Inheritance of telomere length in a bird

Telomere dynamics are intensively studied in human ageing research and epidemiology, with many correlations reported between telomere length and age-related diseases, cancer and death. While telomere length is influenced by environmental factors there is also good evidence for a strong heritable component. In human, the mode of telomere length inheritance appears to be paternal and telomere length differs between sexes, with females having longer telomeres than males. Genetic factors, e.g. sex chromosomal inactivation, and non-genetic factors, e.g. antioxidant properties of oestrogen, have been suggested as possible explanations for these sex-specific telomere inheritance and telomere length differences. To test the influence of sex chromosomes on telomere length, we investigated inheritance and sex-specificity of telomere length in a bird species, the kakapo (Strigops habroptilus), in which females are the heterogametic sex (ZW) and males are the homogametic (ZZ) sex. We found that, contrary to findings in humans, telomere length was maternally inherited and also longer in males. These results argue against an effect of sex hormones on telomere length and suggest that factors associated with heterogamy may play a role in telomere inheritance and sex-specific differences in telomere length.     

ELA and fertility in American Standardbred horses

We have analysed the effects of ELA alleles and sire-dam ELA incompatibility on two measures of fertility, gestation length and foaling rate, in American Standardbred horses. Using multivariate statistical methods, we corrected for the effects of confounding factors such as dam and sire age, parity, inbreeding, and sire-dam kinship. These analyses revealed substantial differences between Standardbred trotters and pacers in the effects of several confounding factors. There appear to be no ELA effects on gestation length in either trotters or pacers. However our results suggest that there may be ELA effects on foaling rate associated with specific dam alleles, with sire-dam incompatibility, and possibly with specific sire alleles, and that these effects differ between trotters and pacers.     

Clustered environments and randomized genes: a fundamental distinction between conventional and genetic epidemiology

Background

In conventional epidemiology confounding of the exposure of interest with lifestyle or socioeconomic factors, and reverse causation whereby disease status influences exposure rather than vice versa, may invalidate causal interpretations of observed associations. Conversely, genetic variants should not be related to the confounding factors that distort associations in conventional observational epidemiological studies. Furthermore, disease onset will not influence genotype. Therefore, it has been suggested that genetic variants that are known to be associated with a modifiable (nongenetic) risk factor can be used to help determine the causal effect of this modifiable risk factor on disease outcomes. This approach, mendelian randomization, is increasingly being applied within epidemiological studies. However, there is debate about the underlying premise that associations between genotypes and disease outcomes are not confounded by other risk factors. We examined the extent to which genetic variants, on the one hand, and nongenetic environmental exposures or phenotypic characteristics on the other, tend to be associated with each other, to assess the degree of confounding that would exist in conventional epidemiological studies compared with mendelian randomization studies.

Methods and Findings

We estimated pairwise correlations between nongenetic baseline variables and genetic variables in a cross-sectional study comparing the number of correlations that were statistically significant at the 5%, 1%, and 0.01% level (α = 0.05, 0.01, and 0.0001, respectively) with the number expected by chance if all variables were in fact uncorrelated, using a two-sided binomial exact test. We demonstrate that behavioural, socioeconomic, and physiological factors are strongly interrelated, with 45% of all possible pairwise associations between 96 nongenetic characteristics (n = 4,560 correlations) being significant at the p < 0.01 level (the ratio of observed to expected significant associations was 45; p-value for difference between observed and expected < 0.000001). Similar findings were observed for other levels of significance. In contrast, genetic variants showed no greater association with each other, or with the 96 behavioural, socioeconomic, and physiological factors, than would be expected by chance.

Conclusions

These data illustrate why observational studies have produced misleading claims regarding potentially causal factors for disease. The findings demonstrate the potential power of a methodology that utilizes genetic variants as indicators of exposure level when studying environmentally modifiable risk factors.     

