An essential textbook for any student or researcher in biology needing to design experiments, sample programs or analyse the resulting data The text begins with a revision of estimation and hypothesis testing methods, covering both classical and Bayesian philosophies, before advancing to the analysis of linear and generalized linear models Topics covered include linear and logistic regression, simple and complex ANOVA models (for factorial, nested, block, split-plot and repeated measures and covariance designs), and log-linear models Multivariate techniques, including classification and ordination, are then introduced Special emphasis is placed on checking assumptions, exploratory data analysis and presentation of results The main analyses are illustrated with many examples from published papers and there is an extensive reference list to both the statistical and biological literature The book is supported by a website that provides all data sets, questions for each chapter and links to software

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Experimental Design and Data Analysis for Biologists

▪ Abstract The focus of most ideas on diversity maintenance is species coexistence, which may be stable or unstable. Stable coexistence can be quantified by the long-term rates at which community members recover from low density. Quantification shows that coexistence mechanisms function in two major ways: They may be (a) equalizing because they tend to minimize average fitness differences between species, or (b) stabilizing because they tend to increase negative intraspecific interactions relative to negative interspecific interactions. Stabilizing mechanisms are essential for species coexistence and include traditional mechanisms such as resource partitioning and frequency-dependent predation, as well as mechanisms that depend on fluctuations in population densities and environmental factors in space and time. Equalizing mechanisms contribute to stable coexistence because they reduce large average fitness inequalities which might negate the effects of stabilizing mechanisms. Models of unstable coexitence...

/pdf/mechanisms-of-maintenance-of-species-diversity-340h1nopps.pdf

Mechanisms of Maintenance of Species Diversity

Every form of behavior is shaped by trial and error. Such stepwise adaptation can occur through individual learning or through natural selection, the basis of evolution. Since the work of Maynard Smith and others, it has been realized how game theory can model this process. Evolutionary game theory replaces the static solutions of classical game theory by a dynamical approach centered not on the concept of rational players but on the population dynamics of behavioral programs. In this book the authors investigate the nonlinear dynamics of the self-regulation of social and economic behavior, and of the closely related interactions among species in ecological communities. Replicator equations describe how successful strategies spread and thereby create new conditions that can alter the basis of their success, i.e., to enable us to understand the strategic and genetic foundations of the endless chronicle of invasions and extinctions that punctuate evolution. In short, evolutionary game theory describes when to escalate a conflict, how to elicit cooperation, why to expect a balance of the sexes, and how to understand natural selection in mathematical terms.

 Comprehensive treatment of ecological and game theoretic dynamics
 Invasion dynamics and permanence as key concepts
 Explanation in terms of games of things like competition between species

/pdf/evolutionary-games-and-population-dynamics-pax1uk4ywa.pdf

Evolutionary games and population dynamics

A high number of tree species, low density of adults of each species, and long distances between conspecific adults are characteristic of many low-land tropical forest habitats. I propose that these three traits, in large part, are the result of the action of predators on seeds and seedlings. A model is presented that allows detailed examination of the effect of different predators, dispersal agents, seed-crop sizes, etc. on these three traits. In short, any event that increases the efficiency of the predators at eating seeds and seedlings of a given tree species may lead to a reduction in population density of the adults of that species and/or to increased distance between new adults and their parents. Either event will lead to more space in the habitat for other species of trees, and therefore higher total number of tree species, provided seed sources are available over evolutionary time. As one moves from the wet lowland tropics to the dry tropics or temperate zones, the seed and seedling predators in ...

Herbivores and the Number of Tree Species in Tropical Forests

The sequence of species observed after a relatively large space is opened up is a consequence of the following mechanisms. "Opportunist" species with broad dispersal powers and rapid growth to maturity usually arrive first and occupy empty space. These species cannot invade and grow in the presence of adults of their own or other species. Several alternative mechanisms may then determine which species replace these early occupants. Three models of such mechanisms have been proposed. The first "facilitation" model suggests that the entry and growth of the later species is dependent upon the earlier species "preparing the ground"; only after this can later species colonize. Evidence in support of this model applies mainly to certain primary successions and in heterotrophic succession. A second "tolerance" model suggests that a predictable sequence is produced by the existence of species that have evolved different strategies for exploiting resources. Later species will be those able to tolerate lower levels...

Mechanisms of succession in natural communities and their role in community stability and organization

A recent monograph by Hurlbert raised several problems concerning the appropriate design of sampling programs to assess the impact upon the abundance of biological populations of, for example, the discharge of effluents into an aquatic ecosystem at a single point. Key to the resolution of these issues is the correct identification of the statistical parameter of interest, which is the mean of the underlying probabilistic "process" that produces the abundance, rather than the actual abundance itself. We describe an appropriate sampling scheme designed to detect the effect of the discharge upon this underlying mean. Although not guaranteed to be universally applicable, the design should meet Hurlbert's objections in many cases. Detection of the effect of the discharge is achieved by testing whether the difference between abundances at a control site and an impact site changes once the discharge begins. This requires taking samples, replicated in time, Before the discharge begins and After it has begun, at both the Control and Impact sites (hence this is called a BACI design). Care needs to be taken in choosing a control site so that it is sufficiently far from the discharge to be largely beyond its influence, yet close enough that it is influenced by the same range of natural phenomena (e.g., weather) that result in long-term changes in the biological populations. The design is not appro- priate where local events cause populations at Control and Impact sites to have different long-term trends in abundance; however, these situations can be detected statistically. We discuss the assumptions of BACI, particularly additivity (and transformations to achieve it) and independence.

https://www.jstor.org/stable/info/1939815

Environmental impact assessment: "pseudoreplication" in time?'

