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 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.     

"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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Optimal offspring size in a small mammal: an exception to the tradeoff invariant life-history rule

Offspring size and number were examined in a captive population of wild guinea pigs ( Cavia aperea ), and findings were compared with models of optimal offspring size for small litters. Median and modal litter size was two, regardless of maternal size or parity. Females producing their second litter tended to have litters that were larger than average. In contrast, young females that were still growing never had litters that were larger than average. Mean offspring size decreased and variation in offspring size tended to decrease with increasing litter size. Optimal offspring size models, in which offspring survival depended on the amount of resources invested, as well as litter size, predict such a trend. Little support was found for Charnov and Downhower's (1995) tradeoff invariant life-history rule that the range in offspring sizes between litters is inversely proportional to the size of the litter. Cavia aperea may be an exception to this rule because pup mass at birth did not reflect total reproductive investment, because conversion of resources into litter mass may not be linearly related to litter size and because resources were not equally partitioned among offspring within large litters. Experimental data are needed to determine the relevance of these results among mammals in general.     

Bypassing the catalytic activity of SIR2 for SIR protein spreading in Saccharomyces cerevisiae

Sir protein spreading along chromosomes and silencing in Saccharomyces cerevisiae requires the NAD+-dependent histone deacetylase activity of Sir2p. We tested whether this requirement could be bypassed at the HM loci and telomeres in cells containing a stably expressed, but catalytically inactive mutant of Sir2p, sir2-345p, plus histone mutants that mimic the hypoacetylated state normally created by Sir2p. Sir protein spreading was rescued in sir2-345 mutants expressing histones in which key lysine residues in their N-termini had been mutated to arginine. Mating in these mutants was also partially restored upon overexpression of Sir3p. Together, these results indicate that histone hypoacetylation is sufficient for Sir protein spreading in the absence of production of 2'-O-acetyl-ADP ribose by sir2p and Sir2p's enzymatic function for silencing can be bypassed in a subset of cells in a given population. These results also provide genetic evidence for the existence of additional critical substrates of Sir2p for silencing in vivo.     

SIR2-deficient Leishmania infantum induces a defined IFN-gamma/IL-10 pattern that correlates with protection

The ability to manipulate the Leishmania genome to create genetically modified parasites by introducing or eliminating genes is considered a powerful alternative for developing a new generation vaccine against leishmaniasis. Previously, we showed that the deletion of one allele of the Leishmania infantum silent information regulatory 2 (LiSIR2) locus was sufficient to dramatically affect amastigote axenic proliferation. Furthermore, LiSIR2 single knockout (LiSIR2(+/-)) amastigotes were unable to replicate in vitro inside macrophages. Because this L. infantum mutant persisted in BALB/c mice for up to 6 wk but failed to establish an infection, we tested its ability to provide protection toward a virulent L. infantum challenge. Strikingly, vaccination with a single i.p. injection of LiSIR2(+/-) single knockout elicits complete protection. Thus, vaccinated BALB/c mice showed a reversal of T cell anergy with specific anti-Leishmania cytotoxic activity and high levels of NO production. Moreover, vaccinated mice simultaneously generated specific anti-Leishmania IgG Ab subclasses suggestive of both type 1 and type 2 responses. A strong correlation was found between the elimination of the parasites and an increased Leishmania-specific IFN-gamma/IL-10 ratio. Therefore, we propose that the polarization to a high IFN-gamma/low IL-10 ratio after challenge is a clear indicator of vaccine success. Furthermore these mutants, which presented attenuated virulence, represent a good model to understand the correlatives of protection in visceral leishmaniasis.     

Geographical variations of the skull in the red fox Vulpes vulpes on the Japanese Islands: an exception to Bergmann's rule

In order to clarify the morphological differences between two subspecies of the red fox (Vulpes vulpes) on the Japanese Islands and test the validity of Bergmann's rule, we examined geographical variations in 25 cranial and 24 dental characters in V. v. schrencki from Hokkaido and V. v. japonica from the other main islands of Japan (Honshu, Shikoku, and Kyushu). Many skull measurements, including the male greatest length, condylobasal length, and the length of upper and lower tooth rows, were significantly larger for V. v. japonica than for V. v. schrencki, whereas most tooth measurements, especially the length of molars and premolars, in V. v. schrencki were larger than those in V. v. japonica. Although the two subspecies were morphologically well-differentiated from each other, the results did not support that they have evolved following Bergmann's rule of adaptation to cold climates. Based on consideration of the relatively large differences of their tooth sizes, which are not easily influenced by food abundance, and previous genetic research on the different migration histories of the two subspecies, the morphological differences detected in the present study may have resulted not only from the present ecological differences between the two subspecies, but also from the difference of migration history and evolutionary constraints.     

Electron-nuclear double resonance spectroscopy of 15N-enriched phthalate dioxygenase from Pseudomonas cepacia proves that two histidines are coordinated to the [2Fe-2S] Rieske-type clusters

We have performed ENDOR spectroscopy at microwave frequencies of 9 and 35 GHz at 2 K on the reduced Rieske-type [2Fe-2S] cluster of phthalate dioxygenase (PDO) from Pseudomonas cepacia. Four samples have been examined: (1) 14N (natural abundance); (2) uniformly 15N labeled; (3) [15N]histidine in a 14N background; (4) [14N]histidine in a 15N background. These studies establish unambiguously that two of the ligands to the Rieske [2Fe-2S] center are nitrogens from histidine residues. This contrasts with classical ferredoxin-type [2Fe-2S] centers in which all ligation is by sulfur of cysteine residues. Analysis of the polycrystalline ENDOR patterns has permitted us to determine for each nitrogen ligand the principal values of the hyperfine tensor and its orientation with respect to the g tensor, as well as the 14N quadrupole coupling tensor. The combination of these results with earlier M?ssbauer and resonance Raman studies supports a model for the reduced cluster with both histidyl ligands bound to the ferrous ion of the spin-coupled [Fe2+ (S = 2), Fe3+ (S = 5/2)] pair. The analyses of 15N hyperfine and 14N quadrupole coupling tensors indicate that the geometry of ligation at Fe2+ is approximately tetrahedral, with the (Fe)2(N)2 plane corresponding to the g1-g3 plane, and that the planes of the histidyl imidazoles lie near that plane, although they could not both lie in the plane. The bonding parameters of the coordinated nitrogens are fully consistent with those of an spn hybrid on a histidyl nitrogen coordinated to Fe. Differences in 14N ENDOR line width provide evidence for different mobilities of the two imidazoles when the protein is in fluid solution. We conclude that the structure deduced here for the PDO cluster is generally applicable to the full class of Rieske-type centers.