A Bayesian framework for comparative quantitative genetics

Bayesian approaches have been extensively used in animal breeding sciences, but similar approaches in the context of evolutionary quantitative genetics have been rare. We compared the performance of Bayesian and frequentist approaches in estimation of quantitative genetic parameters (viz. matrices of additive and dominance variances) in datasets typical of evolutionary studies and traits differing in their genetic architecture. Our results illustrate that it is difficult to disentangle the relative roles of different genetic components from small datasets, and that ignoring, e.g. dominance is likely to lead to biased estimates of additive variance. We suggest that a natural summary statistic for G-matrix comparisons can be obtained by examining how different the underlying multinormal probability distributions are, and illustrate our approach with data on the common frog (Rana temporaria). Furthermore, we derive a simple Monte Carlo method for computation of fraternity coefficients needed for the estimation of dominance variance, and use the pedigree of a natural Siberian jay (Perisoreus infaustus) population to illustrate that the commonly used approximate values can be substantially biased.     

X-ray analysis of phosphoglycerate kinase 2, a sperm-specific isoform from Mus musculus

Phosphoglycerate kinase 2 (PGK2) is an isozyme of the glycolytic pathway that provides ATP required for sperm motility. It is encoded by an autosomal retrogene that is expressed only during spermatogenesis, concomitant with the inactivation of the X-linked Pgk1 gene. PGK2 from the mouse, Mus musculus, has been overexpressed from a plasmid in bacteria and purified. It was crystallized in three forms: as the apoenzyme, as a complex with 3-phosphoglycerate (3PG), and as a complex with 3PG and ATP. The crystal structures were solved to 2.7, 2.0, and 2.7 A resolutions, respectively. The overall fold is nearly identical with previously solved mammalian PGK1 molecules. The apoenzyme is in the "open" form; that is the N-terminal domain that can bind 3PG and the C-terminal domain that binds ATP are too far apart for the substrates to interact. Binding 3PG causes a 13 degree rotation that partially closes the structure and causes helix 13, which is disordered in the unliganded structure, to stabilize. Binding ATP leaves the protein in the open configuration but also causes helix 13 to be ordered. Sequence alignment suggests that the active site of PGK2 is essentially identical to that of the cytoplasmic PGK1, but significant differences accumulate on a side of the C-terminal domain away from the active site. These changes may mediate the binding of this isoform to other proteins within the sperm flagellum, while still allowing the hinging action between the domains that is essential to catalytic activity.     

Modification of the visual background increases the conspicuousness of golden-collared manakin displays

Effective visual communication requires signals that are easyto detect, transmit, receive, and discriminate. Animals canincrease the probability that their visual signals would bedetected by evolving signals that contrast with their visualbackground. Animals can further enhance this contrast by behaviorallymodifying the existing visual background. Male golden-collaredmanakins (Manacus vitellinus) clear leaf litter from the groundto form courts, which are used as display arenas. Using reflectancemeasures of the signal (male plumage) and the visual background(cleared court and adjacent litter), the irradiance measuresof ambient light during display, and published measures of photoreceptorsensitivity of a Passerine, we test the hypothesis that court-clearingaugments the contrast between male plumage and the visual background.We find that the chromatic and brightness contrasts of goldenpatches used during courtship are greater against the clearedcourt than against adjacent litter. In addition, we find thatcleared courts provide a less variable background for thesecolor patches, resulting in displays that consistently contrastthe visual background. These results suggest that behavioralmodification of the visual background may act to increase theconspicuousness of colorful male plumage during display, providingan explanation for why golden-collared manakins, and possiblyother species, build or clear display courts.     

Visual and olfactory cues for mate orientation behaviour in male white-spotted longicorn beetle, Anoplophora malasiaca

Olfactory and visual cues were shown to mediate short‐distance orientation in Anoplophora malasiaca (Thomson) (Coleoptera: Cerambycidae). In a laboratory test, more than 80% (n = 42) of males walked straight upward when presented with an untreated surface with a 75° slope. When a freshly killed female was fixed at a short distance (10 cm ahead and 5 cm to left/right) from the starting point, 50% of males (n = 30) were oriented toward the female before direct contact. Similar behavioural responses were observed when female extract was directly applied to the slope or to a glass rod model fixed on the slope. When black, white, and transparent coloured rods with the extract were presented, the orientation response was significantly greater for black than to white and transparent rods, to which only a negligible response was observed.     

