Assessing the statistical power of genetic analyses to detect multiple mating in fishes

Blue catfish Ictalurus furcatus and channel catfish Ictalurus punctatus , two large-bodied piscivore-omnivores in Lake Texoma, Texas-Oklahoma, U.S.A., showed very high overlap in food use, but substantial differences in use of habitat during the year. Both species primarily ate fishes, aquatic insects, vegetation and detritus, terrestrial insects, seeds and zooplankton, with overall overlap = 98%. Diet breadth indices were very similar (blue catfish=4.31, channel catfish = 4.53). Quantitative and qualitative feeding varied seasonally and food habits changed ontogenetically. Feeding intensity was greatest in winter and lowest in late summer. Aquatic insects were eaten more from May to October and fishes more in winter. At body sizes from 100 to 299 mm L_s , both species primarily ate aquatic insects, terrestrial insects, fishes or zooplankton, whereas the diets of individuals >300 mm L_s of both species were dominated by fishes. Overall, their overlap in distribution across major habitat types was only 58%, with blue catfish most abundant in deep water offshore, and channel catfish more common in shallow cove habitats. Blue catfish that did occur in coves were in the deeper parts of those habitats, essentially not occurring in the littoral zone. In lakes without blue catfish, channel catfish are widely dispersed in various habitats and it is suspected that displacement of channel catfish by blue catfish may influence habitat differences of the two species in Lake Texoma. Because the spatial separation of the species also reflects their typical interspecific differences in unimpounded drainages, however, the habitat differences observed in Lake Texoma probably also reflect evolved, historical differences in ecology of the two species.     

Phenological response of sea turtles to environmental variation across a species' northern range

Variations in environmental parameters (e.g. temperature) that form part of global climate change have been associated with shifts in the timing of seasonal events for a broad range of organisms. Most studies evaluating such phenological shifts of individual taxa have focused on a limited number of locations, making it difficult to assess how such shifts vary regionally across a species range. Here, by using 1445 records of the date of first nesting for loggerhead sea turtles (Caretta caretta) at different breeding sites, on different continents and in different years across a broad latitudinal range (25–39° ′N), we demonstrate that the gradient of the relationship between temperature and the date of first breeding is steeper at higher latitudes, i.e. the phenological responses to temperature appear strongest at the poleward range limit. These findings support the hypothesis that biological changes in response to climate change will be most acute at the poleward range limits and are in accordance with the predictions of MacArthur''s hypothesis that poleward range limit for species range is environmentally limited. Our findings imply that the poleward populations of loggerheads are more sensitive to climate variations and thus they might display the impacts of climate change sooner and more prominently.     

The evolution of trade-offs: testing predictions on response to selection and environmental variation

The concept of phenotypic trade-offs is a central element in evolutionary theory. In general, phenotypic models assume a fixed trade-off function, whereas quantitative genetic theory predicts that the trade-off function will change as a result of selection. For a linear trade-off function selection will readily change the intercept but will have to be relatively stronger to change the slope. We test these predictions by examining the trade-off between fecundity and flight capability, as measured by dorso-longitudinal muscle mass, in four different populations of the sand cricket, Gryllus firmus. Three populations were recently derived from the wild, and the fourth had been in the laboratory for 19 years. We hypothesized that the laboratory population had most likely undergone more and different selection from the three wild populations and therefore should differ from these in respect to both slope and intercept. Because of geographic variation in selection, we predicted a general difference in intercept among the four populations. We further tested the hypothesis that this intercept will be correlated with proportion macropterous and that this relationship will itself vary with environmental conditions experienced during both the nymphal and adult period. Observed variation in the phenotypic trade-off was consistent with the predictions of the quantitative genetic model. These results point to the importance of modeling trade-offs as dynamic rather than static relationships. We discuss how phenotypic models can incorporate such variation. The phenotypic trade-off between fecundity and dorso-longitudinal muscle mass is determined in part by variation in body size, illustrating the necessity of considering trade-offs to be multi factorial rather than simply bivariate relationships.     

