Time‐shift experiments and patterns of adaptation across time and space

Time‐shift experiments provide measures of the mean fitness of a population in environments of different points in time. Here, we show how to use this type of data to decompose mean fitness into (1) the effect of the environment in which the population is transplanted, (2) the effect of the genetic composition of the population and (3) ‘temporal adaptation’, which measures how the population fits the environment at that time. We derive analytical results for the pattern of ‘temporal adaptation’ and show that it is in general maximal in the recent past. The link between ‘temporal adaptation’ and ‘local adaptation’ is discussed, and we show when patterns of adaptation in time and space are expected to be similar. Finally, we illustrate the potential use of this approach using a data set measuring the adaptation of HIV to the immune response of several recently infected patients.     

Niche construction,adaptive preferences,and the differences between fitness and utility

A number of scholars have recently defended the claim that there is a close connection between the evolutionary biological notion of fitness and the economic notion of utility: both are said to refer to an organism’s success in dealing with its environment, and both are said to play the same theoretical roles in their respective sciences. However, an analysis of two seemingly disparate but in fact structurally related phenomena—‘niche construction’ (the case where organisms change their environment to make it fit to their needs) and ‘adaptive preferences’ (the case where agents change their wants to make them fit to what the world has given them)—shows that one needs to be very careful about the postulation of this sort of fitness–utility connection. Specifically, I here use the analysis of these two phenomena to establish when connecting fitness and utility is and is not possible.     

Some bold evolutionary predictions for the future of mating in humans

Why are many human populations presently ‘imploding’ with below‐replacement fertility? Why are more and more young adults in these societies choosing to remain single and/or childless? Based on first principles of evolutionary theory, predictions can be derived for changes over time in the relative frequency distributions of four traits in humans proposed as the most direct determinants of the propensity to mate and reproduce: attractions to sex, legacy, leisure and parenting. In the past, high fitness was most profoundly determined by strong sex drive and strong legacy drive, especially in males. Female fertility was largely controlled by dominant males, who were then free to engage in attractions to both leisure and legacy through ‘memes’ (as well as through genes, or offspring) without any penalty on fitness. Natural selection in the past, therefore, neither strongly favoured nor strongly disfavoured any particular intrinsic female inclinations or preferences that might affect offspring production. The recent, widespread, and continuing rise in the empowerment of women, however, defines a dramatically different contemporary selection regime, where women are now free to indulge in their evolved attractions to leisure and legacy through memes inherited from predecessors, both of which represent compelling distractions from parenthood. The implications for the future survival of marriage and parenthood as cultural institutions look dismal in the short term, but promising in the long term.     

Our use,misuse, and abandonment of a concept: Whither habitat?

The foundational concept of habitat lies at the very root of the entire science of ecology, but inaccurate use of the term compromises scientific rigor and communication among scientists and nonscientists. In 1997, Hall, Krausman & Morrison showed that ‘habitat’ was used correctly in only 55% of articles. We ask whether use of the term has been more accurate since their plea for standardization and whether use varies across the broader range of journals and taxa in the contemporary literature (1998–2012). We searched contemporary literature for ‘habitat’ and habitat‐related terms, ranking usage as either correct or incorrect, following a simplified version of Hall et al.'s definitions. We used generalized linear models to compare use of the term in contemporary literature with the papers reviewed by Hall et al. and to test the effects of taxa, journal impact in the contemporary articles and effects due to authors that cited Hall et al. Use of the term ‘habitat’ has not improved; it was still only used correctly about 55% of the time in the contemporary data. Proportionately more correct uses occurred in articles that focused on animals compared to ones that included plants, and papers that cited Hall et al. did use the term correctly more often. However, journal impact had no effect. Some habitat terms are more likely to be misused than others, notably ‘habitat type’, usually used to refer to vegetation type, and ‘suitable habitat’ or ‘unsuitable habitat’, which are either redundant or nonsensical by definition. Inaccurate and inconsistent use of the term can lead to (1) misinterpretation of scientific findings; (2) inefficient use of conservation resources; (3) ineffective identification and prioritization of protected areas; (4) limited comparability among studies; and (5) miscommunication of science‐based findings. Correct usage would improve communication with scientists and nonscientists, thereby benefiting conservation efforts, and ecology as a science.     

