Fluctuations in the Size of Isolated Single-Species Populations and Natural Selection

This paper discusses the basic types of dynamical behavior of populations obtained in discrete models, such as monotonous dynamics, stable limited cycles, and chaotic variations. All these modes are shown to have possibly arisen in the evolution of limited populations under the effect of density-independent selection. This effect together with that of density-dependent non-selective factors has been termed F-selection, which is characterized by independence of relative fitnesses from population density, whereas populations may be ecologically limited; in other words, absolute fitnesses prove to be a function of population size. The characteristic of F-selection is to be not sensitive to changes in population size but to lead to fluctuations, that create conditions for achieving density-dependent selection.     

Measuring Natural Selection on Proportional Traits: Comparisons of Three Types of Selection Estimates for Resistance and Susceptibility to Herbivore Damage

To compare the strength of natural selection on different traits and in different species, evolutionary biologists typically estimate selection differentials and gradients in standardized units. Measuring selection differentials and gradients in standard deviation units or mean-standardized units facilitates such comparisons by converting estimates with potentially varied units to a common scale. In this note, I compare the performance of variance- and mean-standardized selection differentials and gradients for a unique and biologically important class of traits: proportional traits, that can only vary between zero and one, and their complements (1 minus the trait) using simple algebra and analysis of data from a field-study using morning glories. There is a systematic, mathematical relationship between unstandardized and variance-standardized selection gradients for proportional traits and their complements, but such a general relationship is lacking for mean-standardized gradients, potentially leading investigators to mistakenly conclude that a proportional change in a trait would have little effect on fitness. Despite this potential limitation, mean-standardized selection differentials and gradients represent a useful tool for studying natural selection on proportional traits, because by definition they measure how proportional changes in the mean of a trait lead to proportional changes in relative fitness.Co-ordinating editor: I. Olivieri     

HaploBlocks: Efficient Detection of Positive Selection in Large Population Genomic Datasets

Genomic regions under positive selection harbor variation linked for example to adaptation. Most tools for detecting positively selected variants have computational resource requirements rendering them impractical on population genomic datasets with hundreds of thousands of individuals or more. We have developed and implemented an efficient haplotype-based approach able to scan large datasets and accurately detect positive selection. We achieve this by combining a pattern matching approach based on the positional Burrows–Wheeler transform with model-based inference which only requires the evaluation of closed-form expressions. We evaluate our approach with simulations, and find it to be both sensitive and specific. The computational resource requirements quantified using UK Biobank data indicate that our implementation is scalable to population genomic datasets with millions of individuals. Our approach may serve as an algorithmic blueprint for the era of “big data” genomics: a combinatorial core coupled with statistical inference in closed form.     

群体融合对选择有效性的影响

探讨了群体融合对选择有效性的影响⒚显性完全且选择不利于纯合子 ａａ 时，当群体中隐性基因的频率 ０≤ｑ＜ １／３，群体融合导致选择有效性增加；而当 １／３＜ ｑ≤１ 时，融合使选择有效性减小⒚无显性即选择不利于 Ａａ 和 ａａ 时，群体融合导致选择有效性减小⒚超显性即选择有利于杂合子 Ａａ 而不利于纯合子 Ａ Ａ 和 ａａ 时，当 ０≤ｑ＜ １／２，融合导致选择有效性增加；当 １／２＜ ｑ≤１，融合导致选择有效性减小⒚     

DNA水平自然选择作用的检测

上个世纪60年代,Kimura提出的“中性进化”假说使经典的达尔文自然选择学说遭遇了前所未有的挑战。但新近的研究表明：在DNA水平,越来越多的证据支持“自然选择”的进化理论。这些研究成果得益于近年来大量群体和基因组DNA数据的积累,以及理论群体遗传学的发展。在DNA水平检测选择作用是否存在的方法包括两大类：种内多态性检验和种间差异度检验。前者以Tajima(1989)提出的D检验为代表,后者大都基于“中性条件下,种内与种间进化速率一致”的原理。这些方法以中性假说作为零假设,结合统计检验方法分析DNA数据,被称为“中性检验”。这些方法对于解决一些有关进化的基础理论问题和人类遗传学及生物信息学的深入研究都具有重要意义。本文介绍几个应用广泛的检测方法,以使国内的读者了解它们的基本思路和操作方法。     

On the Explanatory Roles of Natural Selection

Can selection explain why individuals have the traits they do? This question has generated significant controversy. I will argue that the debate encompasses two separable aspects, to detrimental effect: (1) the role of selection in explaining the origin and evolution of biological traits and (2) the implications this may have for explaining why individuals have the traits they do. (1) can be settled on the basis of evolutionary theory while (2) requires additional, extra-scientific assumptions. By making a distinction between traits affected by a single factor and traits affected by multiple factors I show that selection can, under certain conditions, help explain the origin of traits. Resolving the first aspect enables us to critically assess the various incompatible and independent philosophical commitments made within the second aspect of the debate.     

