Is There a Phylogenetic Signal in Prokaryote Proteins?

Using the sequence information from nine completely sequenced bacterial genomes, we extract 32 protein families that are thought to contain orthologous proteins from each genome. The alignments of these 32 families are used to construct a phylogeny with the neighbor-joining algorithm. This tree has several topological features that are different from the conventional phylogeny, yet it is highly reliable according to its bootstrap values. Upon closer study of the individual families used, it is clear that the strong phylogenetic signal comes from three families, at least two of which are good candidates for horizontal transfer. The tree from the remaining 29 families consists almost entirely of noise at the level of bacterial phylum divisions, indicating that, even with large amounts of data, it may not be possible to reconstruct the prokaryote phylogeny using standard sequence-based methods. Received: 22 November 1998 / Accepted: 17 February 1999     

Signal convergence in fruits: a result of selection by frugivores?

The Dispersal Syndrome hypothesis remains contentious, stating that apparently nonrandom associations of fruit characteristics result from selection by seed dispersers. We examine a key assumption under this hypothesis, i.e. that fruit traits can be used as reliable signals by frugivores. We first test this assumption by looking at whether fruit colour allows birds and primates to distinguish between fruits commonly dispersed by birds or primates. Second, we test whether the colours of fruits dispersed by primates are more contrasting to primates than the colours of bird‐dispersed fruits, expected if fruit colour is an adaptation to facilitate the detection by seed dispersers. Third, we test whether fruit colour has converged in unrelated plant species dispersed by similar frugivores. We use vision models based on peak sensitivities of birds’ and primates’ cone cells. We base our analyses on the visual systems of two types of birds (violet and ultraviolet based) and three types of primates (trichromatic primates from the Old and the New Worlds, and a dichromatic New World monkey). Using a Discriminant Function Analysis, we find that all frugivore groups can reliably discriminate between bird‐ and primate‐dispersed fruits. Fruit colour can be a reliable signal to different seed dispersers. However, the colours of primate‐dispersed fruits are less contrasting to primates than those of bird‐dispersed fruits. Fruit colour convergence in unrelated plants is independent of phylogeny and can be better explained by disperser type, which supports the hypothesis that frugivores are important in fruit evolution. We discuss adaptive and nonadaptive hypotheses that can potentially explain the pattern we found.     

Gene-Flow in a Mosaic Hybrid Zone: Is Local Introgression Adaptive?

Genome-wide scans of genetic differentiation between hybridizing taxa can identify genome regions with unusual rates of introgression. Regions of high differentiation might represent barriers to gene flow, while regions of low differentiation might indicate adaptive introgression—the spread of selectively beneficial alleles between reproductively isolated genetic backgrounds. Here we conduct a scan for unusual patterns of differentiation in a mosaic hybrid zone between two mussel species, Mytilus edulis and M. galloprovincialis. One outlying locus, mac-1, showed a characteristic footprint of local introgression, with abnormally high frequency of edulis-derived alleles in a patch of M. galloprovincialis enclosed within the mosaic zone, but low frequencies outside of the zone. Further analysis of DNA sequences showed that almost all of the edulis allelic diversity had introgressed into the M. galloprovincialis background in this patch. We then used a variety of approaches to test the hypothesis that there had been adaptive introgression at mac-1. Simulations and model fitting with maximum-likelihood and approximate Bayesian computation approaches suggested that adaptive introgression could generate a “soft sweep,” which was qualitatively consistent with our data. Although the migration rate required was high, it was compatible with the functioning of an effective barrier to gene flow as revealed by demographic inferences. As such, adaptive introgression could explain both the reduced intraspecific differentiation around mac-1 and the high diversity of introgressed alleles, although a localized change in barrier strength may also be invoked. Together, our results emphasize the need to account for the complex history of secondary contacts in interpreting outlier loci.     

Adaptive changes in bacteria: a consequence of nonlinear transitions in chromosome topology?

Adaptive changes in bacteria are generally considered to result from random mutations selected by the environment. This interpretation is challenged by the non-randomness of genomic changes observed following ageing or starvation in bacterial colonies. A theory of adaptive targeting of sequences for enzymes involved in DNA transactions is proposed here. It is assumed that the sudden leakage of cAMP consecutive to starvation induces a rapid drop in the ATP/ADP ratio that inactivates the homeostasis in control of the level of DNA supercoiling. This phase change enables the emergence of local modifications in chromosome topology in relation to the missing metabolites, a first stage in expression of an adaptive status in which DNA transactions are induced. The nonlinear perspective proposed here is homologous to that already suggested for adaptation of pluricellular organisms during their development. In both cases, phases of robustness in regulation networks for genetic expression are interspaced by critical periods of breakdown of the homeostatic regulations during which, through isolation of nodes from a whole network, specific changes with adaptive value may locally occur.     

