Limitations of entropy maximization in ecology: a reply to Haegeman and Loreau

Haegeman and Loreau published a paper that is primarily a criticism of a maximum entropy model of trait-based community assembly (by Shipley et al.) and purports to show the limitations of this method in ecology. However, they misunderstood the basic purpose, logic and justification of the maximum entropy formalism and, because of this, leveled criticisms of Shipley et al. that are unfounded. Part of the confusion can be traced to sloppy presentation of the underlying approach in Shipley et al. The confusion arises because maximum entropy models are justified based on information theory and Bayesian logic while the interpretation that Haegeman and Loreau present is based on substantive empirical assumptions about microstate allocations and a combinatorial argument that do not apply to maximum entropy models and which I do not apply to my model in particular.     

Reasons to be fussy about cultural evolution

This discussion paper responds to two recent articles in Biology and Philosophy that raise similar objections to cultural attraction theory, a research trend in cultural evolution putting special emphasis on the fact that human minds create and transform their culture. Both papers are sympathetic to this idea, yet both also regret a lack of consilience with Boyd, Richerson and Henrich’s models of cultural evolution. I explain why cultural attraction theorists propose a different view on three points of concern for our critics. I start by detailing the claim that cultural transmission relies not chiefly on imitation or teaching, but on cognitive mechanisms like argumentation, ostensive communication, or selective trust, whose evolved or habitual function may not be the faithful reproduction of ideas or behaviours. Second, I explain why the distinction between context biases and content biases might not always be the best way to capture the interactions between culture and cognition. Lastly, I show that cultural attraction models cannot be reduced to a model of guided variation, which posits a clear separation between individual and social learning processes. With cultural attraction, the same cognitive mechanisms underlie both innovation and the preservation of traditions.     

Integration versus apartheid in post-Roman Britain: a response to Thomas et Al. (2008)

The genetic surveys of the population of Britain conducted by Weale et al. and Capelli et al. produced estimates of the Germani immigration into Britain during the early Anglo-Saxon period, c.430-c.730. These estimates are considerably higher than the estimates of archaeologists. A possible explanation suggests that an apartheid-like social system existed in the early Anglo-Saxon kingdoms resulting in the Germani breeding more quickly than the Britons. Thomas et al. attempted to model this suggestion and showed that it was a possible explanation if all Anglo-Saxon kingdoms had such a system for up to 400 years. I noted that their explanation ignored the probability that Germani have been arriving in Britain for at least the past three millennia, including Belgae and Roman soldiers, and not only during the early Anglo-Saxon period. I produced a population model for Britain taking into account this long term, low level migration that showed that the estimates could be reconciled without the need for introducing an apartheid-like system. In turn, Thomas et al. responded, criticizing my model and arguments, which they considered persuasively written but wanting in terms of methodology, data sources, underlying assumptions, and application. Here, I respond in detail to those criticisms and argue that it is still unnecessary to introduce an apartheid-like system in order to reconcile the different estimates of Germani arrivals. A point of confusion is that geneticists are interested in ancestry, while archaeologists are interested in ethnicity: it is the bones, not the burial rites, which are important in the present context.     

Fisherian and Wrightian perspectives in evolutionary genetics and model-mediated imposition of theoretical assumptions

I investigate how theoretical assumptions, pertinent to different perspectives and operative during the modeling process, are central in determining how nature is actually taken to be. I explore two different models by Michael Turelli and Steve Frank of the evolution of parasite-mediated cytoplasmic incompatility, guided, respectively, by Fisherian and Wrightian perspectives. Since the two models can be shown to be commensurable both with respect to mathematics and data, I argue that the differences between them in the (1) mathematical presentation of the models, (2) explanations, and (3) objectified ontologies stem neither from differences in mathematical method nor the employed data, but from differences in the theoretical assumptions, especially regarding ontology, already present in the respective perspectives. I use my "set up, mathematically manipulate, explain, and objectify" (SMEO) account of the modeling process to track the model-mediated imposition of theoretical assumptions. I conclude with a discussion of the general implications of my analysis of these models for the controversy between Fisherian and Wrightian perspectives.     