Expression of sexual ornaments in a polymorphic species: phenotypic variation in response to environmental risk

Secondary sexual traits may evolve under the antagonistic context of sexual and natural selection. In some polymorphic species, these traits are only expressed during the breeding period and are differently expressed in alternative phenotypes. However, it is unknown whether such phenotypes exhibit phenotypic plasticity of seasonal ornamentations in response to environmental pressures such as in the presence of fish (predation risk). This is an important question to understand the evolution of polyphenisms. We used facultative paedomorphosis in newts as a model system because it involves the coexistence of paedomorphs that retain gills in the adult stage with metamorphs that have undergone metamorphosis, but also because newts exhibit seasonal sexual traits. Our aim was therefore to determine the influence of fish on the development of seasonal ornamentation in the two phenotypes of the palmate newt (Lissotriton helveticus). During the entire newt breeding period, we assessed the importance of phenotype and fish presence with an information‐theoretic approach. Our results showed that paedomorphs presented much less developed ornamentation than metamorphs and those ornamentations varied over time. Fish inhibited the development of sexual traits but differently between phenotypes: in contrast to metamorphs, paedomorphs lack the phenotypic plasticity of sexual traits to environmental risk. This study points out that internal and external parameters act in complex ways in the expression of seasonal sexual ornamentations and that similar environmental pressure can induce a contrasted evolution in alternative phenotypes.     

Relating geographical variation in pollination types to environmental and spatial factors using novel statistical methods

The relative frequencies of functional traits of plant species show notable spatial variation, which is often related to environmental factors. Pollination type (insect-, wind- or self-pollination) is a critical trait for plant reproduction and provision of ecosystem services. Here, we mapped the distribution of pollination types across Germany by combining databases on plant distribution and plant pollination types. Applying a new method, we modelled the composition of pollination types using a set of 12 environmental variables as predictors within a Bayesian framework which allows for the analysis of compositional data in the presence of spatial autocorrelation. A clear biogeographical pattern in the distribution of pollination types was revealed which was adequately captured by our model. The most striking relationship was a relative increase in insect-pollination and a corresponding decrease of selfing with increasing altitude. Further important factors were wind speed, geology and land use. We present a powerful tool to analyse the distribution patterns of plant functional types such as pollination types and their relationship with environmental parameters in a spatially explicit framework.     

The relative power of genome scans to detect local adaptation depends on sampling design and statistical method

Although genome scans have become a popular approach towards understanding the genetic basis of local adaptation, the field still does not have a firm grasp on how sampling design and demographic history affect the performance of genome scans on complex landscapes. To explore these issues, we compared 20 different sampling designs in equilibrium (i.e. island model and isolation by distance) and nonequilibrium (i.e. range expansion from one or two refugia) demographic histories in spatially heterogeneous environments. We simulated spatially complex landscapes, which allowed us to exploit local maxima and minima in the environment in ‘pair’ and ‘transect’ sampling strategies. We compared F_ST outlier and genetic–environment association (GEA) methods for each of two approaches that control for population structure: with a covariance matrix or with latent factors. We show that while the relative power of two methods in the same category (F_ST or GEA) depended largely on the number of individuals sampled, overall GEA tests had higher power in the island model and F_ST had higher power under isolation by distance. In the refugia models, however, these methods varied in their power to detect local adaptation at weakly selected loci. At weakly selected loci, paired sampling designs had equal or higher power than transect or random designs to detect local adaptation. Our results can inform sampling designs for studies of local adaptation and have important implications for the interpretation of genome scans based on landscape data.     

EDDY: a novel statistical gene set test method to detect differential genetic dependencies

Identifying differential features between conditions is a popular approach to understanding molecular features and their mechanisms underlying a biological process of particular interest. Although many tests for identifying differential expression of gene or gene sets have been proposed, there was limited success in developing methods for differential interactions of genes between conditions because of its computational complexity. We present a method for Evaluation of Dependency DifferentialitY (EDDY), which is a statistical test for differential dependencies of a set of genes between two conditions. Unlike previous methods focused on differential expression of individual genes or correlation changes of individual gene–gene interactions, EDDY compares two conditions by evaluating the probability distributions of dependency networks from genes. The method has been evaluated and compared with other methods through simulation studies, and application to glioblastoma multiforme data resulted in informative cancer and glioblastoma multiforme subtype-related findings. The comparison with Gene Set Enrichment Analysis, a differential expression-based method, revealed that EDDY identifies the gene sets that are complementary to those identified by Gene Set Enrichment Analysis. EDDY also showed much lower false positives than Gene Set Co-expression Analysis, a method based on correlation changes of individual gene–gene interactions, thus providing more informative results. The Java implementation of the algorithm is freely available to noncommercial users. Download from: http://biocomputing.tgen.org/software/EDDY.     

