Aspects of “fear” in Japanese quail chicks (coturnix coturnix Japonica) genetically selected for different levels of locomotor activity

Domestic chicks selected for high and low locomotor activity in a novel environment have low and high levels of fearfulness, respectively. Using four commonly employed methods of estimating fear, namely emergence, open-field, response to a bell and tonic immobility tests, we found a similar effect in lines of Japanese quail selected for high and low locomotor activity, i.e. the active line appeared the least fearful. The present findings demonstrate that this effect is common to two gallinaceous species and two selection procedures.     

Behavioural and endocrine fear responses in Japanese quail upon presentation of a novel object in the home cage

Most tests used to study fear in birds involve transferring them to a novel environment, which constitutes a bias in studies aiming at identifying the neural correlates of a specific fear-inducing situation. In order to investigate fear in birds with minimum interference by humans, behavioural and endocrine responses to the presentation of a novel object in the home cage were investigated in two lines of Japanese quail divergently selected for long or short duration of tonic immobility, a behavioural index of fear. Presentation of the novel object induced typical fear responses (avoidance of the object, increased pacing and increased plasma corticosterone levels) that were similar in the two lines of quail. Presentation of a novel object in the home cage thus appears to be a suitable stimulus to induce fear reactions in quail, with minimum interference from other motivational systems. The fact that quail of both lines reacted similarly in this test, while they are known to differ greatly in their behavioural responses to other fear-inducing tests, illustrates the multidimensional nature of fear.     

Cerebellum size is related to fear memory and domestication of chickens

Red Junglefowl (Gallus gallus) were selected for divergent levels of fear of humans during eight generations, causing the selection lines to differ in fear levels as well as in the proportional brain and cerebellum masses. Birds from the two lines were then crossed to obtain an F3 intercross in order to study the correlations between brain mass and fear learning. We exposed 105 F3-animals individually to a fear habituation and memory test at 8 days of age, where the reactions to repeated light flashes were assessed on 2 consecutive days. After culling, the absolute and relative sizes of each of four brain regions were measured. Stepwise regression was used to analyse the effects of the size of each brain region on habituation and memory. There were no effects of any brain region on the habituation on day one. However, birds with a larger absolute size of cerebellum had significantly reduced reactions to the fearful stimuli on day two, indicating a better memory of the stimuli. No other regions had significant effects. We conclude that increased cerebellum size may have been important in facilitating chicken domestication, allowing them to adapt to a life with humans.     

Microarray and EST database estimates of mRNA expression levels differ: The protein length versus expression curve forC. elegans

Background  

Various methods for estimating protein expression levels are known. The level of correlation between these methods is only fair, and systematic biases in each of the methods cannot be ruled out. We here investigate systematic biases in the estimation of gene expression rates from microarray data and from abundance within the Expressed Sequence Tag (EST) database. We suggest that length is a significant factor in biases to measured gene expression rates.     

Inferences about linkage disequilibrium.

Existing theory for inferences about linkage disequilibrium is restricted to a measure defined on gametic frequencies. Unless gametic frequencies are directly observable, they are inferred from genotypic frequencies under the assumption of random union of gametes. Primary emphasis in this paper is given to genotypic data, and disequilibrium coefficients are defined for all subsets of two or more of the four genes, two at each of two loci, carried by an individual. Linkage disequilibrium coefficients are defined for genes within and between gametes, and methods of estimating and testing these coefficients are given for gametic data. For genotypic data, when coupling and repulsion double heterozygotes cannot be distinguished. Burrows' composite measure of linkage disequilibrium is discussed. In particular, the estimate for this measure and hypothesis tests based on it are compared to the usual maximum likelihood estimate of gametic linkage disequilibrium, and corresponding likelihood ratio or contingency chi-square tests. General use of the composite measure, whether or not random union of gametes is an appropriate assumption, is recommended. Attention is given to small samples, where the non-normality of gene frequencies will have greatest effect on methods of inference based on normal theory. Even tools such as Fisher's z-transformation for the correlation of gene frequencies are found to perform quite satisfactorily.     

