Alternative life histories in the Atlantic salmon: genetic covariances within the sneaker sexual tactic in males

Alternative reproductive tactics are ubiquitous in many species. Tactic expression often depends on whether an individual's condition surpasses thresholds that are responsible for activating particular developmental pathways. Two central goals in understanding the evolution of reproductive tactics are quantifying the extent to which thresholds are explained by additive genetic effects, and describing their covariation with condition-related traits. We monitored the development of early sexual maturation that leads to the sneaker reproductive tactic in Atlantic salmon (Salmo salar L.). We found evidence for additive genetic variance in the timing of sexual maturity (which is a measure of the surpassing of threshold values) and body-size traits. This suggests that selection can affect the patterns of sexual development by changing the timing of this event and/or body size. Significant levels of covariation between these traits also occurred, implying a potential for correlated responses to selection. Closer examination of genetic covariances suggests that the detected genetic variation is distributed along at least five directions of phenotypic variation. Our results show that the potential for evolution of the life-history traits constituting this reproductive phenotype is greatly influenced by their patterns of genetic covariance.     

Alternative life histories in sex changing shrimp: a phenotype limited ESS

Summary In many populations of protandrous shrimp, two alternative life histories coexist. One way to interpret this fact is that one age (or size) group consists of a mixture of males and females. This is a nice example of a phenotype limited evolutionarily stable strategy (ESS), in the sense of Parker (1982, p. 187). This paper explores the ESS theory for the mixture.     

Timing in the life histories of insects

This paper presents a heuristic model illustrating some major problems in analyzing seasonal life histories of multigeneration insects. The concept of the critical interval is introduced and defined as the age classes that survive at the end of a period of population growth. These conclusions follow from the results: The optimal age for occupying a habitat depends upon the duration of the habitat as well as the life history of the insect. Two positions of the initial age distribution may give local maxima for fitness. The critical interval should often include the youngest age classes to maximize fitness while the optimal position of the initial age distribution may be at a much older age. In this case, conflicts arise between the positions of the critical interval at the end of one growing period and the initial age distribution at the start of the next. The length of the critical interval that maximizes fitness in a particular environment may be relatively small in which case mortality at the end of a growing period may be high and timing would appear to be poor even though fitness is maximized. In this model, optimum generation lengths exist which are not the shortest attainable. Finally, the length of time that a habitat remains suitable influences all of the above results and must be taken into account in analyzing the adaptedness of life history traits.     

Large-scale analysis of gene expression profiles

The accumulation of DNA microarray data has now made it possible to use gene expression profiles to analyse expression data. A gene expression profile contains the expression data for a given gene over various samples, and can be contrasted with an expression signature, which contains the expression data for a single sample. Gene expression profiles are most revealing when samples are grouped appropriately, either by standard clinical or pathological categories or by categories discovered through cluster analysis techniques. Expression profiles can exist at various levels of abstraction, yielding information across various tissues or across diseases within a particular tissue. Hypothesis tests may be applied to expression profiles on a large scale to identify candidate genes of interest.     

Alternative life histories of the genusLucania: 2. Early ontogeny ofL. goodei,the bluefin killifish

Synopsis This is the second of three papers devoted to the interpretation of morphological development in altricial and precocial species within the genus Lucania. The focus of this paper was the early life history of the bluefin killifish,Lucania goodei. Reproductively mature specimens were collected in the run below Newport Spring, north of St. Marks National Wildlife Refuge in northwest Florida. These specimens were transported to the laboratory, where they served as brood stock for specimens described in this study. Offspring were reared under controlled conditions and were described according to the theory of saltatory ontogeny, which gives a sampling design based on morphological, rather than chronological, progression. The morphological development of these offspring is described on the basis of detailed illustrations, photomicrographs, and measurements of mensural and meristic characters. This account of early ontogeny, in combination with a corresponding study on the early ontogeny of the rainwater killifish,L. parva (Crawford & Balon 1994a), establishes the empirical basis for an altricial-precocial life history model (Crawford & Balon 1994b).     

