Environmentally induced dispersal‐related life‐history syndrome in the tropical butterfly,Bicyclus anynana

Dispersal is a key process for understanding the persistence of populations as well as the capacity of organisms to respond to environmental change. Therefore, understanding factors that may facilitate or constrain the evolution of dispersal is of crucial interest. Assessments of phenotypic variation in various behavioural, physiological and morphological traits related to insect dispersal and flight performance are common, yet very little is known about the genetic associations among these traits. We have used experiments on the butterfly Bicyclus anynana to estimate genetic variation and covariation in seven behavioural, physiological and morphological traits related to flight potential and hence dispersal. Our goal was to characterize the heritabilities and genetic correlations among these traits and thus to understand more about the evolution of dispersal‐related life‐history syndromes in butterflies. Using a version of the animal model, we showed that all of the traits varied between the sexes, and most were either positively or negatively (phenotypically and/or genetically) correlated with body size. Heritable variation was present in most traits, with the highest heritabilities estimated for body mass and thorax ratio. The variance in flight activity among multiple measurements for the same individual was high even after controlling for the prevailing environmental conditions, indicating the importance of behavioural switching and/or inherent randomness associated with this type of movement. A number of dispersal‐related traits showed phenotypic correlations among one another, but only a few of these were associated with significant genetic correlations indicating that covariances between these traits in Bicyclus anynana are mainly environmentally induced.     

A goodness‐of‐fit test for occupancy models with correlated within‐season revisits

Occupancy modeling is important for exploring species distribution patterns and for conservation monitoring. Within this framework, explicit attention is given to species detection probabilities estimated from replicate surveys to sample units. A central assumption is that replicate surveys are independent Bernoulli trials, but this assumption becomes untenable when ecologists serially deploy remote cameras and acoustic recording devices over days and weeks to survey rare and elusive animals. Proposed solutions involve modifying the detection‐level component of the model (e.g., first‐order Markov covariate). Evaluating whether a model sufficiently accounts for correlation is imperative, but clear guidance for practitioners is lacking. Currently, an omnibus goodness‐of‐fit test using a chi‐square discrepancy measure on unique detection histories is available for occupancy models (MacKenzie and Bailey, Journal of Agricultural, Biological, and Environmental Statistics, 9, 2004, 300; hereafter, MacKenzie–Bailey test). We propose a join count summary measure adapted from spatial statistics to directly assess correlation after fitting a model. We motivate our work with a dataset of multinight bat call recordings from a pilot study for the North American Bat Monitoring Program. We found in simulations that our join count test was more reliable than the MacKenzie–Bailey test for detecting inadequacy of a model that assumed independence, particularly when serial correlation was low to moderate. A model that included a Markov‐structured detection‐level covariate produced unbiased occupancy estimates except in the presence of strong serial correlation and a revisit design consisting only of temporal replicates. When applied to two common bat species, our approach illustrates that sophisticated models do not guarantee adequate fit to real data, underscoring the importance of model assessment. Our join count test provides a widely applicable goodness‐of‐fit test and specifically evaluates occupancy model lack of fit related to correlation among detections within a sample unit. Our diagnostic tool is available for practitioners that serially deploy survey equipment as a way to achieve cost savings.     

Evolutionary trade‐off between naturally‐ and sexually‐selected melanin‐based colour traits in worldwide barn owls and allies

Natural selection typically constrains the evolution of sexually‐selected characters. The evolution of naturally‐ and sexually‐selected traits can be intertwined if they share part of their genetic machinery or if sex traits impair foraging success or increase the risk of depredation. The present study investigated phenotypic correlations between naturally‐ and sexually‐selected plumage traits in the Tytonidae (barn owls, grass owls, and masked owls). Phenotypic correlations indicate the extent to which selection on one trait will indirectly influence the evolution of another trait. In this group of birds, the ventral body side varies from white to dark reddish, a naturally‐selected pheomelanin‐based colour trait with important roles in predator–prey interactions. Owls also exhibit eumelanin‐based black spots, for which number and size signal different aspects of individual quality and are used in mate choice. These three plumage traits are strongly heritable and sexually dimorphic, with females being on average darker reddish and more spotted than males. Phenotypic correlations were measured between these three plumage traits in 3958 free‐living barn owls in Switzerland and 10 670 skin specimens from 34 Tyto taxa preserved in museums. Across Tyto taxa, the sexually‐selected plumage spottiness was positively correlated with the naturally‐selected reddish coloration, with redder birds being more heavily spotted. This suggests that they are genetically constrained or that natural and sexual selection are not antagonistically exerted on plumage traits. In a large sample of Swiss nestlings and within 34 Tyto taxa, the three plumage traits were positively correlated. The production of melanin pigments for one plumage trait is therefore not traded off against the production of melanin pigments for another plumage trait. Only in the most heavily‐spotted Tyto taxa do larger‐spotted individuals display fewer spots. This indicates that, at some threshold value, the evolution of many spots constrains the evolution of large spots. These analyses raise the possibility that different combinations of melanin‐based plumage traits may not be selectively equivalent.     