Demographic response to environmental variation in breeding,stopover and non-breeding areas in a migratory passerine

Demographic rates of migratory species passing through several areas during their annual cycle may be affected by environmental conditions at each of these areas. Recent studies provide evidence that their impact is not necessarily immediate, but can be delayed. We studied survival, reproductive success and arrival date at the breeding grounds of red-backed shrikes Lanius collurio, a trans-Saharan migrant, in relation to weather and vegetation on the breeding grounds, the stopover sites during migration and in the wintering areas. These environmental factors are used as proxy of the shrike’s food supply. We analysed detailed demographic data of some 4,600 individuals from 25 years with multistate capture–recapture and mixed models. Survival probabilities of juveniles and breeders of both sexes varied in parallel across time, suggesting that all cohorts were sensitive to similar causes of mortality. Reproductive performance increased with temperature and decreased with rainfall on the breeding area. Moreover, it increased with vegetation cover in the Sahelian stopover area used on autumn migration suggesting a carry-over effect. Arrival date was negatively affected by spring temperatures in the breeding area. Hence, demographic rates were affected by environmental factors on the breeding grounds, but also outside and elsewhere. This suggests that the shrike’s population dynamics are driven by environmental factors operating at various scales of space and time. However, only a small amount of the temporal variation in demographic rates is explained by the environmental factors considered, suggesting that additional factors, such as those operating during migration, might be important.     

Thermodynamic calculations and statistical correlations for oligo-probes design

Optimization of probe design for array-based experiments requires improved predictability of oligonucleotide hybridization behavior. Currently, designing oligonucleotides capable of interacting efficiently and specifically with the relevant target is not a routine procedure. Multiple examples demonstrate that oligonucleotides targeting different regions of the same RNA differ in their hybridization ability. The present work shows how thermodynamic evaluations of oligo-target duplex or oligo self-structure stabilities can facilitate probe design. Statistical analysis of large sets of hybridization data reveals that thermodynamic evaluation of oligonucleotide properties can be used to avoid poor RNA binders. Thermodynamic criteria for the selection of 20 and 21mers, which, with high probability, interact efficiently and specifically with their targets, are suggested. The design of longer oligonucleotides can also be facilitated by the same calculations of ΔG°_T values for oligo-target duplex or oligo self-structure stabilities and similar selection schemes.     

Genetic and environmental factors causing variation in drug response

Large pharmacokinetic variations, ranging in magnitude from 4- to 40-fold, often exist among the members of a given population. These variations create differences in risk of cancer by accelerating metabolic activation of certain environmental carcinogens in some subjects, while retarding such rates in other subjects. To identify specific genetic and environmental causes of large interindividual variations in these rates, several methods have been developed to probe hepatic cytochrome P-450 isozymes responsible for xenobiotic activation. In patients, dynamic interactions occur between genetic and environmental factors causing large interindividual variations in xenobiotic metabolism. Even the same patient can change dosage requirements with time and condition. Appropriate marker drugs can sensitively indicate pharmacokinetic capacity at any given time in a patient or normal volunteer. With respect to genetic factors, twin and family studies are the traditional methods used to test pharmacogenetic hypotheses. Representative examples are cited to illustrate how twin and family studies serve this purpose. Monogenic control of large interindividual variations in the activity of approx. 12 P-450 isozymes has been described. Individual metabolic pathways need to be investigated for drugs biotransformed by multiple pathways. Since many hepatic P-450 isozymes are extremely sensitive to perturbation by numerous environmental alterations, the critical role of selection criteria is stressed to assure that all subjects of twin and family studies are under as uniform environmental conditions as possible. Otherwise, the operation of genetic factors may be concealed or misinterpreted in studies that do not use gene cloning or protein sequence.     

