The effect of gut microbiota elimination in Drosophila melanogaster: A how‐to guide for host–microbiota studies

In recent years, there has been a surge in interest in the effects of the microbiota on the host. Increasingly, we are coming to understand the importance of the gut microbiota in modulating host physiology, ecology, behavior, and evolution. One method utilized to evaluate the effect of the microbiota is to suppress or eliminate it, and compare the effect on the host with that of untreated individuals. In this study, we evaluate some of these commonly used methods in the model organism, Drosophila melanogaster. We test the efficacy of a low‐dose streptomycin diet, egg dechorionation, and an axenic or sterile diet, in the removal of gut bacteria within this species in a fully factorial design. We further determine potential side effects of these methods on host physiology by performing a series of standard physiological assays. Our results showed that individuals from all treatments took significantly longer to develop, and weighed less, compared to normal flies. Males and females that had undergone egg dechorionation weighed significantly less than streptomycin reared individuals. Similarly, axenic female flies, but not males, were much less active when analyzed in a locomotion assay. All methods decreased the egg to adult survival, with egg dechorionation inducing significantly higher mortality. We conclude that low‐dose streptomycin added to the dietary media is more effective at removing the gut bacteria than egg dechorionation and has somewhat less detrimental effects to host physiology. More importantly, this method is the most practical and reliable for use in behavioral research. Our study raises the important issue that the efficacy of and impacts on the host of these methods require investigation in a case‐by‐case manner, rather than assuming homogeneity across species and laboratories.     

Determining population structure and hybridization for two iris species

Identifying processes that promote or limit gene flow can help define the ecological and evolutionary history of a species. Furthermore, defining those factors that make up “species boundaries” can provide a definition of the independent evolutionary trajectories of related taxa. For many species, the historic processes that account for their distribution of genetic variation remain unresolved. In this study, we examine the geographic distribution of genetic diversity for two species of Louisiana Irises, Iris brevicaulis and Iris fulva. Specifically, we asked how populations are structured and if population structure coincides with potential barriers to gene flow. We also asked whether there is evidence of hybridization between these two species outside Louisiana hybrid zones. We used a genotyping‐by‐sequencing approach and sampled a large number of single nucleotide polymorphisms across these species' genomes. Two different population assignment methods were used to resolve population structure in I. brevicaulis; however, there was considerably less population structure in I. fulva. We used a species tree approach to infer phylogenies both within and between populations and species. For I. brevicaulis, the geography of the collection locality was reflected in the phylogeny. The I. fulva phylogeny reflected much less structure than detected for I. brevicaulis. Lastly, combining both species into a phylogenetic analysis resolved two of six populations of I. brevicaulis that shared alleles with I. fulva. Taken together, our results suggest major differences in the level and pattern of connectivity among populations of these two Louisiana Iris species.     

In vivo electrochemical evidence for simultaneous 5-HT and histamine release in the rat substantia nigra pars reticulata following medial forebrain bundle stimulation

Exploring the mechanisms of serotonin [5-hydroxytryptamine (5-HT)] in the brain requires an in vivo method that combines fast temporal resolution with chemical selectivity. Fast-scan cyclic voltammetry is a technique with sufficient temporal and chemical resolution for probing dynamic 5-HT neurotransmission events; however, traditionally it has not been possible to probe in vivo 5-HT mechanisms. Recently, we optimized fast-scan cyclic voltammetry for measuring 5-HT release and uptake in vivo in the substantia nigra pars reticulata (SNR) with electrical stimulation of the dorsal raphe nucleus (DRN) in the rat brain. Here, we address technical challenges associated with rat DRN surgery by electrically stimulating 5-HT projections in the medial forebrain bundle (MFB), a more accessible anatomical location. MFB stimulation elicits 5-HT in the SNR; furthermore, we find simultaneous release of an additional species. We use electrochemical and pharmacological methods and describe physiological, anatomical and independent chemical analyses to identify this species as histamine. We also show pharmacologically that increasing the lifetime of extracellular histamine significantly decreases 5-HT release, most likely because of increased activation of histamine H-3 receptors that inhibit 5-HT release. Despite this, under physiological conditions, we find by kinetic comparisons of DRN and MFB stimulations that the simultaneous release of histamine does not interfere with the quantitative 5-HT concentration profile. We therefore present a novel and robust electrical stimulation of the MFB that is technically less challenging than DRN stimulation to study 5-HT and histamine release in the SNR.     