Comparison between two methods of assaying relative microbial activity in marine environments.

Two methods for determining relative microbial activity in the marine environment were compared. In one method, a single concentration of a labeled substrate was used to calculate rates of substrate utilization; in the other, multiple concentrations of the same substrate (heterotrophic activity method) were used to calculate maximum potential substrate utilization rates. These studies were made on 232 seawater and 79 sediment samples taken from a variety of marine environments. The highest correlations between these two methods were seen in the sediment samples tested. The lowest correlation coerfficient seen in the sediment samples was 0.90, and the highest was 0.98. In seawater samples (six studies), the lowest correlation coefficient was 0.77 and the highest was 0.95. The correlation between these two methods was also substrate concentration dependent. Higher correlation coefficients were observed when higher substrate concentrations were used. Under certain conditions, these two methods appear to be comparable for estimating relative levels of microbial activity in the marine environment.     

Comparison between two methods of assaying relative microbial activity in marine environments.

Two methods for determining relative microbial activity in the marine environment were compared. In one method, a single concentration of a labeled substrate was used to calculate rates of substrate utilization; in the other, multiple concentrations of the same substrate (heterotrophic activity method) were used to calculate maximum potential substrate utilization rates. These studies were made on 232 seawater and 79 sediment samples taken from a variety of marine environments. The highest correlations between these two methods were seen in the sediment samples tested. The lowest correlation coerfficient seen in the sediment samples was 0.90, and the highest was 0.98. In seawater samples (six studies), the lowest correlation coefficient was 0.77 and the highest was 0.95. The correlation between these two methods was also substrate concentration dependent. Higher correlation coefficients were observed when higher substrate concentrations were used. Under certain conditions, these two methods appear to be comparable for estimating relative levels of microbial activity in the marine environment.     

Behavioural evaluation of methods for assessing fear responses in weaned pigs

Models of anxiety and fear of novelty were evaluated using correlations and principal component analysis. A total of 84 pigs (LandracexYorkshire) from nine different litters were subjected to a tonic immobility (TI) test at the age of 2.5 weeks, an elevated plus-maze (EPM) at the age of 6 weeks, a light/dark (L/D) exploration test at the age of 7 weeks and an open-field (OF) test at the age of 8 weeks.The first component from the principal component analysis had the highest correlation with number of entries into open arms in the EPM but was also highly correlated to variables from the other three tests confirming a common aversion-related element in the four experimental tests. The second component was negatively correlated with percent entries into and time spent on open arms in the EPM, but positively correlated with the number of entries into closed arms in the same test, number of lines crossed in the OF and time spent in the lit compartment of the L/D test. The last point illustrates a negative relationship between "anxiety" and "activity" in the EPM and OF. To achieve purer measures of fear of novelty and activity in the tests, the components were rotated using the Varimax criterion. The rotated factor pattern demonstrated a simple structure where variables related to "anxiety" or "fear of novelty" (i.e., percent entries into open arms and time spent on open arms of the EPM) had the highest loading on factor 1, whereas variables related to activity (i.e., number of entries into the closed arms in the EPM, number of lines crossed in the OF and time spent in the lit compartment of the L/D test) had the highest loading on factor 2. TI duration loaded more strongly on factor 1 ("fear of novelty") than on factor 2 ("activity"), but did not represent any pure measure of either fear of novelty or activity.In conclusion, all of the test variables were related to one another. Open-arm avoidance represented the purest measure of fear of novelty, whereas entries into closed arms and number of lines crossed in the OF were the purest measures of activity. The EPM appeared to provide the best way to separate the fear of novelty and activity-related elements, indicating that the EPM may be a useful behavioural model of fear of novelty or avoidance in pigs.     