Ecological determinism in the life histories of baboons

An evolutionary model is presented for the covariation of parameters in ecology, behavior, morphology and social organization observed in interpopulational comparisons of baboons. Ecological determinants, in particular rainfall, shape the optimal life history strategies of individuals within a local population, in terms of the distribution of time and energy for reproductive effort, growth and maintenance. The results are adaptations in body mass, sexual dimorphism and aggression among baboons that are significantly correlated with rainfall. The three common types of baboon social organization, one-male units, multi-male troops and age-graded groups, are discussed as the consequences of male and female life history strategies, and in turn as social environments generating their own selection pressures.     

Differences in the life histories of twoCochlearia species

Cochlearia bavarica Vogt andC. pyrenaica Dc. are closely related and highly endangered species in Bavaria (SE Germany).Cochlearia bavarica (2n=36) is a hybrid ofC. pyrenaica (2n=12) andC. officianalis (2n=24) stabilized by polyploidy.Cochlearia officinalis does not occur in Bavaria. The question being addressed is whether the present non-overlapping distribution of the two Bavarian species, both of which are restricted to calcareous springs with a continuous water supply or drainage ditches, is due to competitive exclusion or to subtle differences of ecological requirements. I did not find any evidence for the second case, i.e. niche differentiation, because both species occurred in all the habitat types that I could define by floristic and ecological criteria. The population structures of bothC. bavarica andC. pyrenaica vary in parallel with different habitat types. Both species have the greatest reproductive output (viable seeds) and the highest population densities in habitats with high light availability and/or low interspecific competition. Thus, I expected that one of the two species might be competitively superior over the other, but that it would fail to reach all its potential sites of occurrence. Cochlearia bavarica individuals (dry mass =5.75 g) grow significantly larger thanC. pyrenaica individuals (3.62 g;P<0.05) and produce more, larger and heavier seeds, possibly due to hybrid vigour. Flowering individuals ofC. bavarica also allocate more biomass to vegetative structures thanC. pyrenaica. The analysis of population dynamics reveals a higher life expectancy and reproductive output inC. bavarica. The calculated population growth rates although negative over the observation period in both species, suggest a significantly higher fitness ofC. bavarica (λ=0.66) compared withC. pyrenaica (λ=0.44). Thus, our data are in line with the competitive exclusion hypothesis andCochlearia bavarica appears as an example of a species with hybridogenous origin possessing higher fitness than its progenitor. However, considering the rarity of both species it seems at present unlikely that the former will displace the latter over a large distributional region.     

Measurement of peptide secretion and gene expression in the same cell

A combined reverse hemolytic plaque-in situ hybridization assay was developed to allow analysis of the relationship between peptide secretion and gene expression within individual cells. We used the pituitary lactotroph as a model system, but this strategy should be widely applicable. It can be used to test hypotheses regarding if and when peptide secretion and gene expression are coupled in any system in which antibodies to the secreted peptide and probes complementary to the mRNA are available. Using the mRNA hybridization signal to identify certain cell types, this method may also be useful in further studies on the biochemical mechanism of peptide secretion. In addition, questions regarding whether a cell known to secrete a given peptide contains other specific mRNAs and the relationship between these mRNAs and the secretion of the peptide can be studied using this strategy. We found striking heterogeneity among lactotrophs in both gene expression and PRL secretion and a lack of correlation of these parameters within individual lactotrophs under every treatment examined. We also present the first direct visualization and quantitation of the percentage of nonsecreting PRL mRNA-containing cells after estradiol treatment and in the presence or absence of the PRL secretagogue, TRH. Finally, we found that in ovariectomized rats, nonsecreting lactotrophs exhibited significantly higher levels of PRL mRNA than lactotrophs that were actively secreting PRL during the assay.     

