Visual processing: the devil is in the details

Ganglion cells convey information from the retina back to the brain. Recent experiments have examined how ganglion cell receptive fields are assembled from many incoming signals.     

The devil lies in details: reply to Stuart Hurlbert

As pointed out in Stuart Hurlbert's recent article, ecologists still at times design their experiments sloppily, creating a situation where various forms of ‘non‐demonic intrusion’ could account for the documented contrasts between treatments and controls. If such contrasts are nevertheless presented to the reader as if they were statistically demonstrated treatment effects, then pseudoreplication is not a pseudoissue and the use of a stigmatizing label of is entirely warranted, as pointed out by Hurlbert. The problems with Hurlbert's concepts start in the context of studies, where the scope of the experiment is to provoke a chain of dramatic and a priori extremely unlikely events, which a given conjecture predicts to happen as a consequence of a given manipulation. As the essence of these experiments is to trigger large dynamical responses in a biological system, they often require much space and/or special conditions, allowing for efficient isolation of the experimental system from potential sources of contamination. These constraints can be incompatible with standard designs (randomization, replication and treatment‐control interspersion). In the context of experiments, where it has been necessary to sacrifice randomization, replication or treatment‐control interspersion, the logic of inferring treatment effects is the same as used when interpreting causes of spontaneous events or events triggered by manipulations with practical purposes. The observed contrasts can be reasonably interpreted as effects of the treatment if and only if their magnitudes and the timing of their emergence makes alternative explanations utterly implausible (which is up to the reader to judge). If the logic of inference is clearly explained and no claim of statistically demonstrated treatment effect is made, the use of stigmatizing labels like ‘pseudoreplication’ is unwarranted. However, it might clarify the literature if such imperfectly designed experiments are referred to as experimental events, to be distinguished from perfectly designed experiments, where mechanical interpretation of contrasts between treatments and controls as treatment effects can be regarded as socially acceptable.     

The precautionary approach in fisheries management: the devil is in the details

The William and Lenore Mote International Symposium 'Targets, thresholds and the burden of proof in fishery management' was held at the Mote Marine Laboratory, Sarasota, FL, USA, from 30 October to 2 November 2000.     

The devil in the details: the emerging role of anticitrulline autoimmunity in rheumatoid arthritis

Rheumatoid arthritis is a chronic inflammatory autoimmune disease of unknown cause. The immune response against citrullinated Ags has recently become the prime suspect for disease pathogenesis. Immunity against citrullinated Ags is thought to play a pivotal role in the disease for several reasons: 1) citrullinated Ags are expressed in the target organ, the inflamed joint; 2) anti-citrullinated protein Abs are present before the disease becomes manifest; and 3) these Abs are highly specific for rheumatoid arthritis. In this review, data from clinical, genetic, biochemical, and animal studies is combined to create a profile of this remarkable autoantibody response. Moreover, a model is proposed of how the anti-citrullinated proteins response is generated and how it could eventually lead to chronic inflammation.     

Centrosome function during stem cell division: the devil is in the details

Cell polarity is inherent to animal development and requires microtubules. In essentially all non-terminally differentiated somatic and male germ-line animal cells, microtubule organisation is governed by centrosomes. Animal development without centrosomes would therefore seem inconceivable. The claim of flies without centrosomes may appear to challenge this notion. Does it?     

The cost of reproduction in the glaucous-winged gull

Summary Experimental enlargement of brood size in the glaucous-winged gull (Larus glaucescens) resulted in increased adult foraging time, decreased adult body weight at the end of the breeding season, and decreased over-winter adult survival. The decreased survival of breeding adults was associated with reduced body condition at the end of breeding (resulting from physiological costs of reproduction). Decreased survival was not due to an increased risk of injury or predation during the breeding season. Brood size did not directly affect the fecundity of surviving birds in the subsequent year. However, brood size may have an indirect effect on subsequent fecundity because the probability of mate loss increased among birds with large broods and the reproductive performance of birds with new mates was reduced. Based on estimates of life-time fitness calculated from fecundity and survivorship, birds with two- or three-chick broods (the normal brood size) have higher fitness than birds with one- or four-chick broods. However, the decreased fitness of birds with four-chick broods was slight, and probably not a sufficient explanation for the absence of natural four-chick broods in the glaucouswinged gull.     