Selection for tonic immobility duration does not affect the response to novelty in quail

Genetic selection on a single fear test, the tonic immobility test, seems to result in selection on fearfulness, i.e. the propensity to exhibit fear responses, whatever the fear tests used. However, the conception of fear as a single variable has been challenged by the recognition that fear is multidimensional. This study was designed to test whether genetic selection on a classic index of fear in birds, tonic immobility duration, is accompanied by changes in the response to a single dimension of fear – novelty.Two lines of quail divergently selected for long (LTI) or short (STI) duration of tonic immobility were exposed to a novel object in their home cage. Quail of both lines showed typical fear reactions in response to novelty but there was no difference between lines. We conclude that genetic selection for tonic immobility duration does not affect all dimensions of fear, notably not novelty. Further studies are needed to investigate the dimensions of fear on which the two lines of quail could have been selected.     

Selection for contextual fear conditioning affects anxiety-like behaviors and gene expression

Conditioned fear and anxiety-like behaviors have many similarities at the neuroanatomical and pharmacological levels, but their genetic relationship is less well defined. We used short-term selection for contextual fear conditioning (FC) to produce outbred mouse lines with robust genetic differences in FC. The high and low selected lines showed differences in fear learning that were stable across various training parameters and were not secondary to differences in sensitivity to the unconditioned stimulus (foot shock). They also showed a divergence in fear potentiated startle, indicating that differences induced by selection generalized to another measure of fear learning. However, there were no differences in performance in a Pavlovian approach conditioning task or the Morris water maze, indicating no change in general learning ability. The high fear learning line showed greater anxiety-like behavior in the open field and zero maze, confirming a genetic relationship between FC and anxiety-like behavior. Gene expression analysis of the amygdala and hippocampus identified genes that were differentially expressed between the two lines. Quantitative trait locus (QTL) analysis identified several chromosomal regions that may underlie the behavioral response to selection; cis-acting expression QTL were identified in some of these regions, possibly identifying genes that underlie these behavioral QTL. These studies support the validity of a broad genetic construct that includes both learned fear and anxiety and provides a basis for further studies aimed at gene identification.     

Fearfulness in red junglefowl and domesticated White Leghorn chickens

It may be hypothesised that reduced fearfulness has been a major target of selection during domestication. We tested 20 domesticated White Leghorn (WL) chickens and their ancestors, red junglefowl (RJF), in four different fear tests (Open Field, Novel Object, Aerial Predator, and Fear for Humans). The tests were designed to measure reactions to different types of potentially fearful stimuli. The correlations between durations of the same four variables from each of the tests (Stand/sit alert, Locomotion, Fly/jump, and Vocalisation) were analysed with principal components analysis (PCA). In the PCA, 33.5% of the variation in responses was explained by a single factor, interpreted as a general fear factor. Higher scores on this were related to stronger fear reactions. Red junglefowl scored significantly higher than White Leghorns on this factor, and also had a longer latency to feed in the Fear of Humans-test, used as an independent measure of fear in the same tests. The results suggest that selection for low fearfulness has been an important element of domestication.     

Fear and stress reactions in two species of duck and their hybrid

Susceptibility to fear and stress has often been studied in birds using selection experiments. Crosses between different species of the same genus have also been used to study the type of transmission observed for "fixed action patterns." In this experiment we used a cross between two species (male muscovy and female pekin ducks) to study the genetic transmission of various characteristics of fear reactions and adrenal activity. Males of the three genetic types (two parental species and the hybrid) were submitted to tonic immobility and fear of man tests. Blood was collected for corticosterone assay before and after physiological stress or injection of 5 microg/kg of immediate synacthen (ACTH agonist). The muscovy duck showed lower levels of fear reactions than the pekin duck in the majority of behavioral tests (six of eight). Corticosterone levels were also nearly always the lowest in muscovy ducks (five of six). Generally speaking, the muscovy duck appeared to be less fearful and less susceptible to stress than the pekin duck. The mule duck was similar to one parent, midway between the two, or showed heterosis for fear of man at 10 weeks of age (more fearful than the two parents). Corticosterone levels were midway between the two parents in the mule duck with only one exception, i.e., where the pekin duck was dominant. The existence of heterosis for fear is surprising, as this character is classically considered to be submitted to stabilizing selection. The transmission of corticosterone levels and other fear characteristics is, however, compatible with stabilizing selection. The results are discussed in terms of adaptability.     