Incorporating Inter‐item Correlations in Item Response Data Analysis

This paper concerns with the analysis of item response data, which are usually measured on a rating scale and are therefore ordinal. These study items tended to be highly inter‐correlated. Rasch models, which convert ordinal categorical scales into linear measurements, are widely used in ordinal data analysis. In this paper, we improve the current methodology in order to incorporate inter‐item correlations. We have advocated the latent variable approach for this purpose, in combination with generalized estimating equations to estimate the Rasch model parameters. The data on a study of families of lung cancer patients demonstrate the utility of our methods.     

Normal‐mode‐based modeling of allosteric couplings that underlie cyclic conformational transition in F1 ATPase

F₁ ATPase, a rotary motor comprised of a central stalk ( γ subunit) enclosed by three α and β subunits alternately arranged in a hexamer, features highly cooperative binding and hydrolysis of ATP. Despite steady progress in biophysical, biochemical, and computational studies of this fascinating motor, the structural basis for cooperative ATPase involving its three catalytic sites remains not fully understood. To illuminate this key mechanistic puzzle, we have employed a coarse‐grained elastic network model to probe the allosteric couplings underlying the cyclic conformational transition in F₁ ATPase at a residue level of detail. We will elucidate how ATP binding and product (ADP and phosphate) release at two catalytic sites are coupled with the rotation of γ subunit via various domain motions in α ₃ β ₃ hexamer (including intrasubunit hinge‐bending motions in β subunits and intersubunit rigid‐body rotations between adjacent α and β subunits). To this end, we have used a normal‐mode‐based correlation analysis to quantify the allosteric couplings of these domain motions to local motions at catalytic sites and the rotation of γ subunit. We have then identified key amino acid residues involved in the above couplings, some of which have been validated against past studies of mutated and γ ‐truncated F₁ ATPase. Our finding strongly supports a binding change mechanism where ATP binding to the empty catalytic site triggers a series of intra‐ and intersubunit domain motions leading to ATP hydrolysis and product release at the other two closed catalytic sites. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

Whole‐field macro‐ and micro‐deformation characteristic of unbound water‐loss in dentin hard tissue

High‐resolution deformation measurements in a functionally graded hard tissue such as human dentin are essential to understand the unbound water‐loss mediated changes and their role in its mechanical integrity. Yet a whole‐field, 3‐dimensional (3D) measurement and characterization of fully hydrated dentin in both macro‐ and micro‐scales remain to be a challenge. This study was conducted in 2 stages. In stage‐1, a stereo‐digital image correlation approach was utilized to determine the water‐loss and load‐induced 3D deformations of teeth in a sagittal section over consecutively acquired frames, from a fully hydrated state to nonhydrated conditions for a period up to 2 hours. The macroscale analysis revealed concentrated residual deformations at the dentin‐enamel‐junction and the apical regions of root in the direction perpendicular to the dentinal tubules. Significant difference in the localized deformation characteristics was observed between the inner and outer aspects of the root dentin. During quasi‐static loadings, further increase in the residual deformation was observed in the dentin. In stage‐2, dentin microstructural variations induced by dynamic water‐loss were assessed with environmental scanning electron microscopy and atomic force microscopy (AFM), showing that the dynamic water‐loss induced distention of dentinal tubules with concave tubular edges, and concurrent contraction of intertubular dentin with convex profile. The findings from the current macro‐ and micro‐scale analysis provided insight on the free‐water‐loss induced regional deformations and ultrastructural changes in human dentin.      

Spatial modeling of data with excessive zeros applied to reindeer pellet‐group counts

We analyze a real data set pertaining to reindeer fecal pellet‐group counts obtained from a survey conducted in a forest area in northern Sweden. In the data set, over 70% of counts are zeros, and there is high spatial correlation. We use conditionally autoregressive random effects for modeling of spatial correlation in a Poisson generalized linear mixed model (GLMM), quasi‐Poisson hierarchical generalized linear model (HGLM), zero‐inflated Poisson (ZIP), and hurdle models. The quasi‐Poisson HGLM allows for both under‐ and overdispersion with excessive zeros, while the ZIP and hurdle models allow only for overdispersion. In analyzing the real data set, we see that the quasi‐Poisson HGLMs can perform better than the other commonly used models, for example, ordinary Poisson HGLMs, spatial ZIP, and spatial hurdle models, and that the underdispersed Poisson HGLMs with spatial correlation fit the reindeer data best. We develop R codes for fitting these models using a unified algorithm for the HGLMs. Spatial count response with an extremely high proportion of zeros, and underdispersion can be successfully modeled using the quasi‐Poisson HGLM with spatial random effects.     