Analysis of two components of flight using recombinant inbred lines of Drosophila melanogaster

Complex activities require precise coordination of their components for successful action. The genetic basis underlying coordination of traits may range from relatively static pleiotropic associations to more flexible genetic associations that recombine in phenotypes under continuous selective modification by the environment. Successful flight in insects depends on the precise integration of numerous component physiological processes. Here we examine the genetic basis of two of its components, flight duration and rate. To study flight we created recombinant inbred populations from stocks of this laboratory known for their significantly longer duration flights. A heritable basis for these traits was found and determined to be positively correlated between sexes. Correlations of flight length with rate were negative within sexes, suggesting a trade-off, but were significant in males only. Composite interval mapping using the recombinant inbred (RI2) design was used to locate the QTLs for these traits and test for pleiotropy. Four QTLs affecting duration or wing beat rate were found on chromosomes II and III. Tests for pleiotropy showed some effects on traits of QTLs were common to both sexes while others were sex-specific. No QTL was pleiotropic for both traits, suggesting that correlations between flight duration and rate of wing beat are determined by a combination of linkage and environmental factors.     

Unbiased Functional Clustering of Gene Variants with a Phenotypic-Linkage Network

Groupwise functional analysis of gene variants is becoming standard in next-generation sequencing studies. As the function of many genes is unknown and their classification to pathways is scant, functional associations between genes are often inferred from large-scale omics data. Such data types—including protein–protein interactions and gene co-expression networks—are used to examine the interrelations of the implicated genes. Statistical significance is assessed by comparing the interconnectedness of the mutated genes with that of random gene sets. However, interconnectedness can be affected by confounding bias, potentially resulting in false positive findings. We show that genes implicated through de novo sequence variants are biased in their coding-sequence length and longer genes tend to cluster together, which leads to exaggerated p-values in functional studies; we present here an integrative method that addresses these bias. To discern molecular pathways relevant to complex disease, we have inferred functional associations between human genes from diverse data types and assessed them with a novel phenotype-based method. Examining the functional association between de novo gene variants, we control for the heretofore unexplored confounding bias in coding-sequence length. We test different data types and networks and find that the disease-associated genes cluster more significantly in an integrated phenotypic-linkage network than in other gene networks. We present a tool of superior power to identify functional associations among genes mutated in the same disease even after accounting for significant sequencing study bias and demonstrate the suitability of this method to functionally cluster variant genes underlying polygenic disorders.     

A new look at relationships between size at maturity and asymptotic size

Comparative studies have revealed positive correlations between size at maturity and asymptotic size in several taxa with asymptotic growth after maturity. Using a simple growth model, we show that positive correlations between size at maturity and asymptotic size are predicted for different individuals in the same species if growth costs of reproduction are inversely related to size at maturity. Several processes might lead to higher growth costs of reproduction for smaller individuals; these include effects of body size on competition for resources required for breeding, on the space available within the body cavity for food processing in gravid individuals, and on the costs of transporting eggs or young in relation to the total energy budget. We confirm several key elements of the growth model using data from female Iguana iguana lizards, including the novel assumption that instantaneous growth rates of adults of the same length will be positively related to their length at maturity. These analyses suggest a simple and possibly general explanation for positive correlations between size at maturity and asymptotic size within-and perhaps also among-species that continue to grow after maturity.     

Speed and Diffusion of Kinesin-2 Are Competing Limiting Factors in Flagellar Length-Control Model

Flagellar length control in Chlamydomonas is a tractable model system for studying the general question of organelle size regulation. We have previously proposed that the diffusive return of the kinesin motor that powers intraflagellar transport can play a key role in length regulation. Here, we explore how the motor speed and diffusion coefficient for the return of kinesin-2 affect flagellar growth kinetics. We find that the system can exist in two distinct regimes, one dominated by motor speed and one by diffusion coefficient. Depending on length, a flagellum can switch between these regimes. Our results indicate that mutations can affect the length in distinct ways. We discuss our theory’s implication for flagellar growth influenced by beating and provide possible explanations for the experimental observation that a beating flagellum is usually longer than its immotile mutant. These results demonstrate how our simple model can suggest explanations for mutant phenotypes.     