Intraocular lens power calculations using a Scheimpflug camera to measure corneal power

We measured corneal power using an Oculus Pentacam^® to assess its accuracy for calculating intraocular lens (IOL) power after myopic refractive surgery. A series of corneal power measurements were performed on 22 patients (43 eyes) who had undergone myopic refractive surgery. In 37 of the 43 eyes, phacoemulsification and IOL implantation subsequently were performed. Conventional keratometry and three corneal measurements (mean true net power, central true net power, and 4.5 mm equivalent K reading) obtained using a Pentacam were analyzed and compared to values derived from the clinical history method. Prediction errors of three Pentacam corneal power measurements inserted in third generation IOL formulas also were compared. Analysis of the variance showed that only two Pentacam corneal measurements, mean true net power and central true net power, were not significantly different from those of the clinical history method. Mean true net power was correlated more closely with the clinical history method corneal power than other corneal power values. The one-sample t-test showed that of three Pentacam corneal measurements combined with third-generation formulas, only the mean true net power inserted in the SRK/T implant power calculation formula was not significantly different from zero. The percentages of eyes within ± 0.50 D and ± 1.00 D of the refractive prediction error of this method were 67.6% and 86.5%, respectively. Mean true net power inserted in the SRK/T formula can be used to calculate directly IOL power after myopic refractive surgery.     

New approaches to direct gradient analysis using environmental scalars and statistical curve-fitting procedures

The conceptual framework of direct gradient analysis (DGA) is discussed in relation to the functional, factorial approach to vegetation. Both approaches use abstract simplified environment gradients with which to correlate vegetation response. Environmental scalars based on physical process models of environment and/or known biological growth processes can be incorporated to make analyses less location specific. An example of an environmental scalar (radiation index) for converting aspect and slope measurements to the more biologically relevant radiation input at a site is given. The problem of the shape of species response curves to environmental gradients is examined using a sample of 1 286 plots from eucalypt forest in southern New South Wales. An important conclusion is that skewed or bimodal response curves may be due to unsatisfactory distribution of observations and/or unrecognized environmental factors. The use of Generalized Linear Modelling (GLM) as a method for providing a statistical basis for DGA is presented. Analyses using GLM, and presence/absence data are presented for a range of eucalypt species (Eucalyptus rossii, E. dalrympleana, E. fastigata etc.). Successful prediction of species distributions (realized niches) can be achieved with mean annual temperature, mean annual rainfall, radiation index and geology. Quadratic terms are required in many cases, indicating bell-shaped response curves. The major variability associated with species niches is shown to be related to a limited number (4) of environmental factors. DGA with biologically relevant scalars and appropriate statistical methods is suitable for studying many problems of species' realized niches and plant community composition.     

The ranging behaviour of a large sexually dimorphic herbivore in response to seasonal and annual environmental variation

The allometric relationships of body size play a principle role in determining how large herbivores respond to the marked spatial and temporal heterogeneity of the savanna biome. Using location data collected over an 8‐year period from five distinct study sites, we investigated the influence of environmental variation (using phenological and rainfall data) on the ranging behaviour of the African elephant (Loxodonta africana), a species that exhibits pronounced sexual dimorphism. Both sexes expanded their annual ranges during years of high rainfall and contracted their ranges during periods of resource scarcity, concurring with the hypothesis that abiotic factors dictate the distribution of large generalist herbivores at the landscape scale. However, female elephant did not exhibit the same consistent response to rainfall at the seasonal scale. Furthermore, male elephant demonstrated a reduction in their daily displacement distances during the dry winter season, and altered their movement rates on the basis of seasonal rainfall. These results suggest that male elephant are able to consistently adapt their movement behaviour according to forage quality and abundance. Smaller‐bodied female elephant on the other hand, are unlikely to exhibit the same flexibility in their ranging behaviour because of their higher relative nutritional demands, lower tolerance to fibrous forage and the social and energetic constraints of group living with juveniles. Our study highlights the major role that body size and sociality plays in the decision making of sexually dimorphic herbivores. These differences can have important implications for effective conservation and management, particularly with regard to demographic (e.g. survival) and ecological (e.g. habitat use) factors.