An Adaptive Immune Response in Drosophila?

The ability to mount an adaptive immune response is thought to be an attribute restricted to vertebrates. A new study conducted in Drosophila demonstrates that invertebrate immunity can adapt to an immune challenge and mount a specific immune response.     

Is Salicylic Acid a Translocated Signal of Systemic Acquired Resistance in Tobacco?

Salicylic acid (SA) is a likely endogenous signal in the development of systemic acquired resistance (SAR) in some dicotyledonous plants. In tobacco mosaic virus (TMV)-resistant Xanthi-nc tobacco, SA levels increase systemically following the inoculation of a single leaf with TMV. To determine the extent to which systemic increases in SA result from SA export from the inoculated leaf, SA produced in TMV-inoculated or healthy leaves was noninvasively labeled with 18O2. Spatial and temporal distribution of 18O-SA indicated that most of the SA detected in the healthy tissues was synthesized in the inoculated leaf. No significant increase in the activity of benzoic acid 2-hydroxylase, the last enzyme involved in SA biosynthesis, was detected in upper uninoculated leaves, although the basal level of enzyme activity was relatively high. No increases in SA level, pathogenesis-related PR-1 gene expression, or TMV resistance in the upper uninoculated leaf were observed if the TMV-inoculated leaf was detached up to 60 hr after inoculation. Apart from the inoculated tissues, the highest increase in SA was observed in the leaf located directly above the inoculated leaf. The systemic SA increase observed during SAR may be explained by phloem transport of SA from the inoculation sites.     

Adaptive strategies and life history characteristics in a warming climate: Salmon in the Arctic?

In the warming Arctic, aquatic habitats are in flux and salmon are exploring their options. Adult Pacific salmon, including sockeye (Oncorhynchus nerka), coho (O. kisutch), Chinook (O. tshawytscha), pink (O. gorbuscha) and chum (O. keta) have been captured throughout the Arctic. Pink and chum salmon are the most common species found in the Arctic today. These species are less dependent on freshwater habitats as juveniles and grow quickly in marine habitats. Putative spawning populations are rare in the North American Arctic and limited to pink salmon in drainages north of Point Hope, Alaska, chum salmon spawning rivers draining to the northwestern Beaufort Sea, and small populations of chum and pink salmon in Canada’s Mackenzie River. Pacific salmon have colonized several large river basins draining to the Kara, Laptev and East Siberian seas in the Russian Arctic. These populations probably developed from hatchery supplementation efforts in the 1960’s. Hundreds of populations of Arctic Atlantic salmon (Salmo salar) are found in Russia, Norway and Finland. Atlantic salmon have extended their range eastward as far as the Kara Sea in central Russian. A small native population of Atlantic salmon is found in Canada’s Ungava Bay. The northern tip of Quebec seems to be an Atlantic salmon migration barrier for other North American stocks. Compatibility between life history requirements and ecological conditions are prerequisite for salmon colonizing Arctic habitats. Broad-scale predictive models of climate change in the Arctic give little information about feedback processes contributing to local conditions, especially in freshwater systems. This paper reviews the recent history of salmon in the Arctic and explores various patterns of climate change that may influence range expansions and future sustainability of salmon in Arctic habitats. A summary of the research needs that will allow informed expectation of further Arctic colonization by salmon is given.     

Telomere-Specialized Retroelements in Drosophila: Adaptive Symbionts of the Genome,Neutral, or in Conflict?

Linear chromosomes shorten in every round of replication. In Drosophila, telomere-specialized long interspersed retrotransposable elements (LINEs) belonging to the jockey clade offset this shortening by forming head-to-tail arrays at Drosophila telomere ends. As such, these telomeric LINEs have been considered adaptive symbionts of the genome, protecting it from premature decay, particularly as Drosophila lacks a conventional telomerase holoenzyme. However, as reviewed here, recent work reveals a high degree of variation and turnover in the telomere-specialized LINE lineages across Drosophila. There appears to be no absolute requirement for LINE activity to maintain telomeres in flies, hence the suggestion that the telomere-specialized LINEs may instead be neutral or in conflict with the host, rather than adaptive.     