The continuity of microevolution and macroevolution

A persistent debate in evolutionary biology is one over the continuity of microevolution and macroevolution – whether macroevolutionary trends are governed by the principles of microevolution. The opposition of evolutionary trends over different time scales is taken as evidence that selection is uncoupled over these scales. I argue that the paradox inferred by trend opposition is eliminated by a hierarchical application of the ‘geometric‐mean fitness’ principle, a principle that has been invoked only within the limited context of microevolution in response to environmental variance. This principle implies the elimination of well adapted genotypes – even those with the highest arithmetic mean fitness over a shorter time scale. Contingent on premises concerning the temporal structure of environmental variance, selectivity of extinction, and clade‐level heritability, the evolutionary outcome of major environmental change may be viewed as identical in principle to the outcome of minor environmental fluctuations over the short‐term. Trend reversals are thus recognized as a fundamental property of selection operating at any phylogenetic level that occur in response to event severities of any magnitude over all time scales. This ‘bet‐hedging’ perspective differs from others in that a specified, single hierarchical selective process is proposed to explain observed hierarchical patterns of extinction.     

Looking for a needle in a haystack: inference about individual fitness components in a heterogeneous population

Studies of wild vertebrates have provided evidence of substantial differences in lifetime reproduction among individuals and the sequences of life history ‘states’ during life (breeding, nonbreeding, etc.). Such differences may reflect ‘fixed’ differences in fitness components among individuals determined before, or at the onset of reproductive life. Many retrospective life history studies have translated this idea by assuming a ‘latent’ unobserved heterogeneity resulting in a fixed hierarchy among individuals in fitness components. Alternatively, fixed differences among individuals are not necessarily needed to account for observed levels of individual heterogeneity in life histories. Individuals with identical fitness traits may stochastically experience different outcomes for breeding and survival through life that lead to a diversity of ‘state’ sequences with some individuals living longer and being more productive than others, by chance alone. The question is whether individuals differ in their underlying fitness components in ways that cannot be explained by observable ‘states’ such as age, previous breeding success, etc. Here, we compare statistical models that represent these opposing hypotheses, and mixtures of them, using data from kittiwakes. We constructed models that accounted for observed covariates, individual random effects (unobserved heterogeneity), first‐order Markovian transitions between observed states, or combinations of these features. We show that individual sequences of states are better accounted for by models incorporating unobserved heterogeneity than by models including first‐order Markov processes alone, or a combination of both. If we had not considered individual heterogeneity, models including Markovian transitions would have been the best performing ones. We also show that inference about age‐related changes in fitness components is sensitive to incorporation of underlying individual heterogeneity in models. Our approach provides insight into the sources of individual heterogeneity in life histories, and can be applied to other data sets to examine the ubiquity of our results across the tree of life.     

Methodological problems in evolutionary biology II. Appraisal of arguments against adaptationism

Methodological analysis shows that the concepts of fitness and adaptation are more complex than the literature suggests. Various arguments against ‘adaptationism’ are inadequate since they are couched in terms of unduly simplistic notions.     

Analysis of the relationship between allozyme heterozygosity and fitness in the rare Gentiana pneumonanthe L.

Especially for rare species occurring in small populations, which are prone to loss of genetic variation and inbreeding, detailed knowledge of the relationship between heterozygosity and fitness is generally lacking. After reporting on allozyme variation and fitness in relation to population size in the rare plant Gentiana pneumonanthe, we present a more detailed analysis of the association between heterozygosity and individual fitness. The aim of this study was to test whether increased fitness of more heterozygous individuals is explained best by the ‘inbreeding’ hypothesis or by the ‘overdominance’ hypothesis. Individual fitness was measured during 8 months of growth in the greenhouse as the performance for six life-history parameters. PCA reduced these parameters to four main Fitness Components. Individual heterozygosity was scored for seven polymorphic allozyme loci. For some of these loci (e.g. Aat3, Pgm1 and 6Pgdh2) heterozygotes showed a significantly higher relative fitness than homozygotes. To test the inbreeding model, regression analyses were performed between each Fitness Component and the number of heterozygous loci per individual. Multiple regressions with the adaptive distance of five loci as independent variables were used to test the overdominance model. Only the inbreeding model was a statistically significant explanation for the relationship between heterozygosity and fitness in G. pneumonanthe. The number of heterozygous loci was significantly negatively correlated with the coefficients of variation of three of the six initially measured fitness parameters. This suggests a lower developmental stability among more homozygous plants and may explain the higher phenotypic variation in small populations of the species observed earlier. The importance of the results for conservation biology is discussed.     

