.     

内蒙古高原不同生境条件下甘蒙锦鸡儿水分调节特性和抗逆性的比较研究

对分布于内蒙古和林格尔（半干旱地区）和阿拉善（强干旱地区）地区的甘蒙锦鸡儿种群水分调节特性和抗逆性进行了比较研究.结果表明,阿拉善种群比和林格尔种群的叶片渗透调节物质含量高、渗透势低、渗透调节能力强,叶片含水量和自由水含量低、束缚水含量和束缚水/自由水比值高,叶水势和气孔导度低,表明阿拉善种群比和林格尔种群有更强的水分调节能力.阿拉善种群丙二醛(MDA)含量大于和林格尔种群,但细胞膜相对透性和超氧自由基含量小于和林格尔种群,表明阿拉善种群自由基清除能力强、细胞膜稳定性高.有效的水分调节能力和较强的抗逆性是甘蒙锦鸡儿适应干旱环境的重要生理基础.     

A diffusion approximation for selection and drift in a subdivided population

The population-genetic consequences of population structure are of great interest and have been studied extensively. An area of particular interest is the interaction among population structure, natural selection, and genetic drift. At first glance, different results in this area give very different impressions of the effect of population subdivision on effective population size (N(e)), suggesting that no single value of N(e) can completely characterize a structured population. Results presented here show that a population conforming to Wright's island model of subdivision with genic selection can be related to an idealized panmictic population (a Wright-Fisher population). This equivalent panmictic population has a larger size than the actual population; i.e., N(e) is larger than the actual population size, as expected from many results for this type of population structure. The selection coefficient in the equivalent panmictic population, referred to here as the effective selection coefficient (s(e)), is smaller than the actual selection coefficient (s). This explains how the fixation probability of a selected allele can be unaffected by population subdivision despite the fact that subdivision increases N(e), for the product N(e)s(e) is not altered by subdivision.     

The Allee Effect in Population Dynamics with a Seasonal Reproduction Pattern

The local consequences of the Allee effect in isolated populations of animal species with a seasonal reproduction pattern that nonmonotonically depends on population density are studied based on a discrete analog of the Bazykin–Ludwig model. Along with the critical population size (below which the population degenerates because of the Allee effect), the limiting population size is discovered: the population with a higher density degenerates because of overpopulation. The effect of the initial population size on possible scenarios of its development is studied in detail. It is shown that an “intermediate” population size that provides the maximum population density is unachievable in some cases.     

Evolutionary stability for large populations

We present a revision of Maynard Smith's evolutionary stability criteria for populations which are very large (though technically finite) and of unknown size. We call this the large population ESS, as distinct from Maynard Smith's infinite population ESS and Schaffer's finite population ESS. Building on Schaffer's finite population model, we define the large population ESS as a strategy which cannot be invaded by any finite number of mutants, as long as the population size is sufficiently large. The large population ESS is not equivalent to the infinite population ESS: we give examples of games in which a large population ESS exists but an infinite population ESS does not, and vice versa. Our main contribution is a simple set of two criteria for a large population ESS, which are similar (but not identical) to those originally proposed by Maynard Smith for infinite populations.     

Regarding the confusion between the population concept and Mayr's "population thinking"

Ernst Mayr said that one of Darwin's greatest contributions was to show scholars the way to population thinking, and to help them discard a mindset of typological thinking. Population thinking rejects a focus on a central representative type, and emphasizes the variation among individuals. However, Mayr's choice of terms has led to confusion, particularly among biologists who study natural populations. Both population thinking and the concept of a biological population were inspired by Darwin, and from Darwin the chain for both concepts runs through Francis Galton who introduced the statistical usage of "population" that appears in Mayr's population thinking. It was Galton's "population" that was modified by geneticists and biometricians in the early 20th century to refer to an interbreeding and evolving community of organisms. Under this meaning, a population is a biological entity and so paradoxically population thinking, which emphasizes variation at the expense of dwelling on entities, is usually not about populations. Mayr did not address the potential for misunderstanding but for him the important part of the population concept was that the organisms within a population were variable, and so he probably thought there should not be confusion between population thinking and the concept of a population.     

A population dynamics model for annual plants subject to inbreeding depression

Summary We present a population dynamics model for annual plants subject to density dependent competition and a decline in mean individual fitness with inbreeding. An analysis of this model provides three distinct sets of parameter values that define the relative influence of inbreeding depression and density on population growth. First, a population with a relatively high finite rate of increase and a relatively small environmental carrying capacity can persist in spite of low levels of inbreeding depression. These types of population may occur during a bottleneck event that is caused by pure predation (or collecting) pressure rather than loss of habitat. Second, there can exist a minimum viable population size when the finite rate of increase is relatively low and the population is also affected by density: the growth or decline of the population will depend on the initial population size. Third, when the population is small enough to be simultaneously effected by density and by inbreeding depression, there can be no viable population.     