Recent models for adaptive personality differences: a review

In this paper we review recent models that provide adaptive explanations for animal personalities: individual differences in behaviour (or suites of correlated behaviours) that are consistent over time or contexts. We start by briefly discussing patterns of variation in behaviour that have been documented in natural populations. In the main part of the paper we discuss models for personality differences that (i) explain animal personalities as adaptive behavioural responses to differences in state, (ii) investigate how feedbacks between state and behaviour can stabilize initial differences among individuals and (iii) provide adaptive explanations for animal personalities that are not based on state differences. Throughout, we focus on two basic questions. First, what is the basic conceptual idea underlying the model? Second, what are the key assumptions and predictions of the model? We conclude by discussing empirical features of personalities that have not yet been addressed by formal modelling. While this paper is primarily intended to guide empiricists through current adaptive theory, thereby stimulating empirical tests of these models, we hope it also inspires theoreticians to address aspects of personalities that have received little attention up to now.     

Modelling beyond data is uninformative: a comment on “State-space modelling reveals proximate causes of harbour seal population declines” by Matthiopoulos et al.

Detailed models have the potential to reveal important processes underlying patterns in data. However, model fitting depends on the availability of sufficient data, and the results obtained from the models depend on detailed assumptions. In a recent paper, Matthiopoulos et al. fitted Bayesian state space models to a limited dataset and attempted to explain the recent trajectory of the harbour seal population in the Moray Firth, in northern Scotland. They went on to suggest that the results could help explain recent declines in other nearby populations. This Comment describes the implications of understating the uncertainty that the model required for convergence, questions the robustness of the results, highlights the differences between the areas, and cautions against extrapolating across these populations. The distinction between models that can be fitted to a dataset and those that provide useful information about the systems that generated the data is also considered.     

Displacement Behaviour Solving a Silent Contradiction

Displacement acts, once a hot topic in ethology, but wrapped in silence for two decades since, have recently been suggested to indicate and relax social tension (Maestripieri et al., 1992; Wiepkema, 1987). The first of these contentions seems to be in contradiction with some of the classical ethological studies of displacement behaviour, in particular those supporting the disinhibition hypothesis, since the latter would not predict any positive correlation between amount of tension (i.c. intensity of the conflict) and the occurrence of displacement acts.A critical examination of these studies reveals that a positive correlation of the sort has been found, but that proponents of the disinhibition hypothesis tried to explain it in terms of their own model, rather than taking it at its face value. (The reason for this is that they viewed it as pleading for the surplus hypothesis which they rejected). It can be shown that at least some of their explanations are grounded on assumptions which are arbitrary. Also, the disinhibition hypothesis does not account for the occurrence of displacement behaviour in contexts with tension but without conflict.This discussion leads to a new interpretation of displacement behaviour, in which tension is the direct cause, whether generated by conflict or otherwise, and relaxation is brought about by a breaking of the cognitive symmetry between actors. It is indicated how this interpretation may be tested with experiments.     

Evolution in response to social selection: the importance of interactive effects of traits on fitness

Social interactions have a powerful effect on the evolutionary process. Recent attempts to synthesize models of social selection with equations for indirect genetic effects (McGlothlin et al. 2010) provide a broad theoretical base from which to study selection and evolutionary response in the context of social interactions. However, this framework concludes that social selection will lead to evolution only if the traits carried by social partners are nonrandomly associated. I suggest this conclusion is incomplete, and that traits that do not covary between social partners can nevertheless lead to evolution via interactive effects on fitness. Such effects occur when there are functional interactions between traits, and as an example I use the interplay in water striders (Gerridae) between grasping appendages carried by males and spines by females. Functional interactive effects between traits can be incorporated into both the equations for social selection and the general model of social evolution proposed by McGlothlin et al. These expanded equations would accommodate adaptive coevolution in social interactions, integrate the quantitative genetic approach to social evolution with game theoretical approaches, and stimulate some new questions about the process of social evolution.     