Measuring the cost of reproduction

Gravid and barren Daphnia pulex were exposed to a variety of predators in laboratory aquaria. Small fish (guppies, sticklebacks and shiner fry) consistently preferred the gravid females, establishing the existence of a behavioural cost of reproduction. However, no such cost was associated with predation by more efficient visual predators (sunfish) or by nonvisual predators (hydras), and the excess of gravid females eaten by backswimmers was found to be attributable to their distribution in the water column. Moreover, the cost associated with predation by small fish was observed only when the Daphnia were presented against a light background, and was abolished when a dark background was substituted. In a further series of experiments with guppies we attempted to show that each egg added to the brood caused a decrease in survival; in two such experiments survival rate was related to body size but not to fecundity, while in a third the effect of body size did not appear, and a negative correlation between survival and fecundity could be demonstrated. Although these experiments unambiguously demonstrate a cost of reproduction they also illustrate the elusiveness of the phenomenom and emphasize the need to develop theories which specify the type and magnitude of costs generated by different ways of life.     

Measuring the cost of reproduction

Summary The timing of the first two broods and the number and size of offspring in each was measured in a series of three experiments for monoclonal cultures of the cladoceran Daphnia pulex reared under standard conditions of ration, temperature and photoperiod. The pattern of total correlations between pairs of life-history variables did not in general support predictions made by hypotheses of reproductive cost. A partial correlation analysis, involving initial size and subsequent growth as well as the life history variables themselves, was performed in an attempt to avoid potential fallacies introduced by the use of total correlations. The only consistent effect found was a positive relationship between the age at reproductive maturity and the mean size of offspring in the first brood. The structure of this segment of the life history is strongly influenced by interactions between size and reproduction, to an extent that precludes the use of simple optimality models.     

小型啮齿动物的繁殖能量代价

繁殖是动物向后代传递和保持遗传信息的方式。因此繁殖的意义是显而易见的,但也需要付出代价。主要代价是能量需求增加。在对小家鼠繁殖能量需求的研究中发现,能量摄入在妊娠期只是稍微增加,而在哺乳期则急剧增加。尽管在妊娠期增加的幅度很小,但这可能反映了消化道和发育的胎儿之间在动物腹中的空间竞争,从而可能使能量摄入受到限制进而影响到繁殖过程。哺乳期间,能量摄入急剧增加,在哺乳后期达到高峰并趋于稳定。对野生鼠的研究也表明,野生鼠妊娠期和哺乳期的能量摄入模式与小家鼠是基本相同的,这样我们在小家鼠研究工作中的发现就具有更普遍的适应意义。对哺乳后期能量摄入的限制机制研究至少已经进行了15 年。能量摄入受消化道消化能力的限制(中心限制假说)或者受乳腺泌乳能力限制(外周限制假说) 的假说,都不能合理地解释一些现有的结果。我们提出了一个新的假说,即能量摄入可能受啮齿动物散热能力的限制(热耗散限制假说)。很久以来,一直认为散热能力是对大型哺乳动物哺乳的一个限制因素,但它在小型啮齿动物中的意义尚不清楚。传统观点认为,啮齿动物哺乳期对褐色脂肪组织产热水平的调节是为了重新分配能量以满足哺乳所需;但现在看来,实际上可能是动物为了避免体温过高而降低其基本的产热水平。我们在这个领域已经有了一些进展,但要利用这些知识来理解即使很简单的生活史权衡等问题也还有很多的工作需要做。     

The devil in the details: interactions between the branch-length prior and likelihood model affect node support and branch lengths in the phylogeny of the Psoraceae