Intra‐population genetic variation in diapause incidence of adult‐diapausing Tetranychus pueraricola (Acari: Tetranychidae)

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Female‐ and male‐specific signals of quality in the barn owl

Most bird studies of female signalling have been confined to species in which females display a male‐ornament in a vestigial form. However, a great deal of benefit may be gained from considering phenotypic traits that are specific to females. This is because (1) sex‐specific traits may signal sex‐specific qualities and (2) females may develop a male‐ornament not because they are selected to do so, but because fathers transmit to daughters the underlying genes for its expression (genetic correlation between the sexes). We investigated these two propositions in the barn owl Tyto alba, a species in which male plumage is lighter in colour and less marked with black spots than that of females. Firstly, we present published evidence that female plumage spottiness reflects parasite resistance ability. We also show that male plumage coloration is correlated with reproductive success, male feeding rate and heart mass. Secondly, cross‐fostering experiments demonstrate that plumage coloration and spottiness are genetically correlated between the sexes. This implies that if a given trait value is selected in one sex, the other sex will indirectly evolve towards a similar value. This prediction is supported by the observation that female plumage coloration and spottiness resembled that of males, in comparisons at the level of Tyto alba alba populations, Tyto alba subspecies and Tyto species. Our results therefore support the hypothesis that sex‐specific traits signal sex‐specific qualities and that a gene for a sex‐specific trait can be expressed in the other sex as the consequence of a genetic correlation between the sexes.     

Semi‐Markov Models with Phase‐Type Sojourn Distributions

Summary Continuous‐time multistate models are widely used for categorical response data, particularly in the modeling of chronic diseases. However, inference is difficult when the process is only observed at discrete time points, with no information about the times or types of events between observation times, unless a Markov assumption is made. This assumption can be limiting as rates of transition between disease states might instead depend on the time since entry into the current state. Such a formulation results in a semi‐Markov model. We show that the computational problems associated with fitting semi‐Markov models to panel‐observed data can be alleviated by considering a class of semi‐Markov models with phase‐type sojourn distributions. This allows methods for hidden Markov models to be applied. In addition, extensions to models where observed states are subject to classification error are given. The methodology is demonstrated on a dataset relating to development of bronchiolitis obliterans syndrome in post‐lung‐transplantation patients.     

THE EVOLUTIONARY STABILITY OF CROSS‐SEX,CROSS‐TRAIT GENETIC COVARIANCES

Although knowledge of the selective agents behind the evolution of sexual dimorphism has advanced considerably in recent years, we still lack a clear understanding of the evolutionary durability of cross‐sex genetic covariances that often constrain its evolution. We tested the relative stability of cross‐sex genetic covariances for a suite of homologous contact pheromones of the fruit fly Drosophila serrata, along a latitudinal gradient where these traits have diverged in mean. Using a Bayesian framework, which allowed us to account for uncertainty in all parameter estimates, we compared divergence in the total amount and orientation of genetic variance across populations, finding divergence in orientation but not total variance. We then statistically compared orientation divergence of within‐sex ( G ) to cross‐sex ( B ) covariance matrices. In line with a previous theoretical prediction, we find that the cross‐sex covariance matrix, B , is more variable than either within‐sex G matrix. Decomposition of B matrices into their symmetrical and nonsymmetrical components revealed that instability is linked to the degree of asymmetry. We also find that the degree of asymmetry correlates with latitude suggesting a role for spatially varying natural selection in shaping genetic constraints on the evolution of sexual dimorphism.     

A Bayesian Chi‐Squared Goodness‐of‐Fit Test for Censored Data Models

Summary We propose a Bayesian chi‐squared model diagnostic for analysis of data subject to censoring. The test statistic has the form of Pearson's chi‐squared test statistic and is easy to calculate from standard output of Markov chain Monte Carlo algorithms. The key innovation of this diagnostic is that it is based only on observed failure times. Because it does not rely on the imputation of failure times for observations that have been censored, we show that under heavy censoring it can have higher power for detecting model departures than a comparable test based on the complete data. In a simulation study, we show that tests based on this diagnostic exhibit comparable power and better nominal Type I error rates than a commonly used alternative test proposed by Akritas (1988, Journal of the American Statistical Association 83, 222–230). An important advantage of the proposed diagnostic is that it can be applied to a broad class of censored data models, including generalized linear models and other models with nonidentically distributed and nonadditive error structures. We illustrate the proposed model diagnostic for testing the adequacy of two parametric survival models for Space Shuttle main engine failures.     

