Evolution: an exception that proves the rule

A careful comparative analysis suggests a simple explanation for a category of exceptions to the general correlation between separate sexes in plants -- dioecy -- and self-incompatibility. In some genera, polyploidy causes failure of self-incompatibility, and dioecy may then evolve.     

Sperm sexing in sheep and cattle: the exception and the rule

Flow cytometric sorting for the preselection of sex has progressed considerably in the 20 years since its inception. This technique has allowed the production of pre-sexed offspring in a multitude of species and become a commercial success in cattle around the world. However, due to the stress inherent to the sex-sorting process, sex-sorted spermatozoa are widely recognized as functionally compromised in terms of their fertilizing lifespan within the female reproductive tract as a result of reduced motility and viability and changed functional state. These characteristics, when compared to non-sorted controls, are manifest in vivo as lower fertility. However, improvements to the technology and a greater understanding of its biological impact have facilitated recent developments in sheep, showing sex-sorting is capable of selecting a functionally superior population in terms of both in vitro and in vivo function. These results are reviewed in the context of recent developments in other species and the reasons for success after artificial insemination with sex-sorted ram spermatozoa are discussed.     

Frequency-dependent selection in hermaphrodites: the rule rather than the exception

It is shown for simple assumptions that frequency-dependent selection in seed plants may have at least three causes, namely: (a) sexual asymmetry; (b) differential genotypic selfing rates; and (c) gene-cytoplasm fertility interactions. Sexual asymmetry is defined as the situation where the ratio of pollen: ovule fertility is not the same for all genotypes or phenotypes in a population. A review of the literature suggests that all three causes of frequency-dependent selection probably occur in nature, and that at least the first cause, sexual asymmetry, is probably widespread in hermaphrodites. It is shown that resource-allocation theory leads to the expectation that sexual asymmetry and, therefore, frequency-dependent selection should be almost universal in hermaphrodite populations which are not largely selfed. A method for obtaining frequency-dependent fitness values is presented and applied to a population of Scots pine ( Pinus sylvestris ) showing strong sexual asymmetry.     

The discovery-dominance trade-off is the exception, rather than the rule

1. Interspecific trade-offs are thought to facilitate coexistence between species at small spatial scales. The discovery-dominance trade-off, analogous to a competition-colonisation trade-off, is considered an important structuring mechanism in ant ecology. A trade-off between species' ability to discover food resources and to dominate them may explain how so many species apparently dependent on similar resources can coexist. 2. The discovery-dominance trade-off is thought to be broken by invasive species in enemy-free space or territorial species whose activity is fuelled by domination of carbohydrate resources. It may also be mediated by factors such as temperature and habitat structure. 3. We investigate the generality and form of the discovery-dominance relationship in an experiment using habitats of contrasting complexity across three continents. In addition, to assess how widespread the discovery-dominance trade-off is, we conducted a systematic review combining all empirical studies (published and from our experiment). 4. From our own fieldwork and meta-analyses of available studies, we find surprisingly little empirical support for the trade-off, with results indicating that mean effect sizes were either not significantly different from 0 or significantly positive. The trade-off was only detected in studies with parasitoids present. Additionally, experimental data from simple and complex habitats within each continent suggest that simple habitats may facilitate both food resource discovery and dominance. 5. We conclude that the discovery-dominance trade-off is the exception, rather than the rule. Instead, these abilities were commonly correlated. Real food resources provide many axes along which partitioning may occur, and discovery-dominance trade-offs are not a prerequisite for coexistence.     

Primary structure analysis proves that protein phosphatases 2C1 and 2C2 are isozymes

The two recently discovered forms of protein phosphatase 2C, termed 2C1 and 2C2, were digested with CNBr or trypsin, and several peptides corresponding to two regions of the protein were sequenced. These studies revealed close homology between the two enzymes with 49 identities over the 62 residues that could be compared directly. The results establish that protein phosphatases 2C1 and 2C2 are the products of different genes. The C-terminus of protein phosphatase 2C2 has also been identified.     

The exception that confirms the rule: a higher-order telomeric G-quadruplex structure more stable in sodium than in potassium

DNA and RNA guanine-quadruplexes (G4s) are stabilized by several cations, in particular by potassium and sodium ions. Generally, potassium stabilizes guanine-quartet assemblies to a larger extent than sodium; in this article we report about a higher-order G4 structure more stable in sodium than in potassium. Repeats of the DNA GGGTTA telomeric motif fold into contiguous G4 units. Using three independent approaches (thermal denaturation experiments, isothermal molecular-beacon and protein-binding assays), we show that the (GGGTTA)₇GGG sequence, folding into two contiguous G4 units, exhibits an unusual feature among G4 motifs: despite a lower thermal stability, its sodium conformation is more stable than its potassium counterpart at physiological temperature. Using differential scanning calorimetry and mutated sequences, we show that this switch in the relative stability of the sodium and potassium conformations (occurring around 45°C in 100 mM cation concentration) is the result of a more favorable enthalpy change upon folding in sodium, generated by stabilizing interactions between the two G4 units in the sodium conformation. Our work demonstrates that interactions between G4 structural domains can make a higher-order structure more stable in sodium than in potassium, even though its G4 structural domains are individually more stable in potassium than in sodium.     