In popular use of Bayesian phylogenetics, a default branch-length prior is almost universally applied without knowing how a different prior would have affected the outcome. We performed Bayesian and maximum likelihood (ML) inference of phylogeny based on empirical nucleotide sequence data from a family of lichenized ascomycetes, the Psoraceae, the morphological delimitation of which has been controversial. We specifically assessed the influence of the combination of Bayesian branch-length prior and likelihood model on the properties of the Markov chain Monte Carlo tree sample, including node support, branch lengths, and taxon stability. Data included two regions of the mitochondrial ribosomal RNA gene, the internal transcribed spacer region of the nuclear ribosomal RNA gene, and the protein-coding largest subunit of RNA polymerase II. Data partitioning was performed using Bayes' factors, whereas the best-fitting model of each partition was selected using the Bayesian information criterion (BIC). Given the data and model, short Bayesian branch-length priors generate higher numbers of strongly supported nodes as well as short and topologically similar trees sampled from parts of tree space that are largely unexplored by the ML bootstrap. Long branch-length priors generate fewer strongly supported nodes and longer and more dissimilar trees that are sampled mostly from inside the range of tree space sampled by the ML bootstrap. Priors near the ML distribution of branch lengths generate the best marginal likelihood and the highest frequency of "rogue" (unstable) taxa. The branch-length prior was shown to interact with the likelihood model. Trees inferred under complex partitioned models are more affected by the stretching effect of the branch-length prior. Fewer nodes are strongly supported under a complex model given the same branch-length prior. Irrespective of model, internal branches make up a larger proportion of total tree length under the shortest branch-length priors compared with longer priors. Relative effects on branch lengths caused by the branch-length prior can be problematic to downstream phylogenetic comparative methods making use of the branch lengths. Furthermore, given the same branch-length prior, trees are on average more dissimilar under a simple unpartitioned model compared with a more complex partitioned models. The distribution of ML branch lengths was shown to better fit a gamma or Pareto distribution than an exponential one. Model adequacy tests indicate that the best-fitting model selected by the BIC is insufficient for describing data patterns in 5 of 8 partitions. More general substitution models are required to explain the data in three of these partitions, one of which also requires nonstationarity. The two mitochondrial ribosomal RNA gene partitions need heterotachous models. We found no significant correlations between, on the one hand, the amount of ambiguous data or the smallest branch-length distance to another taxon and, on the other hand, the topological stability of individual taxa. Integrating over several exponentially distributed means under the best-fitting model, node support for the family Psoraceae, including Psora, Protoblastenia, and the Micarea sylvicola group, is approximately 0.96. Support for the genus Psora is distinctly lower, but we found no evidence to contradict the current classification.     

Oxidative shielding and the cost of reproduction

Life‐history theory assumes that reproduction and lifespan are constrained by trade‐offs which prevent their simultaneous increase. Recently, there has been considerable interest in the possibility that this cost of reproduction is mediated by oxidative stress. However, empirical tests of this theory have yielded equivocal support. We carried out a meta‐analysis to examine associations between reproduction and oxidative damage across markers and tissues. We show that oxidative damage is positively associated with reproductive effort across females of various species. Yet paradoxically, categorical comparisons of breeders versus non‐breeders reveal that transition to the reproductive state is associated with a step‐change reduction in oxidative damage in certain tissues and markers. Developing offspring may be particularly sensitive to harm caused by oxidative damage in mothers. Therefore, such reductions could potentially function to shield reproducing mothers, gametes and developing offspring from oxidative insults that inevitably increase as a consequence of reproductive effort. According to this perspective, we hypothesise that the cost of reproduction is mediated by dual impacts of maternally‐derived oxidative damage on mothers and offspring, and that mothers may be selected to diminish such damage. Such oxidative shielding may explain why many existing studies have concluded that reproduction has little or no oxidative cost. Future advance in life‐history theory therefore needs to take account of potential transgenerational impacts of the mechanisms underlying life‐history trade‐offs.     

Age-related shapes of the cost of reproduction in vertebrates

The shape of the association between age and the cost of reproduction varies across species. However, it is unclear whether there are any general patterns in the way the cost of reproduction varies with life history, taxon or ecological function. Using a simple theoretical method, we identified three characteristic patterns to describe the age-related survival cost of reproduction. The most frequent pattern is an approximately exponential decay (ED) with increasing age. Two additional u-shaped patterns were identified, where the cost of reproduction was higher for young and old individuals compared with intermediate-aged individuals. The majority of these u-shaped curves suggested higher costs of reproduction at older ages (RQ), with the rest suggesting a higher cost at young ages (LQ). While predators were most likely to exhibit ED-shaped cost curves, herbivores were equally likely to exhibit ED and RQ curves; birds were likely to exhibit ED-shaped curves and mammals were split equally between ED and RQ curves. These findings suggest that there may be predictable differences in the age-related shape of the cost of reproduction between species, but further research is required to identify the mechanisms generating such differences.     

A cost of reproduction in Drosophila melanogaster: stress susceptibility

Little is known about physiological mechanisms that underlie the cost of reproduction. We tested the hypothesis that stress susceptibility is a cost of reproduction. In one test of our hypothesis, Drosophila melanogaster females were exposed to a juvenile hormone analog (methoprene) to stimulate egg production followed by stress assays. A sterile stock of D. melanogaster was employed as a control for reproduction. Exposure of fertile females to methoprene resulted in an increase in female reproduction and increased susceptibility to oxidative stress and starvation (compared to solvent controls). Sterile females did not exhibit a decrease in stress resistance. Mating also stimulated egg production. As a second test of our hypothesis, mated females were compared to virgin females. Mated fertile females were relatively susceptible to oxidative stress, but this relationship was not evident when mated and virgin sterile females were compared. The results of the present study support the hypothesis that stress susceptibility is a cost of reproduction.