Calibration of multivariate scatter plots for exploratory analysis of relations within and between sets of variables in genomic research

The scatter plot is a well known and easily applicable graphical tool to explore relationships between two quantitative variables. For the exploration of relations between multiple variables, generalisations of the scatter plot are useful. We present an overview of multivariate scatter plots focussing on the following situations. Firstly, we look at a scatter plot for portraying relations between quantitative variables within one data matrix. Secondly, we discuss a similar plot for the case of qualitative variables. Thirdly, we describe scatter plots for the relationships between two sets of variables where we focus on correlations. Finally, we treat plots of the relationships between multiple response and predictor variables, focussing on the matrix of regression coefficients. We will present both known and new results, where an important original contribution concerns a procedure for the inclusion of scales for the variables in multivariate scatter plots. We provide software for drawing such scales. We illustrate the construction and interpretation of the plots by means of examples on data collected in a genomic research program on taste in tomato.     

Evidence for rapid evolution of phenology in an invasive grass

Evolutionary dynamics of integrative traits such as phenology are predicted to be critically important to range expansion and invasion success, yet there are few empirical examples of such phenomena. In this study, we used multiple common gardens to examine the evolutionary significance of latitudinal variation in phenology of a widespread invasive species, the Asian short‐day flowering annual grass Microstegium vimineum. In environmentally controlled growth chambers, we grew plants from seeds collected from multiple latitudes across the species' invasive range. Flowering time and biomass were both strongly correlated with the latitude of population origin such that populations collected from more northern latitudes flowered significantly earlier and at lower biomass than populations from southern locations. We suggest that this pattern may be the result of rapid adaptive evolution of phenology over a period of less than one hundred years and that such changes have likely promoted the northward range expansion of this species. We note that possible barriers to gene flow, including bottlenecks and inbreeding, have apparently not forestalled evolutionary processes for this plant. Furthermore, we hypothesize that evolution of phenology may be a widespread and potentially essential process during range expansion for many invasive plant species.     

Immobilization strategies for single-chain antibody microarrays

Sandwich ELISA microarrays have great potential for validating disease biomarkers. Each ELISA relies on robust-affinity reagents that retain activity when immobilized on a solid surface or when labeled for detection. Single-chain antibodies (scFv) are affinity reagents that have greater potential for high-throughput production than traditional IgG. Unfortunately, scFv are typically less active than IgG following immobilization on a solid surface and not always suitable for use in sandwich ELISAs. We therefore investigated different immobilization strategies and scFv constructs to determine a more robust strategy for using scFv as ELISA reagents. Two promising strategies emerged from these studies: (i) the precapture of epitope-tagged scFv using an antiepitope antibody and (ii) the direct printing of a thioredoxin (TRX)/scFv fusion protein on glass slides. Both strategies improved the stability of immobilized scFv and increased the sensitivity of the scFv ELISA microarray assays, although the antiepitope precapture method introduced a risk of reagent transfer. Using the direct printing method, we show that scFv against prostate-specific antigen (PSA) are highly specific when tested against 21 different IgG-based assays. In addition, the scFv microarray PSA assay gave comparable quantitative results (R(2) = 0.95) to a commercial 96-well ELISA when tested using human serum samples. In addition, we find that TRX-scFv fusions against epidermal growth factor and toxin X have good LOD. Overall, these results suggest that minor modifications of the scFv construct are sufficient to produce reagents that are suitable for use in multiplex assay systems.     

Mimicry between unequally defended prey can be parasitic: evidence for quasi-Batesian mimicry

The nature of signal mimicry between defended prey (known as Müllerian mimicry) is controversial. Some authors assert that it is always mutualistic and beneficial, whilst others speculate that less well defended prey may be parasitic and degrade the protection of their better defended co-mimics (quasi-Batesian mimicry). Using great tits (Parus major) as predators of artificial prey, we show that mimicry between unequally defended co-mimics is not mutualistic, and can be parasitic and quasi-Batesian. We presented a fixed abundance of a highly defended model and a moderately defended dimorphic (mimic and distinct non-mimetic) species, and varied the relative frequency of the two forms of the moderately defended prey. As the mimic form increased in abundance, per capita predation on the model-mimic pair increased. Furthermore, when mimics were rare they gained protection from predation but imposed no co-evolutionary pressure on models. We found that the feeding decisions of the birds were affected by their individual toxic burdens, consistent with the idea that predators make foraging decisions which trade-off toxicity and nutrition. This result suggests that many prey species that are currently assumed to be in a simple mutualistic mimetic relationship with their co-mimic species may actually be engaged in an antagonistic co-evolutionary process.     