"Switching" in predators which attack several prey species potentially can stabilize the numbers in prey populations. In switching, the number of attacks upon a species is disproportionately large when the species is abundant relative to other prey, and disproportionately small when the species is relatively rare. The null case for two prey species can be written: P1/P2 = cN1/N2, where P1/P2 is the ratio of the two prey expected in the diet, N1/N2 is the ratio given and c is a proportionality constant. Predators were sea—shore snails and prey were mussels and barnacles. Experiments in the laboratory modelled aspects of various natural situations. When the predator had a strong preference (c) between prey the data and the "null case" model were in good agreement. Preference could not altered by subjecting predators to training regimens. When preference was weak the data did not fit the model replicates were variable. Predators could be trained easily to one or other prey species. From a number of experiments it was concluded that in the weak—preference case no switch would occur in nature except where there is an opportunity for predators to become trained to the abundant species. A patchy distribution of the abundant prey could provide this opportunity. Given one prey species, snails caused a decreasing percentage mortality as prey numbers increased. This occurred also with 2 prey species present when preference was strong. When preference was weak the form of the response was unclear. When switching occurred the percentage prey mortality increased with prey density, giving potentially stabilizing mortality. The consequences of these conclusions for prey population regulation and for diversity are discussed.

Switching in General Predators: Experiments on Predator Specificity and Stability of Prey Populations

Population regulation is a fundamental process related to most phenomena in ecology, including evolutionary ecology. I review the conceptual basis for defining reg- ulation as bounded fluctuations in abundance, in contrast to the unbounded fluctuations of random-walk populations. Regulation arises as a result of potentially stabilizing density- dependent processes, even when brought about by "non-equilibrium" mechanisms. Al- though the phenomenon is unambiguous in theory, detecting regulation by finding evidence for density dependence in a series of population estimates faces unsolved statistical prob- lems. So, while there is growing evidence for widespread regulation, severe detection prob- lems remain. I illustrate these with data from bird populations. Whether regulation is typically achieved by local stabilizing mechanisms or via metapopulation dynamics remains to be determined. I summarize recent studies on a particularly well-regulated system - red scale (Aonidiella aurantii) and its controlling parasitoid, Aphytis melinus. We tested and failed to find evidence for eight hypotheses that might account for the system's stability, including spatial heterogeneity in attack rates, a refuge, and metapopulation dynamics. We also failed to find evidence for density-dependent parasitism, but such density dependence might be still size-structured~rthu host.eipen

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Population regulation in theory and practice

The conventional wisdom of biological control of insect pests, and its related ecological theory, is that successful natural enemies in long-lived ecosystems (1) impose a low, stable pest equilibrium, and (2) share the following properties: (a) host-specific; (b) synchronous with the pest; (c) can increase in density rapidly when the pest does; (d) need only one pest individual to complete their life cycle; (e) have a high search rate for the pest; (f) aggregate at areas of high pest density, which is thought to stabilize the interaction. These features are more characteristic of parasitoids than predators. We suggest that a stable pest equilibrium is neither a necessary nor a sufficient condition for control. We show that satisfactory control in model systems is compatible with both local extinction of the pest and polyphagy in the natural enemy. Only one of nine real examples of successful control is convincingly a stable interaction; the remainder show either strong evidence for instability and local e...

http://max2.ese.u-psud.fr/epc/conservation/PDFs/HIPE/Murdoch1985.pdf

Biological Control in Theory and Practice

The plants and Homoptera on three old fields in southeast Michigan were sam- pled. Within fields, correlations between plant and insect diversity were generally weak. But using all samples from three fields, evenness (J) and diversity (H) of the insects were highly correlated with plant evenness and plant diversity, respectively. For example, 72% of the variance in insect H could be accounted for by variation in plant H. Number of species (S) showed a positive but weaker correlation. When correlations were based on the pooled sam- ples from each field, all three statistics for insects were highly correlated with those for the plants. Insect H was also highly correlated with plant structure (foliage height diversity, FHD) over all three fields. These two measures of plant diversity (H and FHD) were highly correlated and were equally good correlates of insect H. Together they accounted for 79% of the variance in insect H. This extends to insects a correlation between plant and animal diversity, already well established for birds and possibly true for lizards and rodents. It leaves open the unresolved question as to whether plant structure or plant species diversity is more important. The diversities of different components of a com- munity seem to be correlated, in the few cases studied, and in particular, animal diversity has been correlated with aspects of the plant diversity. It is not surprising that a greater variety of plants should lead to a greater variety of plant-eaters. However, the reasons for observed correlations between plant structural diversity and animal species diversity are less obvious. In one group of animals the reason ap- pears obvious; different bird species nest and forage at different heights and their diversity is related to the structural diversity of the vegetation (e.g., MacArthur and MacArthur 1961, Recher 1969). In this paper we explore these relationships in in- sects. Plant-sucking bugs (Homoptera) of several old fields were studied because they form a dominant group of insect herbivores in these communities, and because their diversity might be expected to be closely tied to that of plants. Since these insects feed directly on the green plants, unlike the other groups that have been studied, and since at least some of them are host specific (DeLong 1948, Whitcomb 1957), we expected to find correlations with plant species di- versity, but we also measured foliage height diversity (structure). To avoid geographic effects on diversity, and to keep in the same kind of habitat, we sampled several old fields, all within a 1-km radius and all abandoned for the same period of time.

https://www.jstor.org/stable/pdfplus/1934297.pdf

William W. Murdoch

Papers

Environmental impact assessment: "pseudoreplication" in time?'

Switching in General Predators: Experiments on Predator Specificity and Stability of Prey Populations

Population regulation in theory and practice

Biological Control in Theory and Practice

Diversity and Pattern in Plants and Insects