Estimation of covariance matrix of multivariate longitudinal data using modified Choleksky and hypersphere decompositions

Linear models are typically used to analyze multivariate longitudinal data. With these models, estimating the covariance matrix is not easy because the covariance matrix should account for complex correlated structures: the correlation between responses at each time point, the correlation within separate responses over time, and the cross-correlation between different responses at different times. In addition, the estimated covariance matrix should satisfy the positive definiteness condition, and it may be heteroscedastic. However, in practice, the structure of the covariance matrix is assumed to be homoscedastic and highly parsimonious, such as exchangeable or autoregressive with order one. These assumptions are too strong and result in inefficient estimates of the effects of covariates. Several studies have been conducted to solve these restrictions using modified Cholesky decomposition (MCD) and linear covariance models. However, modeling the correlation between responses at each time point is not easy because there is no natural ordering of the responses. In this paper, we use MCD and hypersphere decomposition to model the complex correlation structures for multivariate longitudinal data. We observe that the estimated covariance matrix using the decompositions is positive-definite and can be heteroscedastic and that it is also interpretable. The proposed methods are illustrated using data from a nonalcoholic fatty liver disease study.     

ANALYSIS OF THE GENETIC STRUCTURE OF LIFE HISTORY OF DROSOPHILA MELANOGASTER USING RECOMBINANT EXTRACTED LINES

A model for the evolution of senescence known as “antagonistic pleiotropy” makes the specific prediction that there should be a negative genetic correlation between early- and late-age traits associated with fitness. This model has previously been tested by classical quantitative-genetic means including sib-analysis and artificial selection. We used the approach of chromosome extraction, which has both advantages and disadvantages compared to classical techniques, to test the model further. From four isogenic lines of Drosophila melanogaster, four sets of recombinant extracted lines were constructed using standard balancer-chromosome techniques. The four parental lines and 53 recombinants were reared under controlled laboratory conditions and isolated as pairs for scoring daily fecundity and longevity. Even though the design is not optimal for estimating classical components of genetic variance, it afforded a uniquely direct test of the magnitude of environmental covariances, while giving a detailed genetic picture of part of the genome. There were clear differences among the recombinant series in the distribution of mean longevity and early fecundity. The genetic correlation between early fecundity (sum of egg production for the first five days posteclosion) and female longevity was significantly negative in only one of the recombinant series. When all lines were considered together, the phenotypic correlation between these traits was significantly negative (P < 0.02), while the broad-sense genetic correlation was –0.219 (P < 0.11). This result may be viewed as weakly consistent with the model of antagonistic pleiotropy, but other aspects of the data are at odds with the model.     

Ease of capture in lines of Japanese quail (Coturnix japonica) subjected to contrasting selection for fear or sociability