Epidemic and demographic interaction in the spread of potentially fatal diseases in growing populations.

The spread of a potentially fatal infectious disease is considered in a host population that would increase exponentially in the absence of the disease. Taking into account how the effective contact rate C(N) depends on the population size N, the model demonstrates that demographic and epidemiological conclusions depend crucially on the properties of the contact function C. Conditions are given for the following scenarios to occur: (i) the disease spreads at a lower rate than the populations grows and does not modify the population growth rate: (ii) the disease initially spreads at a faster rate than the population grows and lowers the population growth rate in the long run and the following three subscenarios are possible: (iia) the population still grows exponentially, but at a slower rate; (iib) population growth is limited, but the population size does not decay; (iic) population increase is converted into population decrease.     

Effective population size of a population with stochastically varying size

For a Wright–Fisher model with mutation whose population size fluctuates stochastically from generation to generation, a heterozygosity effective population size is defined by means of the equilibrium average heterozygosity of the population. It is shown that this effective population size is equal to the harmonic mean of population size if and only if the stochastic changes of population size are uncorrelated. The effective population size is larger (resp. smaller) than the harmonic mean when the stochastic changes of population size are positively (resp. negatively) autocorrelated. These results and those obtained so far for other stochastic models with fluctuating population size suggest that the property that effective population sizes are always larger than the harmonic mean under the fluctuation of population size holds only for continuous time models such as diffusion and coalescent models, whereas effective population sizes can be equal to or smaller than the harmonic mean for discrete time models.     

The regulation of the dynamics of human populations

The important aspects of population dynamics are shown in a model along with the changes of population structure, the reasons for these changes and the conditions under which such changes take place. Subsequently, the reasons for these population dynamic processes which can be arranged in a three step scale are shown. Here, it must be differentiated between endogenous processes, due to factors inherent in the population, and exogenous ones caused by external forces effecting structural changes. The population political trends has to be incorporated as a part of the exogenous factors. The questions of regularities in the population dynamics are shown in the examples of important population theories in history. At the same time the theoretically possible borders are described, within which, due to purely physiological reasons, a population dynamic process has to occur. However, these borders will never be reached. Examination of the inertia of the population dynamic processes suggests an examination of the questions about the probability of the self-destructive processes in population dynamics. Considering the strong self-regulatory processes within a population the hypothesis of a population extinction is refuted.     

Sex-specific population dynamics and demography of capercaillie (Tetrao urogallus L.) in a patchy environment

Modeling the population dynamics of patchily distributed species is a challenge, particularly when inference must be based on incomplete and small data sets such as those from most species of conservation concern. Here, we develop an open population spatial capture–recapture (SCR) model with sex-specific detection and population dynamics parameters to investigate population trend and sex-specific population dynamics of a capercaillie (Tetrao urogallus) population in Switzerland living in eight distinct forest patches totaling 22 km² within a region of 908 km² and sampled via scat collection. Our model accounts for the patchy distribution of habitat and the uncertainty introduced by collecting data only every third year, while producing sex by patch population trajectories. The estimated population trajectory was a decline of 2% per year; however, the sex specificity of the model revealed a decline in the male population only, with no evidence of decline in the female population. The decline observed in males was explained by the demography of just two of the eight patches. Our study highlights the flexibility of open population SCR models for assessing population trajectories through time and across space and emphasizes the desirability of estimating sex-stratified population trends especially in species of conservation concern.     

Distinctly different sex ratios in African and European populations of Drosophila melanogaster inferred from chromosomewide single nucleotide polymorphism data

It has been hypothesized that the ratio of X-linked to autosomal sequence diversity is influenced by unequal sex ratios in Drosophila melanogaster populations. We conducted a genome scan of single nucleotide polymorphism (SNP) of 378 autosomal loci in a derived European population and of a subset of 53 loci in an ancestral African population. On the basis of these data and our already available X-linked data, we used a coalescent-based maximum-likelihood method to estimate sex ratios and demographic histories simultaneously for both populations. We confirm our previous findings that the African population experienced a population size expansion while the European population suffered a population size bottleneck. Our analysis also indicates that the female population size in Africa is larger than or equal to the male population size. In contrast, the European population shows a huge excess of males. This unequal sex ratio and the bottleneck alone, however, cannot account for the overly strong decrease of X-linked diversity in the European population (compared to the reduction on the autosome). The patterns of the frequency spectrum and the levels of linkage disequilibrium observed in Europe suggest that, in addition, positive selection must have acted in the derived population.     

Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations

Current estimators of gene flow come in two methods; those that estimate parameters assuming that the populations investigated are a small random sample of a large number of populations and those that assume that all populations were sampled. Maximum likelihood or Bayesian approaches that estimate the migration rates and population sizes directly using coalescent theory can easily accommodate datasets that contain a population that has no data, a so-called 'ghost' population. This manipulation allows us to explore the effects of missing populations on the estimation of population sizes and migration rates between two specific populations. The biases of the inferred population parameters depend on the magnitude of the migration rate from the unknown populations. The effects on the population sizes are larger than the effects on the migration rates. The more immigrants from the unknown populations that are arriving in the sample populations the larger the estimated population sizes. Taking into account a ghost population improves or at least does not harm the estimation of population sizes. Estimates of the scaled migration rate M (migration rate per generation divided by the mutation rate per generation) are fairly robust as long as migration rates from the unknown populations are not huge. The inclusion of a ghost population does not improve the estimation of the migration rate M; when the migration rates are estimated as the number of immigrants Nm then a ghost population improves the estimates because of its effect on population size estimation. It seems that for 'real world' analyses one should carefully choose which populations to sample, but there is no need to sample every population in the neighbourhood of a population of interest.     

具有阶段结构的自食单种群生长模型的稳定性及最有收获策略

本文讨论了一生中具有两个生长阶段－成年与未成年的种群模型,该模型收获成年种群并且成年种群食自身所产的卵,即模型为自食模型,得到了正平衡点全局渐近稳定的条件及收获成年种群的阈值和最优收获策略。     

Conservation genetics of a peripherally isolated population of the wood turtle (<Emphasis Type="Italic">Glyptemys insculpta</Emphasis>) in Iowa

The North American wood turtle, Glyptemys insculpta, is a semi-aquatic species that is considered rare, threatened, or endangered over much of its range. In this study, a particularly vulnerable peripheral isolate population in Iowa has been monitored over a period of 7 years. Population census size, estimated from mark-recapture data, and age structure determined from morphology are compared with genetic variation assessed using microsatellites. For reference, the genetics and demographics of this peripheral isolate are compared to data from a more dense population nearer the core of the species range in West Virginia. Geneflow between the Iowa population and a nearby population in Minnesota also is assessed. Genetic data indicate that the Iowa population is isolated, unique, and diverse. Although the Iowa population has lower allelic richness, lower heterozygosity, and smaller genetic effective population size than does the West Virginia population, the difference is not dramatic despite its lower population size, position at the periphery of the species range, and biogeographic history. The Iowa population is not inbred, and there is no genetic signature of a recent population bottleneck. However, interpretations of recent population dynamics based on genetic data may be unduly encouraging in long-lived species such as G. insculpta. Field data suggest a nearly complete lack of recruitment in Iowa. A number of environmental and anthropogenic factors, including recent increases in summer flooding during egg incubation, may have a more negative impact on the Iowa population than on the West Virginia population.     

Genetic impoverishment of the last black grouse (Tetrao tetrix) population in the Netherlands: detectable only with a reference from the past

We have studied a small isolated population of black grouse (Tetrao tetrix) in the Netherlands to examine the impact of isolation and reduction in numbers on genetic diversity. We compared the genetic diversity in the last extant Dutch population with Dutch museum samples and three other black grouse populations (from England, Austria and Norway, respectively) representing isolated and continuous populations. We found significantly lower allelic richness, observed and expected heterozygosities in the present Dutch population compared to the continuous populations (Austria and Norway) and also to the historical Dutch population. However, using a bottleneck test on each population, signs of heterozygosity excess were only found in the likewise isolated English population despite that strong genetic drift was evident in the present Dutch population in comparison to the reference populations, as assessed both in pairwise F(ST)and STRUCTURE analyses. Simulating the effect of a population reduction on the Dutch population from 1948 onwards, using census data and with the Dutch museum samples as a model for the genetic diversity in the initial population, revealed that the loss in number of alleles and observed heterozygosity was according to genetic drift expectations and within the standard error range of the present Dutch population. Thus, the effect of the strong decline in the number of grouse on genetic diversity was only detectable when using a reference from the past. The lack of evidence for a population reduction in the present Dutch population by using the program bottleneck was attributed to a rapidly found new equilibrium as a consequence of a very small effective population size.     