High‐resolution structures of collagen‐like peptides [(Pro‐Pro‐Gly)4‐Xaa‐Yaa‐Gly‐(Pro‐Pro‐Gly)4]: Implications for triple‐helix hydration and Hyp(X) puckering

Structures of (Pro‐Pro‐Gly)₄‐Xaa‐Yaa‐Gly‐(Pro‐Pro‐Gly)₄ (ppg9‐XYG) where (Xaa, Yaa) = (Pro, Hyp), (Hyp, Pro) or (Hyp, Hyp) were analyzed at high resolution using synchrotron radiation. Molecular and crystal structures of these peptides are very similar to those of the (Pro‐Pro‐Gly)₉ peptide. The results obtained in this study, together with those obtained from related compounds, indicated the puckering propensity of the Hyp in the X position: (1) Hyp(X) residues involved in the Hyp(X):Pro(Y) stacking pairs prefer the down‐puckering conformation, as in ppg9‐OPG, and ppg9‐OOG; (2) Hyp(X) residues involved in the Hyp(X):Hyp(Y) stacking pairs prefer the up‐puckering conformation if there is no specific reason to adopt the down‐puckering conformation. Water molecules in these peptide crystals are classified into two groups, the 1st and 2nd hydration waters. Water molecules in the 1st hydration group have direct hydrogen bonds with peptide oxygen atoms, whereas those in the 2nd hydration group do not. Compared with globular proteins, the number of water molecules in the 2nd hydration shell of the ppg9‐XYG peptides is very large, likely due to the unique rod‐like molecular structure of collagen model peptides. In the collagen helix, the amino acid residues in the X and Y positions must protrude outside of the triple helix, which forces even the hydrophobic side chains, such as Pro, to be exposed to the surrounding water molecules. Therefore, most of the waters in the 2nd hydration shell are covering hydrophobic Pro side chains by forming clathrate structures. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 361–372, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Change of Beclin‐1 dependent on ATP, [Ca2+]i and MMP in PC12 cells following oxygen‐glucose deprivation‐reoxygenation injury

Autophagy is usually up‐regulated to provide more ATP in response to starvation or OGD (oxygen‐glucose deprivation), but the relationship between autophagy and ATP, [Ca²⁺]_i (intracellular free Ca²⁺ concentration) or MMP (mitochondrial membrane potential) during reoxygenation is not yet fully clear. The role of autophagy is unknown in PC12 cells subjected to 2 h OGD with different time points of reoxygenation. In the present study, we showed that Beclin‐1 was up‐regulated beginning at 0 h reoxygenation peaking at 24 h and lasting for 48 h. Cell viability was decreased from 0 to 48 h reoxygenation, reaching its minimum at 10 h reoxygenation. ATP was decreased from 0 to 10 h reoxygenation, reaching its minimum at 4 h reoxygenation. A significant negative correlation was observed between ATP and Beclin‐1 (r = ?0.61, P<0.05) at 0 h reoxygenation, but ATP was not significant related (r = 0.24, P>0.05) to Beclin‐1 at 24 h reoxygenation. Besides, Nimodipine, a calcium antagonist, significantly reduced [Ca²⁺]_i and Beclin‐1, but increased MMP in OGD/R‐treated cells. At 24 h reoxygenation, Beclin‐1 expression reached its maximum, cell viability continued to increase, and ATP was higher than that before OGD. These results suggest that energy metabolism dysfunction can induce autophagy during OGD in PC12 cells. Increased [Ca²⁺]_i and decreased MMP may induce autophagy during reoxygenation in PC12 cells. Autophagy may be a protective effect on PC12 cells treated with different time points of reoxygenation after 2 h OGD.     

Testing random effects in linear mixed‐effects models with serially correlated errors

In linear mixed‐effects models, random effects are used to capture the heterogeneity and variability between individuals due to unmeasured covariates or unknown biological differences. Testing for the need of random effects is a nonstandard problem because it requires testing on the boundary of parameter space where the asymptotic chi‐squared distribution of the classical tests such as likelihood ratio and score tests is incorrect. In the literature several tests have been proposed to overcome this difficulty, however all of these tests rely on the restrictive assumption of i.i.d. measurement errors. The presence of correlated errors, which often happens in practice, makes testing random effects much more difficult. In this paper, we propose a permutation test for random effects in the presence of serially correlated errors. The proposed test not only avoids issues with the boundary of parameter space, but also can be used for testing multiple random effects and any subset of them. Our permutation procedure includes the permutation procedure in Drikvandi, Verbeke, Khodadadi, and Partovi Nia (2013) as a special case when errors are i.i.d., though the test statistics are different. We use simulations and a real data analysis to evaluate the performance of the proposed permutation test. We have found that random slopes for linear and quadratic time effects may not be significant when measurement errors are serially correlated.