Japanese quail (Coturnix japonica) of lines, which have been subjected to contrasting selection for duration of the tonic immobility (TI) reaction or social reinstatement (SR) behaviour over many generations show corresponding differences in underlying fearfulness and sociality. As fearfulness and sociality are particularly influential traits in domesticated species, the finding that such traits respond to artificial selection may have important implications for poultry welfare and performance. However, it is not known if or how such selection has influenced human-animal interactions. The present experiment investigated the influence of fearfulness and SR behaviour on the ease with which birds could be caught and handled. Birds of lines selected for duration of the TI response or SR behaviour were reared in mixed line groups (LTI and STI or HSR and LSR) of 491 and 346 birds, respectively, until 6 weeks of age. When the birds were 2, 4, and 6 weeks of age, they were caught one by one and their individual capture ranks noted. In the group of birds selected for duration of the TI response, birds selected of the line selected for short duration of TI were caught before those selected for long duration of the response. In the group of birds selected for SR motivation, birds of the high line were caught before their low lines counterparts. Coefficients of concordance between capture ranks were significant and capture ranks did not differ significantly across ages. These results imply that selection for low levels of fear or high levels of sociality produces animals that are less disturbed by human interventions than animals selected for the opposite traits. The greater ease of capture of low fear line birds than high fear line birds may be explained by reduced fear of humans. The fact that the birds selected for high levels of SR behaviour are easier to catch than birds selected for low levels of sociality is less readily explicable. One hypothesis is that HSR line chicks tend to be more strongly imprinted on each other and the human caretaker. However, SR behaviour is highly species specific in both lines, existing evidence for line differences in social discrimination is limited and birds of the two lines show similar duration of the TI response. Despite this, whatever their underlying causation, these results demonstrate that genetic selection can be used to reduce negative reactions to human beings and may be of value in the improvement of both animal welfare and productivity.     

Estimating Behavioral Transition Rates: Problems and Solutions

Continuous time Markov chain (CTMC) models offer ethologists a powerful tool. The methods are based on well-established procedures for estimating the rates at which one state (e.g. resting) changes to some other set of states (e.g. feeding, fighting, etc.). Unfortunately, ethological data typically differ in a very critical manner from the type of data to which these methods are usually applied: ethological data are usually heavily censored in the sense that each behavioral state shows frequent transitions to several other possible states. This occurs when several competing processes can each end a bout.
We used computer simulation of various behavioral models with known transition rates to investigate the unknown performance of four of the most popular statistical tests for screening data prior to application of CTMC models; this included a modification of one of these tests derived under the assumption of random censoring. Two of the four tests failed completely and would result in rejection of nearly all data even if the model did fit the assumptions of the CTMC methods. Only Barlow's total-time-on test performed with an acceptable α error rate under all conditions. None of the tests were particularly effective at detecting certain types of departures from the CTMC assumptions.
Guidelines are given as to how much confidence should be attached to apparent changes in transition rates.     

Proliferation assays for estrogenicity testing with high predictive value for the in vivo uterotrophic effect

Proliferation assays based on human cell lines are the most used in vitro tests to determine estrogenic properties of compounds. Our objective was to characterise to what extent these in vitro tests provide alternatives for the in vivo Allen and Doisy test, a uterotrophic assay in immature or ovariectomised rodents with uterus weight as a crucial read-out parameter. In the present study four different human cell lines derived from three different female estrogen-sensitive tissues, i.e. breast (MCF-7/BOS and T47D), endometrial (ECC-1) and ovarian (BG-1) cells, were characterised by investigating their relative ERα and ERβ amounts, as the ERα/ERβ ratio is a dominant factor determining their estrogen-dependent proliferative responses. All four cell lines clearly expressed the ERα type and a very low but detectable amount of ERβ on both the mRNA and protein level, with the T47D cell line expressing the highest level of the ERβ type. Subsequently, a set of reference compounds representing different modes of estrogen action and estrogenic potency were used to investigate the proliferative response in the four cell lines, to determine which cell line most accurately predicts the effect observed in vivo. All four cell lines revealed a reasonable to good correlation with the in vivo uterotrophic effect, with the correlation being highest for the MCF-7/BOS cell line (R2=0.85). The main differences between the in vivo uterotrophic assay and the in vitro proliferation assays were observed for tamoxifen and testosterone. The proliferative response of the MCF-7/BOS cells to testosterone was partially caused by its conversion to estradiol by aromatase or via androstenedione to estrone. It is concluded that of the four cell lines tested, the best assay to include in an integrated testing strategy for replacement of the in vivo uterotrophic assay is the human MCF-7/BOS breast cancer cell line.     