Developmental perspectives on personality: implications for ecological and evolutionary studies of individual differences

Developmental processes can have major impacts on the correlations in behaviour across contexts (contextual generality) and across time (temporal consistency) that are the hallmarks of animal personality. Personality can and does change: at any given age or life stage it is contingent upon a wide range of experiential factors that occurred earlier in life, from prior to conception through adulthood. We show how developmental reaction norms that describe the effects of prior experience on a given behaviour can be used to determine whether the effects of a given experience at a given age will affect contextual generality at a later age, and to illustrate how variation within individuals in developmental plasticity leads to variation in contextual generality across individuals as a function of experience. We also show why niche-picking and niche-construction, behavioural processes which allow individuals to affect their own developmental environment, can affect the contextual generality and the temporal consistency of personality. We conclude by discussing how an appreciation of developmental processes can alert behavioural ecologists studying animal personality to critical, untested assumptions that underlie their own research programmes, and outline situations in which a developmental perspective can improve studies of the functional significance and evolution of animal personality.     

Spike correlations in a songbird agree with a simple markov population model

The relationships between neural activity at the single-cell and the population levels are of central importance for understanding neural codes. In many sensory systems, collective behaviors in large cell groups can be described by pairwise spike correlations. Here, we test whether in a highly specialized premotor system of songbirds, pairwise spike correlations themselves can be seen as a simple corollary of an underlying random process. We test hypotheses on connectivity and network dynamics in the motor pathway of zebra finches using a high-level population model that is independent of detailed single-neuron properties. We assume that neural population activity evolves along a finite set of states during singing, and that during sleep population activity randomly switches back and forth between song states and a single resting state. Individual spike trains are generated by associating with each of the population states a particular firing mode, such as bursting or tonic firing. With an overall modification of one or two simple control parameters, the Markov model is able to reproduce observed firing statistics and spike correlations in different neuron types and behavioral states. Our results suggest that song- and sleep-related firing patterns are identical on short time scales and result from random sampling of a unique underlying theme. The efficiency of our population model may apply also to other neural systems in which population hypotheses can be tested on recordings from small neuron groups.     

Differentiation for flowering time and phenotypic integration in Arabidopsis thaliana in response to season length and vernalization

The response of plants or animals to different environmental regimes may take the form of specialization of their life history patterns to match the prevailing conditions in a geographical area. In turn, the evolution of different life histories implies that there are trade-offs between distinct components of the life cycle. We investigate some of the possible explanations for the existence of distinct types of populations in the weed Arabidopsis thaliana (Brassicaceae), differentiated by flowering schedule. The so-called early flowering and late flowering "ecotypes" are hypothesized to result from adaptation to harsh winters or short seasons as opposed to mild winters or long seasons, respectively. We carried out two experiments in which we studied the reaction of natural populations to an increase in season length and to conditions simulating mild winter or spring. Unfortunately, only one of our accessions turned out to be a late flowering population; however, it did have a fitness disadvantage when the season was too short, although it had a higher reproductive output at the end of longer growing seasons. Most populations reacted to the simulation of a mild winter by extending their vegetative phase and increasing their reproductive output; however, this could be offset by increased winter mortality under harsh conditions. Character correlations (phenotypic integration) showed contrasting patterns of change in response to the two environmental factors: at the shortest season's length many correlations were negative, displaying a trade-off between vegetative and reproductive traits; during longer seasons, all correlations were positive and there was no evidence of vegetative-reproductive trade-offs. Exposure to cold did not trigger any major change in the pattern of character correlations.     