An optimum body size for mammals? Comparative evidence from bats

1. The distribution of body sizes among mammalian species has been modelled by Brown, Marquet & Taper (1993), who suggest that reproductive power (the rate at which energy from the environment is channelled into offspring production) is maximized at a size of 100 g, and the observed size distribution among species reflects the way reproductive power depends on size. The model makes a testable prediction about life-history allometries: namely, that components of reproductive power should not scale linearly with body size but should change sign at the optimum size.
2. A large set of life-history data from a single clade of small mammals, the bats (Order: Chiroptera), was analysed to test this key prediction. The analyses in this study offer no support for the idea that allometries of reproductive power change sign in bats, either at 100 g or at any other size. Furthermore the life-history allometries of bats, which are mostly below the 100 g optimum, were broadly the same as in mammalian taxa larger than the optimum size.
3. These findings together contradict a key prediction of Brown et al. 's (1993) model to explain the skewed body size distribution across mammalian species.     

Innovativeness, population size and cumulative cultural evolution

Henrich [Henrich, J., 2004. Demography and cultural evolution: how adaptive cultural processes can produce maladaptive losses—the Tasmanian case. Am. Antiquity 69, 197-214] proposed a model designed to show that larger population size facilitates cumulative cultural evolution toward higher skill levels. In this model, each newborn attempts to imitate the most highly skilled individual of the parental generation by directly-biased social learning, but the skill level he/she acquires deviates probabilistically from that of the exemplar (cultural parent). The probability that the skill level of the imitator exceeds that of the exemplar can be regarded as the innovation rate. After reformulating Henrich’s model rigorously, we introduce an overlapping-generations analog based on the Moran model and derive an approximate formula for the expected change per generation of the highest skill level in the population. For large population size, our overlapping-generations model predicts a much larger effect of population size than Henrich’s discrete-generations model. We then investigate by way of Monte Carlo simulations the case where each newborn chooses as his/her exemplar the most highly skilled individual from among a limited number of acquaintances. When the number of acquaintances is small relative to the population size, we find that a change in the innovation rate contributes more than a proportional change in population size to the cumulative cultural evolution of skill level.     

Are reproductive skew models evolutionarily stable?

Reproductive skew theory has become a popular way to phrase problems and test hypotheses of social evolution. The diversity of reproductive skew models probably stems from the ease of generating new variations. However, I show that the logical basis of skew models, that is, the way in which group formation is modelled, makes use of hidden assumptions that may be problematical as they are unlikely to be fulfilled in all social systems. I illustrate these problems by re-analysing the basic concessive skew model with staying incentives. First, the model assumes that dispersal is an all-or-nothing response: all subordinates disperse as soon as concessions drop below a certain value. This leads to a discontinuous 'cliff-edge' shape of dominant fitness, and it is not clear that selection will balance a population at such an edge. Second, it is assumed that subordinates have perfect knowledge of their benefits if they stay in the group. I examine the effects of relaxing these two assumptions. Relaxing the first one strengthens reproductive skew theory, but relaxing the latter makes evolutionary stability disappear. In cases where subordinates cannot accurately measure benefits provided by the individual dominant with which they live, so that their behaviour instead evolves as a response to population-wide average benefits, the logic of reproductive skew models does not apply. This warns against too indiscriminate an application of reproductive skew theory to problems in social evolution: for example, transactional models of extra-pair paternity assume perfect knowledge of paternity, which is unlikely to hold true in nature. It is recommended that models specify the mechanisms by which individuals can adjust their behaviour to that of others, and pay attention to changes that occur in evolutionary versus behavioural time.     