双条杉天牛的生物学特性

双条杉天牛Semanotus bifasciatus(Motschulsky)是危害我国重要绿化树种侧柏的重要害虫。通过室内饲养观察及野外调查相结合的方法,观察分析双条杉天牛的各虫态历期、生活习性和发生规律,并得到出蜇率与温湿度的相关性,及在不同的温度条件下,该虫对颜色有不同的趋性,但总体而言,对绿色有较强的趋性,对无害防治具参考价值。     

Do climatically similar regions contain similar alien floras? A comparison between the mediterranean areas of central Chile and California

Aim Taxonomic comparisons of alien floras across climatically similar regions have been proposed as a powerful approach for increasing our understanding of plant invasions across scales. However, detailed comparisons between the alien biotas of climatically similar regions are scarce. This study aims to compare the taxonomic patterns of alien species richness in mediterranean‐type climate areas of central Chile and California, in order to better understand how climatically similar regions converge or diverge in terms of their alien flora. Location Central Chile and California, United States. Methods We compared the alien floras of the state of California in the United States and central Chile, considering within‐region variation and taxonomic composition up to the species level. To test for within‐region variation, administrative units and counties were grouped within seven latitudinal bands for each region. We tested for differences in the relative contributions of the various origins of the naturalized species to each region. We used a family naturalization index to establish which families had relatively higher numbers of naturalized species in each region. We evaluated the similarity, using cluster analyses with Jaccard’s similarity index, of alien taxa between regions and latitudinal bands using presence–absence matrices at the species, genus and family levels. We used principal components analysis to determine the presence of a compositional gradient including all latitudinal bands. Results We recorded 1212 alien plant species in California and 593 in central Chile, of which 491 are shared between the two regions. These figures include 25 species that are native to California and 37 that are native to Chile. A comparison between the alien floras of central Chile and California reveals three major trends: (1) higher naturalized species diversity for California than for Chile, at all taxonomic levels; (2) differences in the proportion of species according to origin, with America, Africa, Asia and Australia providing a larger number of species in California than in Chile; (3) segregation between regions in terms of taxonomic composition of their alien flora, and a rather weak differentiation within regions; and (4) a trend towards higher similarity between the alien floras of latitudinal bands associated with higher levels of human disturbances. Main conclusions The alien floras of central Chile and California are significantly different, but this difference diminishes in highly disturbed areas. Thus, the current high levels of species movement caused by globalization, together with increasing levels of anthropogenic disturbances, should reduce the differentiation of the alien floras in these regions, increasing overall biotic homogenization.     

A simple numerical approach towards improving the two one-sided test for average bioequivalence

For testing average bioequivalence, a simple test that improves upon the two-one sided test (TOST) is derived. The new test uses a critical value that is a non-increasing continuous function of the sample standard deviation, and the function is numerically obtained. Simulation results show that the resulting test performs well in terms of type I error probability; in particular, the test avoids the conservatism of the TOST. Consequently, the test provides better power compared to the TOST, especially when the variance becomes large. Numerical results also show that our test results in power that is very similar to the other improved tests available in the literature. An advantage of our improved test is that it is just as easy to carry out as the TOST. An example is used to illustrate the new test.     

Symmetries,non-Euclidean metrics,and patterns in a Swift–Hohenberg model of the visual cortex

The aim of this work is to investigate the effect of the shift-twist symmetry on pattern formation processes in the visual cortex. First, we describe a generic set of Riemannian metrics of the feature space of orientation preference that obeys properties of the shift-twist, translation, and reflection symmetries. Second, these metrics are embedded in a modified Swift-Hohenberg model. As a result we get a pattern formation process that resembles the pattern formation process in the visual cortex. We focus on the final stable patterns that are regular and periodic. In a third step we analyze the influences on pattern formation using weakly nonlinear theory and mode analysis. We compare the results of the present approach with earlier models.     

Cues For Shelter Use in a Phytophagous Insect

Many insects spend a large proportion of their life inactive, often hiding in shelters. The presence of shelters may, therefore, influence where insects feed. This study examines stimuli affecting the use of shelters by adults of the pine weevil, Hylobius abietis (L.) (Coleoptera, Curculionidae). This species is an economically important forest pest in Europe since the adults feed on the stem bark of newly planted conifer seedlings. When there are hiding or burrowing places present in close proximity to a seedling, pine weevils may hide there and repeatedly return to feed on the same seedling. Experiments were conducted in a laboratory arena with above-ground or below-ground shelters and in the presence or absence of wind. Pine weevils were highly attracted to shelters both above and below ground. Weevils in shelters were often observed assuming a characteristic “resting” posture. Experiments with opaque and transparent shelters showed that visual stimuli are used for orientation towards shelters and also increase the probability of an individual remaining in a shelter. The presence of wind increased the weevils’ propensity to use shelters both above and below ground. The present study indicates that shelters have a major influence on the behavior of the pine weevil and possible implications of the results are discussed.     

NeuroXidence: reliable and efficient analysis of an excess or deficiency of joint-spike events

We present a non-parametric and computationally efficient method named NeuroXidence that detects coordinated firing of two or more neurons and tests whether the observed level of coordinated firing is significantly different from that expected by chance. The method considers the full auto-structure of the data, including the changes in the rate responses and the history dependencies in the spiking activity. Also, the method accounts for trial-by-trial variability in the dataset, such as the variability of the rate responses and their latencies. NeuroXidence can be applied to short data windows lasting only tens of milliseconds, which enables the tracking of transient neuronal states correlated to information processing. We demonstrate, on both simulated data and single-unit activity recorded in cat visual cortex, that NeuroXidence discriminates reliably between significant and spurious events that occur by chance.