Two-sample tests for comparing intra-individual genetic sequence diversity between populations

Consider a study of two groups of individuals infected with a population of a genetically related heterogeneous mixture of viruses, and multiple viral sequences are sampled from each person. Based on estimates of genetic distances between pairs of aligned viral sequences within individuals, we develop four new tests to compare intra-individual genetic sequence diversity between the two groups. This problem is complicated by two levels of dependency in the data structure: (i) Within an individual, any pairwise distances that share a common sequence are positively correlated; and (ii) for any two pairings of individuals which share a person, the two differences in intra-individual distances between the paired individuals are positively correlated. The first proposed test is based on the difference in mean intra-individual pairwise distances pooled over all individuals in each group, standardized by a variance estimate that corrects for the correlation structure using U-statistic theory. The second procedure is a nonparametric rank-based analog of the first test, and the third test contrasts the set of subject-specific average intra-individual pairwise distances between the groups. These tests are very easy to use and solve correlation problem (i). The fourth procedure is based on a linear combination of all possible U-statistics calculated on independent, identically distributed sequence subdatasets, over the two levels (i) and (ii) of dependencies in the data, and is more complicated than the other tests but can be more powerful. Although the proposed methods are empirical and do not fully utilize knowledge from population genetics, the tests reflect biology through the evolutionary models used to derive the pairwise sequence distances. The new tests are evaluated theoretically and in a simulation study, and are applied to a dataset of 200 HIV sequences sampled from 21 children.     

Potential of microsatellites for individual assignment: the North Atlantic redfish (genus Sebastes) species complex as a case study

We used the four redfish taxa (genus Sebastes) from the North Atlantic to evaluate the potential of multilocus genotype information obtained from microsatellites in assigning individuals at two different levels of group divergence. We first tested the hypothesis that microsatellites can diagnostically discriminate individual redfish from different groups. Second, we compared two different methods to quantify the effect of number of loci and likelihood stringency levels on the power of microsatellites for redfish group membership. The potential of microsatellites to discriminate individuals from different taxa was illustrated by a shared allele distance tree in which four major clusters corresponding to each taxa were defined. Concomitant with this strong discrimination, microsatellites also proved to be powerful in reclassifying specimens to the taxon of origin, using either an empirical or simulated method of estimating assignment success. By testing for the effect of both the number of loci and the level of stringency on the assignment success, we found that 95% of all specimens were still correctly reclassified with only four loci at the most commonly used criterion of log0. In contrast, the results obtained at the population level within taxa highlighted several problems of assignment that may occur at low levels of divergence. Namely, a drastic decrease of success with increasing stringency illustrated the lack of power of our set of loci. Strong discrepancy was observed between results obtained from the empirical and simulated methods. Finally, the highest assignment success was obtained when reducing the number of loci used, an observation previously reported in studies of human populations.     

Human handling and presentation of a novel object evoke independent dimensions of fear in Japanese quail

Fear is a concept comprising several dimensions, but the nature of these dimensions and the relationships between them remain elusive. To investigate these dimensions in birds, we have used two genetic lines of quail divergently selected on tonic immobility duration, a behavioural index of fear. These two lines differ in their behavioural response to some, but not all, fear-inducing situations. In the present study, we investigated the contribution of human intervention in the differentiation between the two lines. To do this, fear responses towards a novel object were compared between lines in three conditions: (1) in the home cage without any human intervention, (2) in the home cage after human handling and (3) after placement in a novel environment by human handling. Fear behaviour differed between lines after human handling, with or without placement in a novel environment, but presentation of a novel object in the home cage without any human intervention induced similar fear responses in the two lines of quail. These results lead us to suggest that in quail, human intervention evokes a dimension of fear that differs from that evoked by sudden presentation of a novel object, in that these two dimensions may be selected independently.