Can low-quality parents exploit their high-quality partners to gain higher fitness?

An individual's optimal investment in parental care potentially depends on many variables, including its future fitness prospects, the expected costs of providing care and its partner's expected or observed parental behaviour. Previous models suggested that low-quality parents could evolve to exploit their high-quality partners by reducing care, leading to the paradoxical prediction that low-quality parents could have higher fitness than their high-quality partners. However, these studies lacked a complete and consistent life-history model. Here, we challenge this result, developing a consistent analytical model of parental care strategies given individual variation in quality, and checking our results using agent-based simulations. In contrast to previous models, we predict that high-quality individuals always outcompete low-quality individuals in fitness terms. However, care effort may differ between high- and low-quality parents in either direction: low-quality individuals care more than high-quality individuals if their baseline mortality is higher, but less if their mortality increases more steeply with increasing care. We also highlight the ambiguity of the term ‘quality’ and stress the need for ‘genealogical consistency’ in evolutionary models.     

Genetic and environmental effects on a condition‐dependent trait: feather growth in Siberian jays

Condition, defined as the amount of ‘internal resources’ an individual can freely allocate, is often assumed to be environmentally determined and to reflect an individual’s health and nutritional status. However, an additive genetic component of condition is possible if it ‘captures’ the genetic variance of many underlying traits as many fitness‐related traits appear to do. Yet, the heritability of condition can be low if selection has eroded much of its additive genetic variance, or if the environmental influences are strong. Here, we tested whether feather growth rate – presumably a condition‐dependent trait – has a heritable component, and whether variation in feather growth rate is related to variation in fitness. To this end, we utilized data from a long‐term population study of Siberian jays (Perisoreus infaustus), and found that feather growth rate, measured as the width of feather growth bars (GB), differed between age‐classes and sexes, but was only weakly related to variation in fitness as measured by annual and life‐time reproductive success. As revealed by animal model analyses, GB width was significantly heritable (h² = 0.10 ± 0.05), showing that this measure of condition is not solely environmentally determined, but reflects at least partly inherited genetic differences among individuals. Consequently, variation in feather growth rates as assessed with ptilochronological methods can provide information about heritable genetic differences in condition.     

Replicator Selection and the Extended Phenotype3

Adaptations are often spoken of as ‘for the good of’ some entity, but what is that entity? Groups and species are now rightly unfashionable, so what are we left with? The prevailing answer is Darwin's: ‘the individual’. Individuals clearly do not maximise their own survival so the concept of fitness had to be invented. If fitness is correctly defined in Hamilton's way as ‘inclusive fitness’ it ceases to matter whether we speak of individuals maximising their inclusive fitness or of genes maximising their survival. The two formulations are mutually inter-translatable. Yet some serious mistranslations are quoted from the literature, which have led their authors into actual biological error. The present paper blames the prevailing concentration on the individual for these errors, and advocates a reversion to the replicator as the proper focus of evolutionary attention. A gene is an obvious replicator, but there are others, and the general properties of replicators are discussed. Defenders of the individual as the unit of selection often point to the unity and integration of the genome as expressed phenotypically. This paper ends by attacking even this assumption, not by a reductionist fragmentation of the phenotype, but, on the contrary, by extending it to include more than one individual. Replicators survive by virtue of their effects on the world, and these effects are not restricted to one individual body but constitute a wider ‘extended phenotype’.     

Collective action in an RNA virus

A recent empirical study by Turner and Chao on the evolution of competitive interactions among phage virus strains revealed that a strain grown at high rates of co‐infection evolved towards lowered fitness relative to an ancestral strain. The authors went on to show that the fitness pay‐off matrix between the evolved and ancestral strain conforms to the prisoners’ dilemma. In this paper, I use Turner and Chao’s data to parameterize a simple model of parasite collective action. The prisoners’ dilemma is based on pairwise interactions of a discrete cooperate/defect nature. In contrast, the collective action model explicitly deals with individual–group interactions where the extent of cooperation is a continuous variable. I argue here that the ‘collective action’ modelling approach is more appropriate than the prisoners’ dilemma for the biology of virus evolution, and hence better able to form a predictive framework for further work on related strains of virus, linking mixing ecology, cooperative phenotype and fitness. Furthermore, the collective action model is used to motivate discussion on the evolutionary ecology of viruses, with a focus on the ‘levels of selection’ debate and the evolution of virulence.     

