The Rooting of the Universal Tree of Life Is Not Reliable

Several composite universal trees connected by an ancestral gene duplication have been used to root the universal tree of life. In all cases, this root turned out to be in the eubacterial branch. However, the validity of results obtained from comparative sequence analysis has recently been questioned, in particular, in the case of ancient phylogenies. For example, it has been shown that several eukaryotic groups are misplaced in ribosomal RNA or elongation factor trees because of unequal rates of evolution and mutational saturation. Furthermore, the addition of new sequences to data sets has often turned apparently reasonable phylogenies into confused ones. We have thus revisited all composite protein trees that have been used to root the universal tree of life up to now (elongation factors, ATPases, tRNA synthetases, carbamoyl phosphate synthetases, signal recognition particle proteins) with updated data sets. In general, the two prokaryotic domains were not monophyletic with several aberrant groupings at different levels of the tree. Furthermore, the respective phylogenies contradicted each others, so that various ad hoc scenarios (paralogy or lateral gene transfer) must be proposed in order to obtain the traditional Archaebacteria–Eukaryota sisterhood. More importantly, all of the markers are heavily saturated with respect to amino acid substitutions. As phylogenies inferred from saturated data sets are extremely sensitive to differences in evolutionary rates, present phylogenies used to root the universal tree of life could be biased by the phenomenon of long branch attraction. Since the eubacterial branch was always the longest one, the eubacterial rooting could be explained by an attraction between this branch and the long branch of the outgroup. Finally, we suggested that an eukaryotic rooting could be a more fruitful working hypothesis, as it provides, for example, a simple explanation to the high genetic similarity of Archaebacteria and Eubacteria inferred from complete genome analysis.     

The intracellular events triggered by the self-incompatibility response inPapaver rhoeas

Summary In recent years self-incompatibility (SI) has come to be recognised as an important model system for studying cell-cell interactions and signalling in flowering plants. In this article we discuss the intracellular events associated with the SI response in the field poppy,Papaver rhoeas. The SI response inP. rhoeas is known to involve a Ca²⁺-based signalling pathway, activated following molecular interactions on the surface of incompatible pollen tubes. Evidence demonstrates that, following a transient increase in the concentration of cytosolic free Ca²⁺ ([Ca²⁺];) initiated by the SI response, phosphorylation of certain cytosolic proteins occurs, followed by activation of pollen gene expression. The magnitude of this transient Ca²⁺ wave and the localisation of cytosolic [Ca²⁺]i following the SI response are discussed. We also describe the character of the proteins specifically phosphorylated in the SI response and the nature of the protein kinases involved in their phosphorylation. Finally, we consider the possibility that the end result of the SI response inP. rhoeas may be analogous to programmed-cell-death mechanisms such as those seen in developmental processes and defence responses in various plant cells.     

Song recognition by temporal cues in a group of closely related bushcricket species (genus Tettigonia)

Female phonotaxis of Tettigonia viridissima and T. caudata was investigated on a walking compensator to determine the temporal parameters of the male song used for song recognition, and to compare them with the previously described pulse rate filtering of T. cantans. The T. cantans song is continuous with a ≈30-Hz pulse rate. The T. caudata song has a higher pulse rate (≈40 Hz) and duty cycle than T. cantans and a distinct verse structure. The T. viridissima song is continuous with a double-pulse pattern. While the pulse rate is essential for song recognition in T. cantans, neither pulse rate not verse structure were essential for song recognition in T. caudata: females responded to signals above a minimum duty cycle. T. viridissima females did not require the double-pulse structure, but a single long pulse, equivalent to the duration of the double pulses and interval between them, was effective. Song attractiveness was limited by a minimum duration of the merged double pulse, and by minimum and maximum duration of the interval between them. Pulse rate recognition had little if any importance in either of the species investigated. Thus, the three congeners use different mechanisms for temporal song recognition. Accepted: 18 June 1998     

Visual Ecology and Perception of Coloration Patterns by Domestic Chicks

This article suggests how we might understand the way potential predators see coloration patterns used in aposematism and visual mimicry. We start by briefly reviewing work on evolutionary function of eyes and neural mechanisms of vision. Often mechanisms used for achromatic vision are accurately modeled as adaptations for detection and recognition of the generality of optical stimuli, rather than specific stimuli such as biological signals. Colour vision is less well understood, but for photoreceptor spectral sensitivities of birds and hymenopterans there is no evidence for adaptations to species-specific stimuli, such as those of food or mates. Turning to experimental work, we investigate how achromatic and chromatic stimuli are used for object recognition by foraging domestic chicks (Gallus gallus). Chicks use chromatic and achromatic signals in different ways: discrimination of large targets uses (chromatic) colour differences, and chicks remember chromatic signals accurately. However, detection of small targets, and discrimination of visual textures requires achromatic contrast. The different roles of chromatic and achromatic information probably reflect their utility for object recognition in nature. Achromatic (intensity) variation exceeds chromatic variation, and hence is more informative about change in reflectance – for example, object borders, while chromatic signals yield more information about surface reflectance (object colour) under variable illumination. This revised version was published online in July 2006 with corrections to the Cover Date.     

Chlamydia trachomatis: identification of susceptibility markers for ocular and sexually transmitted infection by immunogenetics

The aim of this review is to present a concise overview of all data available on the immunogenetics of Chlamydia trachomatis infections, both sexually transmitted urogenital and ocular infections. Currently, candidate gene approaches are used to identify genes related to the susceptibility to and severity of C. trachomatis infections. The main focus in the review will be on data obtained by the study of human cohorts.