Termite mounds as browsing hotspots: an exception to the rule

In African savannas, termite mounds usually serve as browsing hotspots for mammals because of their soil fertility. Van der Plas et al., in this issue, describe that browsers avoid the unpalatable, evergreen tree species on mounds of Macrotermes natalensis in a mesic savanna, preferring mainly leguminous species with high leaf N and P concentrations in the matrix. This exception is probably a consequence of the fertile soils of the study area, and highlights the importance of environmental context for assessing ecological interactions.     

The ovaries of Mecoptera: basic similarities and one exception to the rule

Two entirely different types of ovaries (ovarioles) have been described in mecopterans. In the representatives of Meropeidae, Bittacidae, Panorpodidae and Panorpidae the ovarioles are of the polytrophic-meroistic type. Four regions: a terminal filament, germarium, vitellarium and ovariole stalk can be distinguished in the ovarioles. The germaria house numerous germ cell clusters. Each cluster arises as a result of 2 consecutive mitoses of a cystoblast and consists of 4 sibling cells. The oocyte always differentiates from one of the central cells of the cluster, whereas the remaining 3 cells develop into large, polyploid nurse cells. The vitellaria contain 7-12 growing egg chambers (= oocyte-nurse cell complexes). In contrast, the ovaries of the snow flea, Boreus hyemalis, are devoid of nurse cells and therefore panoistic (secondary panoistic). The ovarioles are composed of terminal filaments, vitellaria and ovariole stalks only; in adult females functional germaria are absent. Histochemical tests suggest that amplification of rDNA takes place in the oocyte nuclei. Resulting dense nucleolar masses undergo fragmentation into multiple polymorphic nucleoli. The classification of extant mecopterans as well as the phylogenetic relationships between Mecoptera and Siphonaptera are discussed in the context of presented data.     

Sex-specific recombination rates in Parus major and P. caeruleus, an exception to Huxley's rule

Huxley's rule predicts lower recombination rates in the heterogametic sex than in the homogametic one. The genotyping of Parus major and P. caeruleus families at 8 microsatellite and 4 enzyme loci yielded contradicting data. Significant genotypic disequilibrium was observed between esterase-1, esterase-2 and esterase-3 in adults of P. major and between esterase-2/esterase-3 and esterase-2/microsatellite PK-12 in P. caeruleus. Support comes from linkage analyses of nuclear families. In P. major, the recombination rate of esterase-2/esterase -3 in males is significantly lower than in females (theta(male) = 0.076, theta(female) = 0.145). The opposite is found for the recombination rates of esterase-1/esterase-2 and esterase-2/esterase-3 in P. caeruleus (EST-1/EST-2: theta(female) = 0.218, theta(male) = 0.5, EST-2/EST-3: theta(female) = 0.109, theta(male) = 0.194). We conclude that the basis of differences in recombination rates cannot be heterogamety, per se, but must have multiple genetic causes including chromosomal rearrangments that have evolved after the cladogenesis of the two species.     

Exception to the exception rule: synthetic and naturally occurring single chromosome Vibrio cholerae

The genome of Vibrio cholerae, the etiological agent of cholera, is an exception to the single chromosome rule found in the vast majority of bacteria and has its genome partitioned between two unequally sized chromosomes. This unusual two-chromosome arrangement in V. cholerae has sparked considerable research interest since its discovery. It was demonstrated that the two chromosomes could be fused by deliberate genome engineering or forced to fuse spontaneously by blocking the replication of Chr2, the secondary chromosome. Recently, natural isolates of V. cholerae with chromosomal fusion have been found. Here, we summarize the pertinent findings on this exception to the exception rule and discuss the potential utility of single-chromosome V. cholerae to address fundamental questions on chromosome biology in general and DNA replication in particular.     

An exception to the rule: common vampire bats do not learn taste aversions

Conditioned taste aversions function by preventing an organism from ingesting a food previously associated with gastrointestinal malaise. Taste-aversion learning has been observed in many animals: molluscs to mammals, insects to birds. However, among mammals, neither bats nor monophagous species have been investigated adequately. Here we show that although three dietary generalists (one insectivorous and two frugivorous bats) readily acquired taste aversions, the common vampire bat, Desmodus rotundus, a monophageous feeder on vertebrate blood, did not learn to associate a novel flavour with aversive gastrointestinal events. We interpret these data as consistent with the hypothesis that taste aversions are an adaptive specialization of learning. Copyright 2003 The Association for the Study of Animal Behaviour. Published by Elsevier Science Ltd. All rights reserved.      