Do facts have a place in science?

The use of the word ‘fact’ in science is discussed. It is suggested that the everyday meaning of the term is assumed when it is used in science and that this can create problems. Some possible ways of overcoming these difficulties are indicated.     

Handling ‘immunocompetence’ in ecological studies: do we operate with confused terms?

‘Immunocompetence’ is a term used in avian immunological ecology to refer to the ability of an individual to overcome potential parasite infections. However, there are multiple ecological definitions of this term currently used and all of them are rather liberal in immunological terms. This prevents much of the potential intellectual interchange between avian ecologists and immunologists, which decelerates the development of immunological ecology as a scientific discipline. We therefore highlight that the term should be handled with care. In any individual host‐parasite interrelationship the demands on host immunity are distinct and thus also the measurements of immunity in any particular case should be aimed differently. Although ornithologists often aspire to obtain a single variable for immunity in their research, due to the enormous diversity of parasites possessing the ability to infect the host, there is no single value for anti‐parasite resistance, i.e. no overall ‘immunocompetence’ per se exists. We propose to use more rigorous terminology, consistent with the one used in classical immunology. The term ‘immunocompetence’ (defined as the ability to produce anti‐parasite or anti‐antigen immune response) should be used as 0/1 character. The magnitude of a particular immune response (i.e. a continuous quantitative trait) should be referred to as ‘immune responsiveness’. Most importantly, both terms should always be used only with respect to a certain parasite taxon or antigen studied as otherwise they lose their explanatory value.     

Genetic quality and sexual selection: an integrated framework for good genes and compatible genes

Why are females so choosy when it comes to mating? This question has puzzled and marveled evolutionary and behavioral ecologists for decades. In mating systems in which males provide direct benefits to the female or her offspring, such as food or shelter, the answer seems straightforward — females should prefer to mate with males that are able to provide more resources. The answer is less clear in other mating systems in which males provide no resources (other than sperm) to females. Theoretical models that account for the evolution of mate choice in such nonresource-based mating systems require that females obtain a genetic benefit through increased offspring fitness from their choice. Empirical studies of nonresource-based mating systems that are characterized by strong female choice for males with elaborate sexual traits (like the large tail of peacocks) suggest that additive genetic benefits can explain only a small percentage of the variation in fitness. Other research on genetic benefits has examined nonadditive effects as another source of genetic variation in fitness and a potential benefit to female mate choice. In this paper, we review the sexual selection literature on genetic quality to address five objectives. First, we attempt to provide an integrated framework for discussing genetic quality. We propose that the term ‘good gene’ be used exclusively to refer to additive genetic variation in fitness, ‘compatible gene’ be used to refer to nonadditive genetic variation in fitness, and ‘genetic quality’ be defined as the sum of the two effects. Second, we review empirical approaches used to calculate the effect size of genetic quality and discuss these approaches in the context of measuring benefits from good genes, compatible genes and both types of genes. Third, we discuss biological mechanisms for acquiring and promoting offspring genetic quality and categorize these into three stages during breeding: (i) precopulatory (mate choice); (ii) postcopulatory, prefertilization (sperm utilization); and (iii) postcopulatory, postfertilization (differential investment). Fourth, we present a verbal model of the effect of good genes sexual selection and compatible genes sexual selection on population genetic variation in fitness, and discuss the potential trade-offs that might exist between mate choice for good genes and mate choice for compatible genes. Fifth, we discuss some future directions for research on genetic quality and sexual selection.     