CORRELATED EVOLUTION OF SEXUAL SYSTEM AND LIFE-HISTORY TRAITS IN MOSSES

In mosses, separate and combined sexes are evolutionarily labile, yet factors selecting for this variation are unknown. In this study, we investigate phylogenetic correlations between sexual system and five life-history traits (asexual reproduction, chromosome number, gametophore length, spore size, and seta length). We assigned states to species on a large-scale phylogeny of mosses and used maximum likelihood analyses to test for the correlations and investigate the sequence of trait acquisition. Mosses in lineages with separate sexes were significantly more likely to be large, whereas those in lineages with combined sexes had higher chromosome numbers. Moreover, evolutionary transitions to separate sexes were more likely to occur in lineages with small spores. There was no support for a correlation between asexual reproduction and separate sexes. These results suggest that sexual system evolution is influenced by traits affecting mate availability and the dispersal of gametes and spores, and provides evidence for the existence of syndromes of life-history traits in mosses.     

Mhc polymorphisms fail to explain the heritability of phytohaemagglutinin-induced skin swelling in a wild passerine

Genetic estimates of the variability of immune responses are rarely examined in natural populations because of confounding environmental effects. As a result, and because of the difficulty of pinpointing the genetic determinants of immunity, no study has to our knowledge examined the contribution of specific genes to the heritability of an immune response in wild populations. We cross-fostered nestling house sparrows to disrupt the association between genetic and environmental effects and determine the heritability of the response to a classic immunological test, the phytohaemagglutinin (PHA)-induced skin swelling. We detected significant heritability estimates of the response to PHA, of body mass and tarsus length when nestlings were 5 and 10 days old. Variation at Mhc genes, however, did not explain a significant portion of the genetic variation of nestling swelling to PHA. Our results suggest that while PHA-induced swelling is influenced by the nest of origin, the importance of additive genetic variation relative to non-additive genetic variation and the genetic factors that influence the former in wild populations still need to be identified for this trait.     

Activation in a frontoparietal cortical network underlies individual differences in the performance of an embedded figures task

The Embedded Figures Test (EFT) requires observers to search for a simple geometric shape hidden inside a more complex figure. Surprisingly, performance in the EFT is negatively correlated with susceptibility to illusions of spatial orientation, such as the Roelofs effect. Using fMRI, we previously demonstrated that regions in parietal cortex are involved in the contextual processing associated with the Roelofs task. In the present study, we found that similar parietal regions (superior parietal cortex and precuneus) were more active during the EFT than during a simple matching task. Importantly, these parietal activations overlapped with regions found to be involved during contextual processing in the Roelofs illusion. Additional parietal and frontal areas, in the right hemisphere, showed strong correlations between brain activity and behavioral performance during the search task. We propose that the posterior parietal regions are necessary for processing contextual information across many different, but related visuospatial tasks, with additional parietal and frontal regions serving to coordinate this processing in participants proficient in the task.     

Effects of Genetic and Environmental Factors on Trait Network Predictions From Quantitative Trait Locus Data

The use of high-throughput genomic techniques to map gene expression quantitative trait loci has spurred the development of path analysis approaches for predicting functional networks linking genes and natural trait variation. The goal of this study was to test whether potentially confounding factors, including effects of common environment and genes not included in path models, affect predictions of cause–effect relationships among traits generated by QTL path analyses. Structural equation modeling (SEM) was used to test simple QTL-trait networks under different regulatory scenarios involving direct and indirect effects. SEM identified the correct models under simple scenarios, but when common-environment effects were simulated in conjunction with direct QTL effects on traits, they were poorly distinguished from indirect effects, leading to false support for indirect models. Application of SEM to loblolly pine QTL data provided support for biologically plausible a priori hypotheses of QTL mechanisms affecting height and diameter growth. However, some biologically implausible models were also well supported. The results emphasize the need to include any available functional information, including predictions for genetic and environmental correlations, to develop plausible models if biologically useful trait network predictions are to be made.     