Extending the range of additivity in using inclusive fitness

Inclusive fitness is a concept widely utilized by social biologists as the quantity organisms appear designed to maximize. However, inclusive fitness theory has long been criticized on the (uncontested) grounds that other quantities, such as offspring number, predict gene frequency changes accurately in a wider range of mathematical models. Here, we articulate a set of modeling assumptions that extend the range of scenarios in which inclusive fitness can be applied. We reanalyze recent formal analyses that searched for, but did not find, inclusive fitness maximization. We show (a) that previous models have not used Hamilton''s definition of inclusive fitness, (b) a reinterpretation of Hamilton''s definition that makes it usable in this context, and (c) that under the assumption of probabilistic mixing of phenotypes, inclusive fitness is indeed maximized in these models. We also show how to understand mathematically, and at an individual level, the definition of inclusive fitness, in an explicit population genetic model in which exact additivity is not assumed. We hope that in articulating these modeling assumptions and providing formal support for inclusive fitness maximization, we help bridge the gap between empiricists and theoreticians, which in some ways has been widening, demonstrating to mathematicians why biologists are content to use inclusive fitness, and offering one way to utilize inclusive fitness in general models of social behavior.     

Natural selection and the maximization of fitness

The notion that natural selection is a process of fitness maximization gets a bad press in population genetics, yet in other areas of biology the view that organisms behave as if attempting to maximize their fitness remains widespread. Here I critically appraise the prospects for reconciliation. I first distinguish four varieties of fitness maximization. I then examine two recent developments that may appear to vindicate at least one of these varieties. The first is the ‘new’ interpretation of Fisher's fundamental theorem of natural selection, on which the theorem is exactly true for any evolving population that satisfies some minimal assumptions. The second is the Formal Darwinism project, which forges links between gene frequency change and optimal strategy choice. In both cases, I argue that the results fail to establish a biologically significant maximization principle. I conclude that it may be a mistake to look for universal maximization principles justified by theory alone. A more promising approach may be to find maximization principles that apply conditionally and to show that the conditions were satisfied in the evolution of particular traits.     

Response to Selection and Inbreeding Depression in a Dynamic Population for Amount of Inbreeding

A method for predicting response to selection and inbreeding depression in a dynamic population for amount of inbreeding was derived and illustrated with an example of selection under full-sib mating.     

Adaptation and Natural Selection revisited

In Adaptation and Natural Selection, George C. Williams linked the distinction between group and individual adaptation with the distinction between group and individual selection. Williams’ Principle, as we will call it, says that adaptation at a level requires selection at that level. This is a necessary but not a sufficient condition; for example, group adaptation requires group selection, but the fact that group selection influences a trait’s evolution does not suffice for the resulting trait frequency to be a group adaptation. What more is required? In this paper, we describe an answer to this question that has been developed in multilevel selection theory. We also discuss an alternative framework for defining units of adaptation that violates Williams’ Principle.     

The Structure of Evolution by Natural Selection

We attempt a conclusive resolution of the debate over whether the principle of natural selection (PNS), especially conceived as the `principle' of the `survival of the fittest', is a tautology. This debate has been largely ignored for the past 15 years but not, we think, because it has actually been settled. We begin by describing the tautology objection, and situating the problem in the philosophical and biology literature. We then demonstrate the inadequacy of six prima facie plausible reasons for believing that the tautology debate has been satisfactorily resolved (the PNS is strictly a methodological principle; scientific theories can contain tautologies; the scope of the PNS has been reduced; theories should be understood as models and not exceptionless laws; the widespread acceptance of the propensity interpretation of fitness; and the abandonment of operationalism and verificationism). We proceed to a detailed discussion of Brandon's law (D) describing the PNS, and show that law (D) seriously misrepresents the structure of evolution by natural selection. In the final sections, we provide and defend a novel reinterpretation of the structure of the principle (or, we prefer, model) of evolution by natural selection.     

自然条件下同级消费者中种群平均规模的博弈论研究

给出了一种新的博弈——非合作n人条件博弈,并给出了它的求解方法．以这种博弈为工具,在适当的假定下研究了无人类的理想地域上同级消费者中各个种群的平均规模．结论是:当个体的平均食量充分小时,该种群的平均规模等于前一级消费者或生产者的最大承受量;否则该种群的平均规模与前一级消费者或生产者的最大承受量成正比,与个体的平均食量和该级消费者中种群的数目都成反比．     

色木槭天然次生林群落结构特征

对色木槭天然次生林群落进行研究,测定了该群落主要乔木树种的重要值,分析了该群落的种类组成,物种多样性。结果表明：色木槭天然次生林乔木层共有16个种群,其中色木槭、蒙古栎、糠椴、山榆占明显优势,为该层的优势种和建群种;径级以<15 cm的株数最多,占总株数的87.82%,林分幼树更新数量充足。群落的Simpson指数为0.833、Shannon-wiener多样性指数为2.101、丰富度指数为2.291、均匀性指数为0.758和生态优势度指数为0.113。乔木层立木以低龄种群在群落中占优势,为了促进群落将向地带性典型植被类型演替,提出了抚育管理的建议。     