Does GABA Act as a Signal in Plants?: Hints from Molecular Studies

GABA is a non-protein amino acid that accumulates rapidly in plant tissues in response to biotic and abiotic stress. There have been a number of suggestions as to the role that GABA might play in plants, ranging from a straightforward involvement in N metabolism to a signal mediating plant-animal and plant-microbe interactions. It has also been several proposed that it might function as an intracellular signalling molecule in plants. Here, we discuss recent evidence that plant cells respond at the molecular level to the presence of applied GABA. We argue that these data might serve as the basis for investigating the possible signalling role for GABA in plant development and stress responses in more detail.Key Words: 14-3-3 proteins, GABA, signalling, gene expression, stress, senescenceGABA (γ-aminobutyric acid), which comprises a significant fraction of the free amino acid pool in plant cells, was first identified in potato tubers over half a century ago, but its functions remained obscure for many years. In animal systems, GABA is present at high levels in the brain where it acts as an important neurotransmitter. GABA is synthesised in a pathway known as the GABA shunt, which operates not only in the animals, but in bacteria, fungi and plants too.^1,2 The function of GABA in plants has attracted renewed attention in the last decade following the discovery that intracellular and/or extracellular GABA concentrations increase rapidly in response to a range of stresses. Subsequently, a number of possible roles for GABA and the GABA shunt in plants have been suggested.^1,2 These include acting as a buffering mechanism in C and N metabolism, cytosolic pH regulation, protection against oxidative stress and defence against herbivorous pests. It has been proposed recently that one common function of GABA might be to mediate interactions between plants and other organisms, including bacterial and fungal pathogens, nematodes and insect pests.³ On the other hand, because of the rapid increases in GABA concentration in response to stress, it has sometimes been inferred that GABA might act as an intracellular signalling molecule in plants. However, few studies have adopted molecular approaches to GABA function, and molecular responses are largely unknown.     

How Fast Does a Signal Propagate through Proteins?

As the molecular basis of signal propagation in the cell, proteins are regulated by perturbations, such as mechanical forces or ligand binding. The question arises how fast such a signal propagates through the protein molecular scaffold. As a first step, we have investigated numerically the dynamics of force propagation through a single (Ala) protein following a sudden increase in the stretching forces applied to its end termini. The force propagates along the backbone into the center of the chain on the picosecond scale. Both conformational and tension dynamics are found in good agreement with a coarse-grained theory of force propagation through semiflexible polymers. The speed of force propagation of 50Å ps⁻¹ derived from these simulations is likely to determine an upper speed limit of mechanical signal transfer in allosteric proteins or molecular machines.     

Threat,Signal or Waste? Meaning of Corpses in two Dulotic Ant Species

Ant corpses, besides representing threat of infection by pathogens and parasites, can also be used during interspecific conflicts to inhibit the activity of the attacked colony, or they can be consumed as food. In the view of the former, the signal properties of corpses can be manifold. Besides discriminating nestmates and foes, the corpses of different ant species may act as cues for foragers, signaling the presence of other rival species, and triggering appropriate responses (e.g., alarm, retreat or foraging). In our study, we examined the responses of the facultative slave-maker Formica sanguinea and those of the obligate Polyergus rufescens towards corpses of nestmates, non-nestmate conspecifics, heterospecific slave-makers and their slaves, and corpses of non-enslaved host species under laboratory conditions. Both dulotic species responded differently to corpses of different origin. In F. sanguinea, the most intensive response was elicited by the corpses of P. rufescens and its slave, but also the corpses of non-nestmate conspecifics and their slaves elicited many adverse responses. In P. rufescens, the corpses of non-nestmate conspecifics and their slaves elicited the most adverse response. Both dulotic species distinguished corpses of their slaves from corpses of non-enslaved hosts. Based on our results, ant corpses are not meaningless objects scattered in the field, but cues carrying information that trigger different behavioral responses, and in F. sanguinea they can even represent an important food source.     

Shock,Stress or Signal? Implications of Freshwater Flows for a Top-Level Estuarine Predator

Physicochemical variability in estuarine systems plays an important role in estuarine processes and in the lifecycles of estuarine organisms. In particular, seasonality of freshwater inflow to estuaries may be important in various aspects of fish lifecycles. This study aimed to further understand these relationships by studying the movements of a top-level estuarine predator in response to physicochemical variability in a large, temperate south-east Australian estuary (Shoalhaven River). Mulloway (Argyrosomus japonicus, 47–89 cm total length) were surgically implanted with acoustic transmitters, and their movements and migrations monitored over two years via fixed-position VR2W acoustic receivers configured in a linear array along the length of the estuary. The study period included a high degree of abiotic variability, with multiple pulses (exponentially high flows over a short period of time) in fresh water to the estuary, as well as broader seasonal variation in flow, temperature and conductivity. The relative deviation of fish from their modal location in the estuary was affected primarily by changes in conductivity, and smaller fish (n = 4) tended to deviate much further downstream from their modal position in the estuary than larger fish (n = 8). High-flow events which coincided with warmer temperatures tended to drive mature fish down the estuary and potentially provided a spawning signal to stimulate aggregation of adults near the estuary mouth; however, this relationship requires further investigation. These findings indicate that pulse and press effects of freshwater inflow and associated physicochemical variability play a role in the movements of mulloway, and that seasonality of large freshwater flows may be important in spawning. The possible implications of river regulation and the extraction of freshwater for consumptive uses on estuarine fishes are discussed.     