Improved methods for estimating abundance and related demographic parameters from mark‐resight data

Over the past decade, there has been much methodological development for the estimation of abundance and related demographic parameters using mark‐resight data. Often viewed as a less‐invasive and less‐expensive alternative to conventional mark recapture, mark‐resight methods jointly model marked individual encounters and counts of unmarked individuals, and recent extensions accommodate common challenges associated with imperfect detection. When these challenges include both individual detection heterogeneity and an unknown marked sample size, we demonstrate several deficiencies associated with the most widely used mark‐resight models currently implemented in the popular capture‐recapture freeware Program MARK. We propose a composite likelihood solution based on a zero‐inflated Poisson log‐normal model and find the performance of this new estimator to be superior in terms of bias and confidence interval coverage. Under Pollock's robust design, we also extend the models to accommodate individual‐level random effects across sampling occasions as a potentially more realistic alternative to models that assume independence. As a motivating example, we revisit a previous analysis of mark‐resight data for the New Zealand Robin (Petroica australis) and compare inferences from the proposed estimators. For the all‐too‐common situation where encounter rates are low, individual detection heterogeneity is non‐negligible, and the number of marked individuals is unknown, we recommend practitioners use the zero‐inflated Poisson log‐normal mark‐resight estimator as now implemented in Program MARK.     

Assessment of 3D models for allergen research

Allergenic proteins must crosslink specific IgE molecules, bound to the surface of mast cells and basophils, to stimulate an immune response. A structural understanding of the allergen–IgE interface is needed to predict cross‐reactivities between allergens and to design hypoallergenic proteins. However, there are less than 90 experimentally determined structures available for the approximately 1500 sequences of allergens and isoallergens cataloged in the Structural Database of Allergenic Proteins. To provide reliable structural data for the remaining proteins, we previously produced more than 500 3D models using an automated procedure, with strict controls on template choice and model quality evaluation. Here, we assessed how well the fold and residue surface exposure of 10 of these models correlated with recently published experimental 3D structures determined by X‐ray crystallography or NMR. We also discuss the impact of intrinsically disordered regions on the structural comparison and epitope prediction. Overall, for seven allergens with sequence identities to the original templates higher than 27%, the backbone root‐mean square deviations were less than 2 Å between the models and the subsequently determined experimental structures for the ordered regions. Further, the surface exposure of the known IgE epitopes on the models of three major allergens, from peanut (Ara h 1), latex (Hev b 2), and soy (Gly m 4), was very similar to the experimentally determined structures. For the three remaining allergens with lower sequence identities to the modeling templates, the 3D folds were correctly identified. However, the accuracy of those models is not sufficient for a reliable epitope mapping. © Proteins 2013. © 2012 Wiley Periodicals, Inc.     

Inclusive fitness is an indispensable approximation for understanding organismal design

For some decades most biologists interested in design have agreed that natural selection leads to organisms acting as if they are maximizing a quantity known as “inclusive fitness.” This maximization principle has been criticized on the (uncontested) grounds that other quantities, such as offspring number, predict gene frequency changes accurately in a wider range of mathematical models. Here, we adopt a resolution offered by Birch, who accepts the technical difficulties of establishing inclusive fitness maximization in a fully general model, while concluding that inclusive fitness is still useful as an organizing framework. We set out in more detail why inclusive fitness is such a practical and powerful framework, and provide verbal and conceptual arguments for why social biology would be more or less impossible without it. We aim to help mathematicians understand why social biologists are content to use inclusive fitness despite its theoretical weaknesses. Here, we also offer biologists practical advice for avoiding potential pitfalls.     

Self-assembly DNA-conjugated polymer for detection of single nucleotide polymorphism

We developed a self-assembly DNA-conjugated polymer based on polyacrylic acid (PAA) for DNA chip fabrication. A 20-mer single-stranded DNA (ssDNA, probe-1), and 3-(2-pyridyldithio)propionyl hydrazide (PDPH), for promoting self-assembled immobilization, were both covalently attached to PAA as sidechains. This DNA-conjugated PAA was then spontaneously immobilized on a gold substrate. Probe-1 on the immobilized polymer was hybridized to a 34-mer ssDNA (probe-2), which had the sequence desired for analyzing the target DNA. The fluorescence intensity after incubating the P-1 DNA-conjugated polymer with probe-2 DNA was much higher than with control sequence in the first hybridization. The interactions between target DNA and the DNA-conjugated PAA were investigated by fluorescence measurement. The interaction of fully matched target DNA with this immobilized DNA conjugated polymer has been studied at different ion strength conditions. SNP sequences as targets showed less than 15% the intensity of fully matched target DNA in the second hybridization, indicating that the gold surfaces coated with the DNA-conjugated PAA was highly specific to fully matched DNA. The DNA-conjugated PAA immobilized on a gold substrate is characterized by reduced nonspecific adsorption, due to less electrostatic repulsion as well as the polymer coating. Therefore, DNA-conjugated PAA can be used for probe DNA immobilization method.     