Learning Natural Selection from the Site Frequency Spectrum

Genetic adaptation to external stimuli occurs through the combined action of mutation and selection. A central problem in genetics is to identify loci responsive to specific selective constraints. Many tests have been proposed to identify the genomic signatures of natural selection by quantifying the skew in the site frequency spectrum (SFS) under selection relative to neutrality. We build upon recent work that connects many of these tests under a common framework, by describing how selective sweeps affect the scaled SFS. We show that the specific skew depends on many attributes of the sweep, including the selection coefficient and the time under selection. Using supervised learning on extensive simulated data, we characterize the features of the scaled SFS that best separate different types of selective sweeps from neutrality. We develop a test, SFselect, that consistently outperforms many existing tests over a wide range of selective sweeps. We apply SFselect to polymorphism data from a laboratory evolution experiment of Drosophila melanogaster adapted to hypoxia and identify loci that strengthen the role of the Notch pathway in hypoxia tolerance, but were missed by previous approaches. We further apply our test to human data and identify regions that are in agreement with earlier studies, as well as many novel regions.     

Teleosemantics Without Natural Selection

Ruth Millikan and others advocate theories which attempt to naturalize wide mental content (e.g. beliefs’ truth conditions) in terms of function in the teleological sense, where a function is constituted in part by facts concerning past natural selection involving ancestors of a current entity. I argue that it is a mistake to base content on selection. Content should instead be based on functions which though historical, do not involve selection. I sketch an account of such functions.     

Fitness effects of derived deleterious mutations in four closely related wild tomato species with spatial structure

A key issue in evolutionary biology is an improved understanding of the genetic mechanisms by which species adapt to various environments. Using DNA sequence data, it is possible to quantify the number of adaptive and deleterious mutations, and the distribution of fitness effects of new mutations (its mean and variance) by simultaneously taking into account the demography of a given species. We investigated how selection functions at eight housekeeping genes of four closely related, outcrossing species of wild tomatoes that are native to diverse environments in western South America (Solanum arcanum, S. chilense, S. habrochaites and S. peruvianum). We found little evidence for adaptive mutations but pervasive evidence for strong purifying selection in coding regions of the four species. In contrast, the strength of purifying selection seems to vary among the four species in non-coding (NC) regions (introns). Using F(ST)-based measures of fixation in subdivided populations, we suggest that weak purifying selection has affected the NC regions of S. habrochaites, S. chilense and S. peruvianum. In contrast, NC regions in S. arcanum show a distribution of fitness effects with mutations being either nearly neutral or very strongly deleterious. These results suggest that closely related species with similar genetic backgrounds but experiencing contrasting environments differ in the variance of deleterious fitness effects.     

Causation, fitness effects and morphology of macropterism in Chorthippus parallelus (Orthoptera: Acrididae)

ABSTRACT. 1. Chorthippus parallelus (Zett.) displays an apparent'flight polyphenism'despite the fact that macropterous individuals cannot fly.
2. Photoperiod is used as an environmental cue controlling the polyphenism: long day lengths increasing the proportion of macropterous adults.
3. Macropterous females start mating when older and are less fecund than brachypters.
4. In contrast to other studies the response may not be due to cues associated with a reduced environmental quality and we speculate that macropterism is not a dispersal mechanism in the Gomphocerinae.     

油松种群自然更新格局的研究

种群的空间格局系指某一种群个体在其生存空间内相对静止的散布形式。它是种群的重要属性之一,是种的生物学特性对其所生存的环境条件在特定时期适应和选择的结果。空间格局的阐明,无论在理论生态学的研究上抑或     

Natural selection and gynodioecy in Thymus vulgaris L.

Thymus vulgaris L. is a gynodioecious species with hermaphrodites (mF) and females (mS) widely distributed in southern France and in which reproduction of which is exclusively sexual. Numerous samples have been collected in the French Mediterranean region and the percentage of mS varies from 5 to 95% in different populations. By studying environmental conditions—the area covered at ground level by vegetation, stones and rocks—high percentages of mS are found to be related to a high vegetation cover and an absence or a scarcity of stones. Grasslands and old fields favour mS, while rocky sites favour mF. This relationship, which has been found both on the plains and on a mountain, is related to the most important reproductive characteristics of T. vulgaris —genetic control of male sterility, mode of pollination, percentage of selling and seed production. These relationships agree with the assumption that unstable environmental conditions such as grasslands or old fields in southern France favour maximum seed production and outcrossing. The greater stability of uncultivated areas such as rocky sites allows for the maintenance of autogamy. Consequently, it is natural selection which adjusts the percentage of male sterility in natural populations of Thymus vulgaris.