华南长江和西江流域鲤科宽鳍鱲和马口鱼不同线粒体DNA谱系之间的体形分化

本文研究了两种鲤科鱼类,即分布于华南长江与西江的宽鳍鱲和马口鱼的不同线粒体DNA谱系之间的体形差异。近期基于线粒体DNA的这两个物种的系统发育分析认为这两个类元内包含多个谱系(宽鳍鱲A-D和马口鱼1-5)。本文采用几何形态度量学的方法研究了这些不同线粒体DNA谱系间是否存在体形方面的差异。在宽鳍鱲的4个不同的线粒体DNA谱系中,有3个被纳入本研究内容。结果显示:在宽鳍鱲的3个线粒体DNA谱系中,2个具有体形的差异。在马口鱼的5个线粒体DNA谱系中,3个被纳入本文的研究。结果显示所有3个谱系均存在体形差异。因此,线粒体DNA的谱系差异很大程度上表现在谱系间的体形差异方面,表明线粒体DNA谱系可能对应于不同的物种。     

Possible implications for allosteric models of hemoglobin of the laws of combination with carbon monoxide under photodissociating conditions

It is shown that the data obtained by Brunori et al. on binding of carbon monoxide to hemoglobin in photodissociating conditions is explained by a simple allosteric model, the two-configuration exclusive-binding induced-fit model together with the simplest kinetic assumptions. Alternative models are considered. It is possible to calculate from the data of Brunori et al a dissociation rate constant for carbon monoxide which agrees well with an independently determined rate constant.     

Revising the distributive networks models of West, Brown and Enquist (1997) and Banavar, Maritan and Rinaldo (1999): metabolic inequity of living tissues provides clues for the observed allometric scaling rules

Basic assumptions of two distributive network models designed to explain the 3/4 power scaling between metabolic rate and body mass are re-analysed. It is shown that these models could have consistently accounted for the observed scaling patterns if and only if body mass M had scaled as L4, where L is body length, in the model of Banavar et al. (1999, Nature 399, 130-132), or if spatial volume VF occupied by the distributive network had scaled as M3/4 in the model of West et al. (1997, Science 276, 122-126). Lack of agreement between these predictions and observational evidence invalidates both models rendering them mathematically controversial. It is further shown that consideration of distributive networks can nevertheless yield realistic values of scaling exponents under the major assumption that living organisms are designed so as to keep the mass-specific metabolic rate of important functional tissues in the vicinity of a size-independent optimum value. Mass-specific metabolic rate of subsidiary mechanical tissues can be small and vary with body mass. Different patterns of spatial distribution of metabolically active biomass within the organism result in different patterns of allometric scaling. From the available evidence the presumable optimum value of mass-specific metabolic rate of living matter is estimated to be in the vicinity of 1-10 W kg-1.     

Neutral Models with Generalised Speciation

Hubbell’s neutral theory claims that ecological patterns such as species abundance distributions can be explained by a stochastic model based on simple assumptions. One of these assumptions, the point mutation assumption, states that every individual has the same probability to speciate. Etienne et al. have argued that other assumptions on the speciation process could be more realistic, for example, that every species has the same probability to speciate (Etienne, et al. in Oikos 116:241–258, 2007). They introduced a number of neutral community models with a different speciation process, and conjectured formulas for their stationary species abundance distribution. Here we study a generalised neutral community model, encompassing these modified models, and derive its stationary distribution, thus proving the conjectured formulas.     

Across islands and continents, mammals are more successful invaders than birds (Reply to Rodriguez-Cabal et al.)

In their reply to Jeschke (2008), Rodriguez-Cabal et al. (2009) argue that the underlying 'data are inadequate to draw strong conclusions about the tens rule or invasibility of islands and continents'. They point out that especially for taxa such as insects or plants, many species introductions are unknown, hence fractions of species that have become established are often overestimated. I agree but would like to add that in Jeschke (2008), I analysed the two well-studied taxa of mammals and birds. Even data from these taxa are imperfect, so they need to be analysed carefully. At least from my perspective, the analyses underlying Jeschke (2008) were done carefully. I thus stand by my original conclusions.     