Isolation by oceanographic distance explains genetic structure for Macrocystis pyrifera in the Santa Barbara Channel

Ocean currents are expected to be the predominant environmental factor influencing the dispersal of planktonic larvae or spores; yet, their characterization as predictors of marine connectivity has been hindered by a lack of understanding of how best to use oceanographic data. We used a high-resolution oceanographic model output and Lagrangian particle simulations to derive oceanographic distances (hereafter called transport times) between sites studied for Macrocystis pyrifera genetic differentiation. We build upon the classical isolation-by-distance regression model by asking how much additional variability in genetic differentiation is explained when adding transport time as predictor. We explored the extent to which gene flow is dependent upon seasonal changes in ocean circulation. Because oceanographic transport between two sites is inherently asymmetric, we also compare the explanatory power of models using the minimum or the mean transport times. Finally, we compare the direction of connectivity as estimated by the oceanographic model and genetic assignment tests. We show that the minimum transport time had higher explanatory power than the mean transport time, revealing the importance of considering asymmetry in ocean currents when modelling gene flow. Genetic assignment tests were much less effective in determining asymmetry in gene flow. Summer-derived transport times, in particular for the month of June, which had the strongest current speed, greatest asymmetry and highest spore production, resulted in the best-fit model explaining twice the variability in genetic differentiation relative to models that use geographic distance or habitat continuity. The best overall model also included habitat continuity and explained 65% of the variation in genetic differentiation among sites.     

Sources of (co)variation in alternative siring routes available to male great tits (Parus major)

Males of socially monogamous species can increase their siring success via within‐pair and extra‐pair fertilizations. In this study, we focused on the different sources of (co)variation between these siring routes, and asked how each contributes to total siring success. We quantified the fertilization routes to siring success, as well as behaviors that have been hypothesized to affect siring success, over a five‐year period for a wild population of great tits Parus major. We considered siring success and its fertilization routes as “interactive phenotypes” arising from phenotypic contributions of both members of the social pair. We show that siring success is strongly affected by the fecundity of the social (female) partner. We also demonstrate that a strong positive correlation between extra‐pair fertilization success and paternity loss likely constrains the evolution of these two routes. Moreover, we show that more explorative and aggressive males had less extra‐pair fertilizations, whereas more explorative females laid larger clutches. This study thus demonstrates that (co)variation in siring routes is caused by multiple factors not necessarily related to characteristics of males. We thereby highlight the importance of acknowledging the multilevel structure of male fertilization routes when studying the evolution of male mating strategies.     

A wireless video camera for viewing tree cavities

ABSTRACT Investigators have used a variety of methods to inspect nest cavities, including wireless battery‐powered video cameras mounted on telescoping poles. Using such a monitoring system to inspect cavities located well above ground can be difficult because the weight of the camera can cause flexing of the telescoping pole, making it difficult to insert the camera into cavity entrances. We constructed a system made from commercially available products that transmits wireless video images from nest cavities, and is both lightweight (198 g) and relatively inexpensive (about $520 US). During a study of Pileated Woodpeckers (Dryocopus pileatus), we inspected more than 100 cavities using our monitoring system and found that images were clear enough to allow us to count eggs and nestlings, and determine the sex of adults and nestlings. Because of its light weight, our wireless camera system allows quick inspection of cavities (typically less than 2 min). Although we used our cavity‐monitoring system to inspect cavities used by Pileated Woodpecker, we believe that the diameter of the camera could be reduced from 5.6 cm to 4.7 cm to allow inspection of cavities with smaller entrances.     

Nonparametric All‐Pairs Multiple Comparisons

Nonparametric all‐pairs multiple comparisons based on pairwise rankings can be performed in the one‐way design with the Steel‐Dwass procedure. To apply this test, Wilcoxon's rank sum statistic is calculated for all pairs of groups; the maximum of the rank sums is the test statistic. We provide exact calculations of the asymptotic critical values (and P‐values, respectively) even for unbalanced designs. We recommend this asymptotic method whenever large sample sizes are present. For small sample sizes we recommend the use of the new statistic according to Baumgartner , Weiss , and Schindler (1998, Biometrics 54 , 1129–1135) instead of Wilcoxon's rank sum for the multiple comparisons. We show that the resultant procedure can be less conservative and, according to simulation results, more powerful than the original Steel‐Dwass procedure. We illustrate the methods with a practical data set.     