High-affinity binding at quadruplex–duplex junctions: rather the rule than the exception

Quadruplex-duplex (Q–D) junctions constitute unique structural motifs in genomic sequences. Through comprehensive calorimetric as well as high-resolution NMR structural studies, Q–D junctions with a hairpin-type snapback loop coaxially stacked onto an outer G-tetrad were identified to be most effective binding sites for various polycyclic quadruplex ligands. The Q–D interface is readily recognized by intercalation of the ligand aromatic core structure between G-tetrad and the neighboring base pair. Based on the thermodynamic and structural data, guidelines for the design of ligands with enhanced selectivity towards a Q–D interface emerge. Whereas intercalation at Q–D junctions mostly outcompete stacking at the quadruplex free outer tetrad or intercalation between duplex base pairs to varying degrees, ligand side chains considerably contribute to the selectivity for a Q–D target over other binding sites. In contrast to common perceptions, an appended side chain that additionally interacts within the duplex minor groove may confer only poor selectivity. Rather, the Q–D selectivity is suggested to benefit from an extension of the side chain towards the exposed part of the G-tetrad at the junction. The presented results will support the design of selective high-affinity binding ligands for targeting Q–D interfaces in medicinal but also technological applications.     

"Guilt by association" is the exception rather than the rule in gene networks

Gene networks are commonly interpreted as encoding functional information in their connections. An extensively validated principle called guilt by association states that genes which are associated or interacting are more likely to share function. Guilt by association provides the central top-down principle for analyzing gene networks in functional terms or assessing their quality in encoding functional information. In this work, we show that functional information within gene networks is typically concentrated in only a very few interactions whose properties cannot be reliably related to the rest of the network. In effect, the apparent encoding of function within networks has been largely driven by outliers whose behaviour cannot even be generalized to individual genes, let alone to the network at large. While experimentalist-driven analysis of interactions may use prior expert knowledge to focus on the small fraction of critically important data, large-scale computational analyses have typically assumed that high-performance cross-validation in a network is due to a generalizable encoding of function. Because we find that gene function is not systemically encoded in networks, but dependent on specific and critical interactions, we conclude it is necessary to focus on the details of how networks encode function and what information computational analyses use to extract functional meaning. We explore a number of consequences of this and find that network structure itself provides clues as to which connections are critical and that systemic properties, such as scale-free-like behaviour, do not map onto the functional connectivity within networks.     

When the exception becomes the rule: The disappearance of limiting similarity in the Lotka-Volterra model

We investigate the transition between limiting similarity and coexistence of a continuum in the competitive Lotka-Volterra model. It is known that there exist exceptional cases in which, contrary to the limiting similarity expectation, all phenotypes coexist along a trait axis. Earlier studies established that the distance between surviving phenotypes is in the magnitude of the niche width 2σ provided that the carrying capacity curve differs from the exceptional one significantly enough. In this paper we studied the outcome of competition for small perturbations of the exceptional (Gaussian) carrying capacity. We found that the average distance between the surviving phenotypes goes to zero when the perturbation vanishes. The number of coexisting species in equilibrium is proportional to the negative logarithm of the perturbation. Nevertheless, the niche width provides a good order of magnitude for the distance between survivors if the perturbations are larger than 10%. Therefore, we conclude that limiting similarity is a good framework of biological thinking despite the lack of an absolute lower bound of similarity.     

SIR2 calls upon the ER

Resveratrol induces longevity in C. elegans through the action of SIR2. Recently published work shows that resveratrol induces genes of the unfolded protein stress response of the endoplasmic reticulum. Paradoxically, these stress genes are repressed by SIR2, suggesting that resveratrol increases life span by inhibiting this SIR2 action.     

Sea lamprey Petromyzon marinus: an exception to the rule of homing in anadromous fishes

Anadromous fishes are believed to make regular circuits of migration in the sea before homing to their natal rivers. Sea lamprey Petromyzon marinus is an anadromous fish that is an exception to this life-history pattern. It also differs from other anadromous fishes in that its adult phase is parasitic, a feeding strategy that should make homing problematic for lamprey cohorts that become widely dispersed through transport by the diverse hosts they parasitize. We sequenced a portion of the mitochondrial DNA control region from sea lampreys collected from 11 North American east coast rivers to test for genetic evidence of homing. There were no significant differences (chi2=235.1, p=0.401) in haplotype frequencies among them, with almost 99 per cent of haplotypic diversity occurring within populations. These findings, together with concordant genetic results from other geographical regions and ancillary information on pheromonal communication, suggest that sea lamprey does not home but rather exhibits regional panmixia while using a novel 'suitable river' strategy to complete its life cycle.     

Mutations that Allow SIR2 Orthologs to Function in a NAD+-Depleted Environment

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