Prediction and uncertainty in the analysis of gene expression profiles

We have developed a complete statistical model for the analysis of tumor specific gene expression profiles. The approach provides investigators with a global overview on large scale gene expression data, indicating aspects of the data that relate to tumor phenotype, but also summarizing the uncertainties inherent in classification of tumor types. We demonstrate the use of this method in the context of a gene expression profiling study of 27 human breast cancers. The study is aimed at defining molecular characteristics of tumors that reflect estrogen receptor tatus. In addition to good predictive performance with respect to pure classification of the expression profiles, the model also uncovers conflicts in the data with respect to the classification of some of the tumors, highlighting them as critical cases for which additional investigations are appropriate.     

Adaptive quality-based clustering of gene expression profiles

MOTIVATION: Microarray experiments generate a considerable amount of data, which analyzed properly help us gain a huge amount of biologically relevant information about the global cellular behaviour. Clustering (grouping genes with similar expression profiles) is one of the first steps in data analysis of high-throughput expression measurements. A number of clustering algorithms have proved useful to make sense of such data. These classical algorithms, though useful, suffer from several drawbacks (e.g. they require the predefinition of arbitrary parameters like the number of clusters; they force every gene into a cluster despite a low correlation with other cluster members). In the following we describe a novel adaptive quality-based clustering algorithm that tackles some of these drawbacks. RESULTS: We propose a heuristic iterative two-step algorithm: First, we find in the high-dimensional representation of the data a sphere where the "density" of expression profiles is locally maximal (based on a preliminary estimate of the radius of the cluster-quality-based approach). In a second step, we derive an optimal radius of the cluster (adaptive approach) so that only the significantly coexpressed genes are included in the cluster. This estimation is achieved by fitting a model to the data using an EM-algorithm. By inferring the radius from the data itself, the biologist is freed from finding an optimal value for this radius by trial-and-error. The computational complexity of this method is approximately linear in the number of gene expression profiles in the data set. Finally, our method is successfully validated using existing data sets. AVAILABILITY: http://www.esat.kuleuven.ac.be/~thijs/Work/Clustering.html     

Whole-genome expression profiles identify gene batteries in Drosophila

Microarray studies make it possible to obtain gene expression data on a whole-genome scale. Arbeitman et al. present microarray data generated at multiple time points throughout Drosophila melanogaster development, and identify new genes engaged in a broad spectrum of processes, including the patterning of the early embryo and senescence in adults.     

Peripheral blood gene expression profiles in COPD subjects

To identify non-invasive gene expression markers for chronic obstructive pulmonary disease (COPD), we performed genome-wide expression profiling of peripheral blood samples from 12 subjects with significant airflow obstruction and an equal number of non-obstructed controls. RNA was isolated from Peripheral Blood Mononuclear Cells (PBMCs) and gene expression was assessed using Affymetrix U133 Plus 2.0 arrays.Tests for gene expression changes that discriminate between COPD cases (FEV1< 70% predicted, FEV1/FVC < 0.7) and controls (FEV1> 80% predicted, FEV1/FVC > 0.7) were performed using Significance Analysis of Microarrays (SAM) and Bayesian Analysis of Differential Gene Expression (BADGE). Using either test at high stringency (SAM median FDR = 0 or BADGE p < 0.01) we identified differential expression for 45 known genes. Correlation of gene expression with lung function measurements (FEV1 & FEV1/FVC), using both Pearson and Spearman correlation coefficients (p < 0.05), identified a set of 86 genes. A total of 16 markers showed evidence of significant correlation (p < 0.05) with quantitative traits and differential expression between cases and controls. We further compared our peripheral gene expression markers with those we previously identified from lung tissue of the same cohort. Two genes, RP9and NAPE-PLD, were identified as decreased in COPD cases compared to controls in both lung tissue and blood. These results contribute to our understanding of gene expression changes in the peripheral blood of patients with COPD and may provide insight into potential mechanisms involved in the disease.     

Mouse maps of gene expression in the brain

The completion of the Allen Brain Atlas generated a great deal of press interest and enthusiasm from the research community. What does it do, and what other complementary resources increase its functionality?