Adaptive innate immunity? Responsive-mode prophylaxis in the mealworm beetle,Tenebrio molitor.

A primary infection by a parasite may indicate a higher risk of being reinfected in the near future (since infection may indicate that enemies are becoming more abundant). Acquired immunity does not exist in invertebrates despite the fact that they also face increased risks of reinfection following primary exposure. However, when subjected to immune insult, insects can produce immune responses that persist for long enough to provide prophylaxis. Because these immune responses are costly, persistence must be maintained through a selective advantage. We tested for the possibility that these long-lasting immune responses provided increased resistance to later infections by experimentally mimicking a primary immune insult (pre-challenge) in larvae of the mealworm beetle, Tenebrio molitor, with lipopolysaccharides (LPS) prior to early or late exposure to spores of the entomopathogenic fungus Metarhizium anisopliae. We found that pre-challenged larvae produced a long-lasting antimicrobial response, which provided a survival benefit when the larvae were exposed to fungal infection. These results suggest that the observed response is functionally "adaptive".     

Do Female Western Mosquitofish,Gambusia affinis,Prefer Ornaments That Males Lack?

Some species in the family Poeciliidae are known for extravagant male ornaments and courtship behavior (e.g., guppies), but the majority of poeciliids are characterized by coercive male copulation attempts that seem to circumvent female choice. In some lineages with male ornaments, female sensory bias may have preceded the evolution of corresponding male signals. We examined female preferences for colorful ornaments in Western mosquitofish, Gambusia affinis, in which males lack ornamentation and reproduce primarily through coercive mating attempts. We found that females exhibited a positional affinity for males that were artificially ornamented with blue coloration over males that had been treated with a transparent ornament. Females exhibited the opposite effect for males treated with red ornaments. In contrast, focal females did not exhibit behavioral discrimination between two live stimulus females or two models (silver fishing lures) with blue vs. transparent ornaments. This suggests a sexual context for female discrimination between males based on ornament color and whether an ornament was present. Because tribe Gambusiini is the basal branch of family Poeciliidae, the results of this study are consistent with the hypothesis that female responsiveness to male coloration is the ancestral poeciliid character state.     

Display of an Inedible Prop as a Signal of Aggression? Adaptive Significance of Leaf‐Display by the Turquoise‐Browed Motmot,Eumomota superciliosa

The incorporation of an inedible object (prop) into a behavioral display is rare among birds. Only four avian taxa have been reported to display with a prop, and in all studied species, prop use has been found to play a role in mate acquisition. However, little is known about the context and adaptive significance of prop use by the motmots. Both male and female motmots perform a leaf‐display, whereby a leaf is held horizontally in the tip of the bill for an extended period. I collected observational data on leaf‐display by the turquoise‐browed motmots (Eumomota superciliosa) to investigate the potential role of this display as a mate‐choice or agonistic signal. Observations of 61 leaf‐displays by 27 individuals indicate that males and females are similarly likely to perform the leaf‐display, that the leaf‐display is performed throughout the long‐breeding season, and that the display is performed by both paired and unpaired birds. These observations suggest that the leaf‐display does not play a role in mate‐attraction. However, the leaf‐display was often performed in association with a chase or fight with a same‐sex individual, and the display was sometimes performed in conjunction with an agonistic display at nest sites, suggesting that the leaf‐display may function in both sexes as a signal of aggressive intent or as a signal of status.     

Adaptive decision making or differential mortality: what causes offspring emergence in a gregarious parasitoid?

Hosts represent a limited resource for the developing offspring of parasitic insects laying eggs in or on spatially discrete resources like fruits, seeds, or other insects. The quality of hosts differs with respect to the value and amount of resources they provide for the feeding larvae. Accordingly, the size of a clutch of eggs laid on a given host should be a function of host quality, because severe competition between developing larvae can lead to increased mortality and/or decreased size of the offspring, both causing a fitness loss for the offspring and the mother. Therefore, females should be selected for the ability to estimate host quality and to adjust their clutch size accordingly. Using the parasitic wasp Nasonia vitripennis (Walker) (Hymenoptera: Pteromalidae) this study investigated the respective contribution of developmental mortality of offspring vs. the clutch size decision of the mother as a determinant of final offspring emergence per host. In addition, taking offspring size into account, the study examined the fitness consequences of female oviposition decisions. Developmental mortality was very low in all quality classes of hosts except previously frozen and thus dead host pupae. Females laid reduced clutch sizes on dead, previously parasitized, and smaller hosts. In contrast to offspring number, offspring size did not differ between host qualities. We conclude that females are able to sense the quality of a host and adjust the number of eggs they lay to mitigate larval competition.