Missing inaction: the dangers of ignoring missing data

The most common approach to dealing with missing data is to delete cases containing missing observations. However, this approach reduces statistical power and increases estimation bias. A recent study shows how estimates of heritability and selection can be biased when the 'invisible fraction' (missing data due to mortality) is ignored, thus demonstrating the dangers of neglecting missing data in ecology and evolution. We highlight recent advances in the procedures of handling missing data and their relevance and applicability.     

The dangers of ignoring stock complexity in fishery management: the case of the North Sea cod

The plight of the marine fisheries is attracting increasing attention as unsustainably high exploitation levels, exacerbated by more extreme climatic conditions, are driving stocks to the point of collapse. The North Atlantic cod (Gadus morhua), a species which until recently formed a major component of the demersal fisheries, has undergone significant declines across its range. The North Sea stock is typical of many, with a spawning stock biomass that has remained below the safe biological limit since 2000 and recruitment levels near the lowest on record. Cod within the North Sea are currently managed as a single stock, and yet mounting empirical evidence supports the existence of a metapopulation of regionally variable, genetically distinct, sub-stocks. Applying the same management strategies to multiple stocks that differ in their resilience to exploitation inevitably results in the overfishing and likely collapse of the weaker components. Indeed, recent studies have identified two North Sea spawning stocks that have undergone disproportionally large collapses with very substantial reductions in egg production. Similarly affected cod stocks in the northwest Atlantic have shown little evidence of recovery, despite fishery closures. The possible implications of ignoring sub-structuring within management units for biocomplexity, local adaptation and ecosystem stability are considered.     

Evolution as a cognition process: Towards an evolutionary epistemology

Recently, biologist and philosophers have been much attracted by an evolutionary view of knowledge, so-called evolutionary epistemology. Developing this insight, the present paper argues that our cognitive abilities are the outcome of organic evolution, and that, conversely, evolution itself may be described as a cognition process. Furthermore, it is argued that the key to an adequate evolutionary epistemology lies in a system-theoretical approach to evolution which grows from, but goes beyond, Darwin's theory of natural selection.     

Cavefish as a model system in evolutionary developmental biology

The Mexican tetra Astyanax mexicanus has many of the favorable attributes that have made the zebrafish a model system in developmental biology. The existence of eyed surface (surface fish) and blind cave (cavefish) dwelling forms in Astyanax also provides an attractive system for studying the evolution of developmental mechanisms. The polarity of evolutionary changes and the environmental conditions leading to the cavefish phenotype are known with certainty, and several different cavefish populations have evolved constructive and regressive changes independently. The constructive changes include enhancement of the feeding apparatus (jaws, taste buds, and teeth) and the mechanosensory system of cranial neuromasts. The homeobox gene Prox 1, which is expressed in the expanded taste buds and cranial neuromasts, is one of the genes involved in the constructive changes in sensory organ development. The regressive changes include loss of pigmentation and eye degeneration. Although adult cavefish lack functional eyes, small eye primordia are formed during embryogenesis, which later arrest in development, degenerate, and sink into the orbit. Apoptosis and lens signaling to other eye parts, such as the cornea, iris, and retina, result in the arrest of eye development and ultimate optic degeneration. Accordingly, an eye with restored cornea, iris, and retinal photoreceptor cells is formed when a surface fish lens is transplanted into a cavefish optic cup, indicating that cavefish optic tissues have conserved the ability to respond to lens signaling. Genetic analysis indicates that multiple genes regulate eye degeneration, and molecular studies suggest that Pax6 may be one of the genes controlling cavefish eye degeneration. Further studies of the Astyanax system will contribute to our understanding of the evolution of developmental mechanisms in vertebrates.     

Tangled nature: a model of evolutionary ecology

We discuss a simple model of co-evolution. In order to emphasize the effect of interaction between individuals, the entire population is subjected to the same physical environment. Species are emergent structures and extinction, origination and diversity are entirely a consequence of co-evolutionary interaction between individuals. For comparison, we consider both asexual and sexually reproducing populations. In either case, the system evolves through periods of hectic reorganization separated by periods of coherent stable coexistence.     

Sexual conflict and the evolutionary ecology of mating patterns: water striders as a model system

Two core ideas in the study of mating systems and sexual selection are (1) the existence of a conflict between the sexes over mating decisions, and (2) that variation in ecological conditions drives the evolution of adaptive mating strategies and the diversification of mating systems. A recent burst of experimental studies of mating behavior and sexual selection in water striders has focused on the interaction of these ideas and led to new insights into the evolutionary ecology of mating systems and sexual selection.     