Brief Communication: Latent toxoplasmosis and salivary testosterone concentration--important confounding factors in second to fourth digit ratio studies

A sexually dimorphic characteristic, the second to fourth digit ratio (2D:4D ratio), has been shown to reflect the prenatal concentration of sex steroid hormones and to correlate with many personality, physiological, and life history traits. The correlations are usually stronger for the right than the left hand. Most studies have shown that the 2D:4D ratio does not vary with age or postnatal concentration of sex steroid hormones. Recently, a strong association between left hand 2D:4D ratio and infection with a common human parasite Toxoplasma has been reported. We hypothesized that the confounding effect of Toxoplasma infection on left hand 2D:4D ratio could be responsible for the stronger association between different traits and right hand rather than left hand 2D:4D ratio. This confounding effect of toxoplasmosis could also be responsible for the difficulty in finding an association between 2D:4D ratio and age or postnatal steroid hormone concentration. To test this hypothesis, we analyzed the association between sex and age and 2D:4D ratio in a population of 194 female and 106 male students with and without controlling for the confounding variables of Toxoplasma infection and testosterone concentration. Our results showed that the relationship between age and sex and 2D:4D ratio increased sharply when Toxoplasma infection and testosterone concentration were controlled. These results suggest that left hand 2D:4D ratio is more susceptible to postnatal influences and that the confounding factors of Toxoplasma infection, testosterone concentration and possibly also age, should be controlled in future 2D:4D ratio studies. Because of a stronger 2D:4D dimorphism in Toxoplasma-infected than Toxoplasma-free subjects, we predict that 2D:4D ratio dimorphism as well as right hand/left hand 2D:4D ratio dimorphism will be higher in countries with a high prevalence of Toxoplasma infection than in those with a low prevalence.     

Paying attention pays off: Kea improve in loose-string cooperation by attending to partner

Previous studies showed that kea are able to cooperate in experiments based on the loose-string paradigm, but success rates were low, except when tested in stable dyads. We trained kea with low success rates to attend to the handling of the string by a human partner. This vastly improved subsequent coordination during cooperation with kea partners. Furthermore, we tested the kea dyads with a delayed entry set-up (delays of 2, 4 or 6 s) and with two different lengths of string. Increasing length of delay and reducing string length had negative effects on the success rate. This suggests that a complete understanding of the actions was not present as the kea were not able to fully overcome factors that inhibit coordination. Lastly, we tested the three subjects showing the greatest ability to wait for the partner in a partner-choice paradigm: one subject in the central position could pull a loose string with one partner after another in the order it preferred. As a result, the second subjects had much longer waiting times than previously experienced. We could show that the central kea learned to visit both set-ups and that the second partner was able to wait for the partner to arrive before attempting to pull on the string, averaging twice as long as in the standard delay. Taken together, the results from this study highlight that cooperation in the loose-string paradigm is largely dependent on coordination of the subjects. While attention to the partner's actions greatly improved performance, the greater waiting times achieved in the final set-up also suggest that utilizing more ecologically relevant (subject is busy VS subject is held back) delays could further improve the performance of non-human subjects in the delayed loose-string paradigm.     

Interruptions in the expanded ATTCT repeat of spinocerebellar ataxia type 10: repeat purity as a disease modifier?

Spinocerebellar ataxia type 10 (SCA10) is one of numerous genetic disorders that result from simple repeat expansions. SCA10 is caused by expansion of an intronic ATTCT pentanucleotide repeat tract. It is clinically characterized by progressive ataxia, seizures, and anticipation, which can vary within and between families. We report two SCA10 families showing distinct frequencies of seizures and correlations of repeat length with age at onset. One family displayed uninterrupted ATTCT expansions, whereas the other showed multiple interruptions of the repeat by nonconsensus repeat units, which differed both in the length and/or sequence of the repeat unit. Disease-causing microsatellite expansions have been assumed to be composed of uninterrupted pure repeats. Our findings for SCA10 challenge this convention and suggest that the purity of the expanded repeat element may be a disease modifier.