Evaluation of two unstructured mathematical models for the penicillin G fedbatch fermentation

The mathematical model for the penicillin G fed-batch fermentation proposed by Heijnen et al. (1979) is compared with the model of Bajpai & Reuß (1980). Although the general structure of these models is similar, the difference in metabolic assumptions and specific growth and production kinetics results in a completely different behaviour towards product optimization. A detailed analysis of both models reveals some physical and biochemical shortcomings. It is shown that it is impossible to make a reliable estimation of the model parameters, only using experimental data of simple constant glucose feed rate fermentations with low initial substrate amount. However, it is demonstrated that some model parameters might be key factors in concluding whether or not altering the substrate feeding strategy has an important influence on the final amount of product.It is illustrated that feeding strategy optimization studies can be a tool in designing experiments for parameter estimation purposes.     

A local influence approach applied to binary data from a psychiatric study

Recently, a lot of concern has been raised about assumptions needed in order to fit statistical models to incomplete multivariate and longitudinal data. In response, research efforts are being devoted to the development of tools that assess the sensitivity of such models to often strong but always, at least in part, unverifiable assumptions. Many efforts have been devoted to longitudinal data, primarily in the selection model context, although some researchers have expressed interest in the pattern-mixture setting as well. A promising tool, proposed by Verbeke et al. (2001, Biometrics 57, 43-50), is based on local influence (Cook, 1986, Journal of the Royal Statistical Society, Series B 48, 133-169). These authors considered the Diggle and Kenward (1994, Applied Statistics 43, 49-93) model, which is based on a selection model, integrating a linear mixed model for continuous outcomes with logistic regression for dropout. In this article, we show that a similar idea can be developed for multivariate and longitudinal binary data, subject to nonmonotone missingness. We focus on the model proposed by Baker, Rosenberger, and DerSimonian (1992, Statistics in Medicine 11, 643-657). The original model is first extended to allow for (possibly continuous) covariates, whereafter a local influence strategy is developed to support the model-building process. The model is able to deal with nonmonotone missingness but has some limitations as well, stemming from the conditional nature of the model parameters. Some analytical insight is provided into the behavior of the local influence graphs.     

Socially isolated? How parents and neighbourhood adults influence youth behaviour in disadvantaged communities

William Julius Wilson’s model of adult joblessness, community disorganization and their effects on youth problem behaviour de-emphasizes the range in children’s outcomes across socially disorganized communities, and says little about the factors that influence this variation. It also does not address the processes by which family structure and relationships affect the well-being of African-American and poor youth. My work is part of a larger research agenda that has begun to address these issues by focusing on the differential rates of sexual activity among youth living in disadvantaged environments, and developing models to explain this variation. This work suggests that units of socially cohesive, stable adults exist among the social networks of successful children and families in poor neighbourhoods. It also points to the existence and functioning of alternative two-parent family structures and offers hypotheses for how family environment interacts with neighbourhood context to influence youth behaviour.     

Beyond learning fixed rules and social cues: abstraction in the social arena

Abstraction is a central idea in many areas of physical comparative cognition such as categorization, numerical competence or problem solving. This idea, however, has rarely been applied to comparative social cognition. In this paper, I propose that the notion of abstraction can be applied to the social arena and become an important tool to investigate the social cognition and behaviour processes in animals. To make this point, I present recent evidence showing that chimpanzees know about what others can see and about what others intend. These data do not fit either low-level mechanisms based on stimulus-response associations or high-level explanations based on metarepresentational mechanisms such as false belief attribution. Instead, I argue that social abstraction, in particular the development of concepts such as seeing in others, is key to explaining the behaviour of our closest relative in a variety of situations.