Evolve III: A discrete events model of an evolutionary ecosystem

Evolve III is a discrete events model of an evolutionary ecosystem. The model includes three levels of organization: population, organism and genetic structure. Each of these components was modeled independently, so that selective replacement of subsystems can be used to create families of models capable of testing alternative hypotheses about the real system. To demonstrate the use of the model we describe an experiment on the relationship between adaptability of populations and the variability of the environment. Populations cultured in a constant environment usually dominated those cultured in a variable environment when both were placed in a variable environment at an early stage of development, whereas the opposite is the case at later stages of development. This agrees with experiments on laboratory microcosms and lends credence to the potential predictive value of the model.     

Capsella as a model system to study the evolutionary relevance of floral homeotic mutants

Several lines of evidence suggest that homeotic changes played a considerable role during the evolution of flowers. This, however, is difficult to reconcile with the predominant evolutionary theory which rejects any drastic, saltational change of the phenotype as reasonable mode of evolution due to its assumed negative impact on the fitness of the affected organism. A better understanding of the evolutionary potential of homeotic transitions requires a study of the performance of respective mutant varieties in the wild. Here we introduce ``Stamenoid petals' (Spe), a variety of Capsella bursa-pastoris (shepherd's purse), as a suitable model to study the evolutionary potential of floral homeotic mutants. In the flowers of the Spe variety all petals are transformed into stamens, while all other floral organs are unaffected. In contrast to most other homeotic mutants the Spe variety occurs on several locations in relatively large and stable populations in the wild. Due to its close relationship to the model plant Arabidopsis thaliana, the Spe variety of C. bursa-pastoris can be rigorously studied, from the molecular genetic basis of the phenotype to its consequences on the fitness in wild habitats. Investigations on Spe may thus help to clarify whether homeotic transformations have the potential to contribute to macroevolution.     

Aldolase of lactic Acid bacteria: a case history in the use of an enzyme as an evolutionary marker

[This corrects the article on p. 453 in vol. 37.].     

Microbial metabolism as an evolutionary response: the cybernetic approach to modeling

The growth and metabolic capabilities of microorganisms depend on their interactions with the culture medium. Many media contain two or more key substrates, and an organism may have different preferences for the components. Microorganisms adjust their preferences according to the prevailing conditions so as to favor their own survival. Cybernetic modeling describes this evolutionary strategy by defining a goal that an organism tries to attain optimally at all times. The goal is often, but not always, maximization of growth, and it may require the cells to manipulate their metabolic processes in response to changing environmental conditions. The cybernetic approach overcomes some of the limitations of metabolic control analysis (MCA), but it does not substitute MCA. Here we review the development of the cybernetic modeling of microbial metabolism, how it may be combined with MCA, and what improvements are needed to make it a viable technique for industrial fermentation processes.     

On the application of statistical physics to evolutionary biology

There is a close analogy between statistical thermodynamics and the evolution of allele frequencies under mutation, selection and random drift. Wright's formula for the stationary distribution of allele frequencies is analogous to the Boltzmann distribution in statistical physics. Population size, 2N, plays the role of the inverse temperature, 1/kT, and determines the magnitude of random fluctuations. Log mean fitness, , tends to increase under selection, and is analogous to a (negative) energy; a potential function, U, increases under mutation in a similar way. An entropy, S_H, can be defined which measures the deviation from the distribution of allele frequencies expected under random drift alone; the sum gives a free fitness that increases as the population evolves towards its stationary distribution. Usually, we observe the distribution of a few quantitative traits that depend on the frequencies of very many alleles. The mean and variance of such traits are analogous to observable quantities in statistical thermodynamics. Thus, we can define an entropy, S_Ω, which measures the volume of allele frequency space that is consistent with the observed trait distribution. The stationary distribution of the traits is ; this applies with arbitrary epistasis and dominance. The entropies S_Ω, S_H are distinct, but converge when there are so many alleles that traits fluctuate close to their expectations. Populations tend to evolve towards states that can be realised in many ways (i.e., large S_Ω), which may lead to a substantial drop below the adaptive peak; we illustrate this point with a simple model of genetic redundancy. This analogy with statistical thermodynamics brings together previous ideas in a general framework, and justifies a maximum entropy approximation to the dynamics of quantitative traits.