Ernst Haeckel (1834–1919) and the monophyly of life

Ernst Haeckel, who first introduced the term ‘monophyly’ into the biological literature, has in the past been appealed to in adjudication of the modern use of that concept. A contextual analysis of his writings reveals an inconsistent use of the term ‘monophyly’ by Haeckel. Morphological phylogeny was decoupled in Haeckel’s thinking from the evolutionary history of taxa. Monophyly could mean the derivation of one taxon from another, ancestral one, where these taxa could be species or of supraspecific rank. Monophyly could also mean the phylogenetic differentiation of a diversity of organismal ‘forms’ (morphologies) from a common primitive ‘form’ (morphological stage). And finally, monophyly, as also polyphyly, could apply to the origin of specific anatomical structures, in which case the monophyly/polyphyly of anatomical structures needed not to correlate with the monophyly/polyphyly of the taxon characterized by these structures. With respect to the issue of the unity and reality of monophyletic taxa, Haeckel’s writings again are indeterminate as is his stance on the monophyletic origin of life.     

关于一些植物学术语的中译等问题（二）

（１）在各种花对称的分类中,Ｅｈｒｅｎｄｏｒｆｅｒ的分类包括了被子植物花对称方面从原始到进化的各种类型,最为全面广德国学者Ｓｔｒａｓｂｕｒｅｒ在１９１１年编著的第１１版植物学教科书中将具２对称面的荷包牡丹属的花称为ｂｉｌａｔｅｒａｌ或ｄｉｓｙｍｍｅｔｒｉｓｃｈ．这个类型代表了被子植物花的一种较进化的构造,应该予以肯定。由于被指定为描述具２对称面的花的术语ｂｉｌａｔｅｒａｌ与被指定为描述具丑对称面的花的术语ｂｉｌａｔｅｒａｌｌｙｓｙｍｍｅｔｒｉｃａｌ颇为相似,而易引起混淆．为避兔发生混淆．建议不再应用这二术语．在描述具２对称面的花时,选用ｄｉｓｙｍｍｅｔｒｉｃａｌ,中文译为双面对称的,在描述具１对称面的花时,选用ｚｙｇｏｍｏｒｐｈｉｃ（左右对称的）或ｍｏｎｏｓｙｍｍｅｔｒｉｃａｌ,后者的中文可译为单面对称的。（２）赞同将术语ｔｅｐａｌ译为花被片,而不赞同译为“被片”。     

Receptins: a novel term for an expanding spectrum of natural and engineered microbial proteins with binding properties for mammalian proteins

A new term ‘receptin’, derived from recipere (lat.), is proposed to denote microbial binding proteins that interact with mammalian target proteins. An example of such a ‘receptin’ is staphyloccocal protein A which binds to the Fc part of many mammalian immunoglobulins. Several other types of ‘receptins’ are listed. This term may easily be distinguished from the similar term ‘receptor’, describing a binding site on a cell surface, mostly eukaryotic, where a secondary effect is induced inside the cell upon binding to a ligand. A receptin, however, does not necessarily have to induce a secondary event. Receptins include so called MSCRAMMs, adhesins, and also engineered receptins, affibodies, and engineered ligands. It denotes any protein of microbial origin, cell‐bound or soluble, which can bind to a mammalian protein. It fulfills the need for an umbrella terminology for a large group of binding structures. In contrast, the term ‘lectin’ represents a group of proteins with affinity for carbohydrate structures. The new term ‘receptin’ includes a number of key microbial proteins involved in host–parasite interactions and in virulence. Some receptins are promising vaccine candidates. Copyright © 1999 John Wiley & Sons, Ltd.     

The Definition and Measurement of Individual Condition in Evolutionary Studies

Over the past four decades, as the use of the term condition has become more frequent, the meaning of the term has become increasingly vague. This is especially true in evolutionary theory where condition is now equated with reproductive value, genetic quality, or defined as the ‘total pool of resources available for reproduction.’ Condition with the latter meaning is essentially impossible to measure empirically because it is associated with multiple attributes, such as nutritional state, health, experience, foraging success, ability to cope with environmental pressures, and social status, that collectively affect individual fitness. The addition of qualifying terms that often precede condition (e.g., phenotypic, energetic, and nutritional) and the usage of terms that describe an individual's state (e.g., physiological state, energetic state, and nutritional state) add confusion to the issue. It is therefore important to evaluate the meaning of condition, the limits of its usefulness, and how it can be best measured. We suggest using a more narrow definition of condition, amenable to empirical study, would benefit evolutionary and behavioral studies.