Intraspecific morphological variation of the middle ear in the European badger,Meles meles (Carnivora: Mustelidae)

Many studies have been conducted about the information contained in the anatomy of the mammalian middle ear. Most of these only use a few specimens. Thus we aim to provide a quantitative analysis of the intraspecific and interspecific variations of the middle ear, focusing on the auditory bulla. For that purpose, we focused on the mustelids, as a quite generalist taxon and, more specifically, on the European badger, Meles meles. Our study includes two types of statistical methods. We first compared the mean of a subjectively chosen measure between individuals of the same species and between individuals of different species. We then used a multidimensional scaling procedure to cluster individuals according to different measures. We conclude that the middle ear varies effectively less intraspecifically than interspecifically. However, we think that the few anatomical parameters to measure in the auditory bulla involve using more specimens or focusing on geometric morphometrics in studies focusing on middle ear.     

Five interval estimators for proportion ratio under a stratified randomized clinical trial with noncompliance

It is not uncommon that we may encounter a randomized clinical trial (RCT) in which there are confounders which are needed to control and patients who do not comply with their assigned treatments. In this paper, we concentrate our attention on interval estimation of the proportion ratio (PR) of probabilities of response between two treatments in a stratified noncompliance RCT. We have developed and considered five asymptotic interval estimators for the PR, including the interval estimator using the weighted-least squares (WLS) estimator, the interval estimator using the Mantel-Haenszel type of weight, the interval estimator derived from Fieller's Theorem with the corresponding WLS optimal weight, the interval estimator derived from Fieller's Theorem with the randomization-based optimal weight, and the interval estimator based on a stratified two-sample proportion test with the optimal weight suggested elsewhere. To evaluate and compare the finite sample performance of these estimators, we apply Monte Carlo simulation to calculate the coverage probability and average length in a variety of situations. We discuss the limitation and usefulness for each of these interval estimators, as well as include a general guideline about which estimators may be used for given various situations.     

TRAIT COMPENSATION AND SEX‐SPECIFIC AGING OF PERFORMANCE IN MALE AND FEMALE PROFESSIONAL BASKETBALL PLAYERS

Phenotypic traits are often influenced by dynamic resource allocation trade‐offs which, when occurring over the course of individual lifespan, may manifest as trait aging. Although aging is studied for a variety of traits that are closely tied to reproduction or reproductive effort, the aging of multiple traits related to fitness in other ways are less well understood. We took advantage of almost 30 years of data on human whole‐organism performance in the National Basketball Association (USA) to examine trends of aging in performance traits associated with scoring. Given that patterns of aging differ between sexes in other animal species, we also analyzed a smaller dataset on players in the Women's National Basketball Association to test for potential sex differences in the aging of comparable traits. We tested the hypothesis that age‐related changes in a specific aspect of overall performance can be compensated for by elevated expression of another, related aspect. Our analyses suggest that the aging of performance traits used in basketball is generally characterized by senescence in males, whereas age‐related changes in basketball performance are less evident in females. Our data also indicate a different rate of senescence of different performance traits associated with scoring over a male's lifetime.     

Dorsal pattern polymorphism in female Iberian wall lizards: differences in morphology,dorsal coloration,immune response,and reproductive investment

Sex‐specific colour polymorphisms have been extensively documented in many different taxa. When polymorphism in colour pattern is restricted to females, the condition is known as female‐limited pattern polymorphism (FPP), which has been less commonly addressed in vertebrates. FPP is present in several lizard species, although most research on lizards has focused on carotenoid‐ and pteridine‐based coloration and not on melanin‐based polymorphisms. In the present study, we focus on Iberian wall lizards, Podarcis hispanicus, where two female melanin‐based dorsal patterns can be clearly distinguished: striped and reticulated‐blotched. We indirectly tested the hypothesis that selection acts differentially among P. hispanicus female morphs to create alternative morph‐specific phenotypic optima at different levels by investigating whether morphs differ in fitness proxies. We specifically examined whether the two female dorsal pattern morphs differed in adult morphology, dorsal coloration, immune response, reproductive investment, and growth. We did not find a relationship between melanin‐based coloration and hatchling growth and immune response, despite a correlation between these traits possibly being expected as a result of pleiotropy in the melanocortin system. However, our results show that female dorsal morphs in P. hispanicus differ in terms of adult morphology, dorsal coloration, and reproductive investment. Reticulated‐blotched P. hispanicus females had deeper heads and longer femora, less melanin, and more brownish coloration, and also had larger and heavier hatchlings than striped females.