A management policy for sika deer based on sex-specific hunting

We consider here a management policy for a sika deer (Cervus nippon) population in the eastern part of Hokkaido. Deer populations are characterized by a large intrinsic rate of population increase, no significant density effects on population growth before population crash, and a relatively simple life history. Our goals of management for the deer population are (1) to avoid irruption with severe damage to agriculture and forestry, (2) to avoid the risk of extinction of the deer population, and (3) to maintain a sustainable yield of deer. To make a robust program on the basis of uncertain information about the deer population, we consider three levels of relative population size and four levels of hunting pressures. We also take into consideration a critical level for extinction, an optimal level, and an irruption level. The hunting pressure for females is set to increase with the population size. We also recommend catching males if the population size is between the critical and optimal levels and catching females and males if the population size is larger than the optimal level. We must avoid cases of irruption or threatened population under various sets of uncertain parameter values. The simulation results suggest that management based on sex-specific hunting is effective to diminish the annual variation in hunting yield. Received: April 8, 1998 / Accepted: December 25, 1998     

Self-organized dynamics in spatially structured populations

Self-organization and pattern formation represent the emergence of order in temporal and spatial processes. Self-organization in population ecology is gaining attention due to the recent advances concerning temporal fluctuations in the population size of dispersal-linked subunits. We shall report that spatially structured models of population renewal promote the emergence of a complex power law order in spatial population dynamics. We analyse a variety of population models showing that self-organization can be identified as a temporal match in population dynamics among local units, and how the synchrony changes in time. Our theoretical results are concordant with analyses of population data on the Canada lynx.     

Formulating variable carrying capacity by exploring a resource dynamics-based feedback mechanism underlying the population growth models

Most of the population growth models comprise the concept of carrying capacity presume that a stable population would have a saturation level characteristic. This indicates that the population growth models have a common implicit feature of resource-limited growth, which contributes at a later stage of population growth by forming a numerical upper bound on the population size. However, a general underlying resource dynamics of the models has not been previously explored, which is the focus of present study. In this paper, we found that there exists a conservation of energy relationship comprising the terms of available resource and population density, jointly interpreted here as total available vital energy in a confined environment. We showed that this relationship determines a density-dependent functional form of relative population growth rate and consequently the parametric equations are in the form depending upon the population density, resource concentration, and time. Thus, the derived form of relative population growth rate is essentially a feedback type, i.e., updating parametric values for the corresponding population density. This resource dynamics-based feedback approach has been implemented for formulating variable carrying capacity in a confined environment. Particularly, at a constant resource replenishment rate, a density-dependent population growth equation similar to the classic logistic equation is derived, while one of the regulating factors of the underlying resource dynamics is that the resource consumption rate is directly proportional to the resource concentration. Likewise two other population growth equations similar to two known popular growth equations are derived based on this resource dynamics-based feedback approach. Using microcosm-derived data of fungus T. virens, we fitted one derived population growth model against the datasets, and concluded that this approach is practically implementable for studying a single population growth regulation in a confined environment.     

Population growth rate and its determinants: an overview

We argue that population growth rate is the key unifying variable linking the various facets of population ecology. The importance of population growth rate lies partly in its central role in forecasting future population trends; indeed if the form of density dependence were constant and known, then the future population dynamics could to some degree be predicted. We argue that population growth rate is also central to our understanding of environmental stress: environmental stressors should be defined as factors which when first applied to a population reduce population growth rate. The joint action of such stressors determines an organism's ecological niche, which should be defined as the set of environmental conditions where population growth rate is greater than zero (where population growth rate = r = log(e)(N(t+1)/N(t))). While environmental stressors have negative effects on population growth rate, the same is true of population density, the case of negative linear effects corresponding to the well-known logistic equation. Following Sinclair, we recognize population regulation as occurring when population growth rate is negatively density dependent. Surprisingly, given its fundamental importance in population ecology, only 25 studies were discovered in the literature in which population growth rate has been plotted against population density. In 12 of these the effects of density were linear; in all but two of the remainder the relationship was concave viewed from above. Alternative approaches to establishing the determinants of population growth rate are reviewed, paying special attention to the demographic and mechanistic approaches. The effects of population density on population growth rate may act through their effects on food availability and associated effects on somatic growth, fecundity and survival, according to a 'numerical response', the evidence for which is briefly reviewed. Alternatively, there may be effects on population growth rate of population density in addition to those that arise through the partitioning of food between competitors; this is 'interference competition'. The distinction is illustrated using a replicated laboratory experiment on a marine copepod, Tisbe battagliae. Application of these approaches in conservation biology, ecotoxicology and human demography is briefly considered. We conclude that population regulation, density dependence, resource and interference competition, the effects of environmental stress and the form of the ecological niche, are all best defined and analysed in terms of population growth rate.