TYPE I ERROR RATES FOR TESTING GENETIC DRIFT WITH PHENOTYPIC COVARIANCE MATRICES: A SIMULATION STUDY

Studies of evolutionary divergence using quantitative genetic methods are centered on the additive genetic variance–covariance matrix ( G ) of correlated traits. However, estimating G properly requires large samples and complicated experimental designs. Multivariate tests for neutral evolution commonly replace average G by the pooled phenotypic within‐group variance–covariance matrix ( W ) for evolutionary inferences, but this approach has been criticized due to the lack of exact proportionality between genetic and phenotypic matrices. In this study, we examined the consequence, in terms of type I error rates, of replacing average G by W in a test of neutral evolution that measures the regression slope between among‐population variances and within‐population eigenvalues (the Ackermann and Cheverud [AC] test) using a simulation approach to generate random observations under genetic drift. Our results indicate that the type I error rates for the genetic drift test are acceptable when using W instead of average G when the matrix correlation between the ancestral G and P is higher than 0.6, the average character heritability is above 0.7, and the matrices share principal components. For less‐similar G and P matrices, the type I error rates would still be acceptable if the ratio between the number of generations since divergence and the effective population size (t/N_e) is smaller than 0.01 (large populations that diverged recently). When G is not known in real data, a simulation approach to estimate expected slopes for the AC test under genetic drift is discussed.     

An Asymmetric Opening of HIV-1 Envelope Mediates Antibody-Dependent Cellular Cytotoxicity

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Cubicle Refusal and Rearing Accommodation as Possible Mastitis Risk Factors in Cubicle-Housed Dairy Heifers

Fifty-nine of the 65 dairy farms with cubicle sheds in the Norwegian county of Oppland in 1990 were included in a study of rearing accommodation, cubicle refusal and mastitis incidence. The farmers recorded the favoured resting location of the individual cows and heifers throughout the final week of pregnancy as well as during calving. The observations were matched with individual records of mastitis cases during the first 30 days after calving. Mastitis incidence in the heifers was analysed by logistic regression using rearing accommodation and cubicle refusal as independent variables, controlling for herd as a clustering factor. Cubicle refusal was found in 29% of the heifers, but in only 3% of older cows. The results of the analysis indicated a tendency for cubicle refusal to be associated with an increased mastitis incidence among the heifers (OR = 2.2, c.i._95%OR = 0.9–5.4, P = 0.08). Cubicle refusal accounted for 21% (0–32%) of the mastitis cases in the study population (PAF = 0.21).     

Removal of birch as a means of protecting raised bog mossy vegetation <Emphasis Type="Italic">Ledo</Emphasis>-<Emphasis Type="Italic">Sphagnetum magellanici</Emphasis>

Raised bogs dominated by the vegetation association Ledo-Sphagnetum magellanici Sukopp 1959 em. Neuhäusl 1969 are a valuable and ecologically important plant community that occurs in Central Europe. They develop in impervious depressions with precipitation as the only water source, and are particularly sensitive to drainage, climate change, eutrophication and overgrowing by trees and shrubs. The high pressure of threat justifies taking protective measures. This research focused on the effects of the removal of birch from two bogs, which were dominated by two birch species (Betula pubescens, B. pendula) and also included stands of Scots pine (Pinus sylvestris); the bogs are located in northeastern Poland and showed signs of drying. The trees were removed in early spring 2008. To capture the response to tree cutting, vegetation monitoring was performed for 7 years. The results were compared to pre-cutting environmental conditions (precipitation, temperature, air transpiration). At the first site, which was drained at the beginning of the twentieth century, the ground water level initially decreased; then, from 2010 onwards, the level stabilised and exhibited a negative correlation with the average annual air temperature. While the second site exhibited no significant differences in the ground water table, a correlation with the average annual rainfall was found. At both sites, there was an increase in the coverage of species appropriate for raised bogs, Oxycocco-Sphagnatea Br.-Bl. et R. Tx. 1943, whereas only the second site had significant coverage of these species. These actions improved the habitat conditions and initiated the process of raised bog restoration at that site because Oxycocco-Sphagnatea species cover and frequency increased.     

Acceleration of plastoquinone pool reduction by alternative pathways precedes a decrease in photosynthetic CO2 assimilation in preheated barley leaves

Heat stress causes inhibition of photosynthetic CO₂ assimilation, affects light photosynthetic reactions and accelerates alternative pathways of plastoquinone pool reduction (APPR). We have studied all these heat-sensitive processes after preheating to a broad range of physiological temperatures (24–46°C) to explore a role of these alternative pathways during heat stress. Primarily, the effective quantum yield of PSII photochemistry was reduced (at 40°C). This PSII downregulation was accompanied by the stimulation of APPR and preceded reduction of photosynthetic CO₂ assimilation by 2°; it occurred after preheating at 42°C because of inhibition in Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase) activation process. Thus, we suggest that the heat-induced stimulation of APPR is not associated with the heat-induced inhibition of Calvin cycle as it was reported for other types of stresses. A possible role of APPR in the compensation of PSII downregulation is briefly discussed.     

Amino acid contacts in proteins adapted to different temperatures: hydrophobic interactions and surface charges play a key role

Thermophiles, mesophiles, and psychrophiles have different amino acid frequencies in their proteins, probably because of the way the species adapt to very different temperatures in their environment. In this paper, we analyse how contacts between sidechains vary between homologous proteins from species that are adapted to different temperatures, but displaying relatively high sequence similarity. We investigate whether specific contacts between amino acids sidechains is a key factor in thermostabilisation in proteins. The dataset was divided into two subsets with optimal growth temperatures from 0–40 and 35–102°C. Comparison of homologues was made between low-temperature species and high-temperature species within each subset. We found that unspecific interactions like hydrophobic interactions in the core and solvent interactions and entropic effects at the surface, appear to be more important factors than specific contact types like salt bridges and aromatic clusters. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.