Mutational meltdown in primary endosymbionts: selection limits Muller's ratchet

Background Primary bacterial endosymbionts of insects (p-endosymbionts) are thought to be undergoing the process of Muller's ratchet where they accrue slightly deleterious mutations due to genetic drift in small populations with negligible recombination rates. If this process were to go unchecked over time, theory predicts mutational meltdown and eventual extinction. Although genome degradation is common among p-endosymbionts, we do not observe widespread p-endosymbiont extinction, suggesting that Muller's ratchet may be slowed or even stopped over time. For example, selection may act to slow the effects of Muller's ratchet by removing slightly deleterious mutations before they go to fixation thereby causing a decrease in nucleotide substitutions rates in older p-endosymbiont lineages. Methodology/Principal Findings To determine whether selection is slowing the effects of Muller's ratchet, we determined the age of the Candidatus Riesia/sucking louse assemblage and analyzed the nucleotide substitution rates of several p-endosymbiont lineages that differ in the length of time that they have been associated with their insect hosts. We find that Riesia is the youngest p-endosymbiont known to date, and has been associated with its louse hosts for only 13–25 My. Further, it is the fastest evolving p-endosymbiont with substitution rates of 19–34% per 50 My. When comparing Riesia to other insect p-endosymbionts, we find that nucleotide substitution rates decrease dramatically as the age of endosymbiosis increases. Conclusions/Significance A decrease in nucleotide substitution rates over time suggests that selection may be limiting the effects of Muller's ratchet by removing individuals with the highest mutational loads and decreasing the rate at which new mutations become fixed. This countering effect of selection could slow the overall rate of endosymbiont extinction.

In vivo expression technology (IVET) selection of genes of Rhizobium leguminosarum biovar viciae A34 expressed in the rhizosphere

IVET was used to identify genes that are specifically expressed in the rhizosphere of the pea-nodulating bacterium Rhizobium leguminosarum A34. A library of R. leguminosarum A34 cloned in the integration vector pIE1, with inserts upstream of a promoter-less purN:gfp:gusA, was conjugated into purN host RU2249 and recombined into the genome. After removal of colonies that expressed the reporter genes of the vector under laboratory conditions, the library was inoculated into a nonsterile pea rhizosphere. The key result is that 29 rhizosphere-induced loci were identified. Sequence analysis of these clones showed that a wide variety of R. leguminosarum A34 genes are expressed specifically in the rhizosphere including those encoding proteins involved in environmental sensing, control of gene expression, metabolic reactions and membrane transport. These genes are likely to be important for survival and colonization of the pea rhizosphere.

In vivo selection for metastasis promoting genes in the mouse

Here, we report the identification of a metastasis promoting factor by a forward genetic screen in mice. A retroviral cDNA library was introduced into the nonmetastatic cancer cell line 168FARN, which was then orthotopically transplanted into mouse mammary fat pads, followed by selection for cells that metastasize to the lung. The genes encoding the disulfide isomerase ERp5 and beta-catenin were found to promote breast cancer invasion and metastasis. Disulfide isomerases (thiol isomerases), which catalyze disulfide bond formation, reduction, and isomerization, have not previously been implicated in cancer cell signaling and tumor metastasis. Overexpression of ERp5 promotes both in vitro migration and invasion and in vivo metastasis of breast cancer cells. These effects were shown to involve activation of ErbB2 and phosphoinositicle 3-kinase (PI3K) pathways through dimerization of ErbB2. Activation of ErbB2 and PI3K subsequently stimulates RhoA and beta-catenin, which mediate the migration and invasion of tumor cells. Inhibition of ErbB2 and PI3K reverses the phenotypes induced by ERp5. Finally, ERp5 was shown to be up-regulated in human surgical samples of invasive breast cancers. These data identify a link between disulfide isomerases and tumor development, and provide a mechanism that modulates ErbB2 and PI3K signaling in the promotion of cancer progression.

Modelling habitat selection and distribution of the critically endangered Jerdon's courser Rhinoptilus bitorquatus in scrub jungle: an application of a new tracking method

1. Jerdon's courser Rhinoptilus bitorquatus is a nocturnally active cursorial bird that is only known to occur in a small area of scrub jungle in Andhra Pradesh, India, and is listed as critically endangered by the IUCN. Information on its habitat requirements is needed urgently to underpin conservation measures. We quantified the habitat features that correlated with the use of different areas of scrub jungle by Jerdon's coursers, and developed a model to map potentially suitable habitat over large areas from satellite imagery and facilitate the design of surveys of Jerdon's courser distribution. 2. We used 11 arrays of 5-m long tracking strips consisting of smoothed fine soil to detect the footprints of Jerdon's coursers, and measured tracking rates (tracking events per strip night). We counted the number of bushes and trees, and described other attributes of vegetation and substrate in a 10-m square plot centred on each strip. We obtained reflectance data from Landsat 7 satellite imagery for the pixel within which each strip lay. 3. We used logistic regression models to describe the relationship between tracking rate by Jerdon's coursers and characteristics of the habitat around the strips, using ground-based survey data and satellite imagery. 4. Jerdon's coursers were most likely to occur where the density of large (>2 m tall) bushes was in the range 300-700 ha(-1) and where the density of smaller bushes was less than 1000 ha(-1). This habitat was detectable using satellite imagery. 5. Synthesis and applications. The occurrence of Jerdon's courser is strongly correlated with the density of bushes and trees, and is in turn affected by grazing with domestic livestock, woodcutting and mechanical clearance of bushes to create pasture, orchards and farmland. It is likely that there is an optimal level of grazing and woodcutting that would maintain or create suitable conditions for the species. Knowledge of the species' distribution is incomplete and there is considerable pressure from human use of apparently suitable habitats. Hence, distribution mapping is a high conservation priority. A two-step procedure is proposed, involving the use of ground surveys of bush density to calibrate satellite image-based mapping of potential habitat. These maps could then be used to select priority areas for Jerdon's courser surveys. The use of tracking strips to study habitat selection and distribution has potential in studies of other scarce and secretive species.

A fast linear-in-the-parameters classifier construction algorithm using orthogonal forward selection to minimize leave-one-out misclassification rate

We propose a simple and computationally efficient construction algorithm for two class linear-in-the-parameters classifiers. In order to optimize model generalization, a forward orthogonal selection (OFS) procedure is used for minimizing the leave-one-out (LOO) misclassification rate directly. An analytic formula and a set of forward recursive updating formula of the LOO misclassification rate are developed and applied in the proposed algorithm. Numerical examples are used to demonstrate that the proposed algorithm is an excellent alternative approach to construct sparse two class classifiers in terms of performance and computational efficiency.

Trade-off associated with selection for increased ability to resist parasitoid attack in Drosophila melanogaster

Costs of resistance are widely assumed to be important in the evolution of parasite and pathogen defence in animals, but they have been demonstrated experimentally on very few occasions. Endoparasitoids are insects whose larvae develop inside the bodies of other insects where they defend themselves from attack by their hosts' immune systems (especially cellular encapsulation). Working with Drosophila melanogaster and its endoparasitoid Leptopilina boulardi, we selected for increased resistance in four replicate populations of flies. The percentage of flies surviving attack increased from about 0.5% to between 40% and 50% in five generations, revealing substantial additive genetic variation in resistance in the field population from which our culture was established. In comparison with four control lines, flies from selected lines suffered from lower larval survival under conditions of moderate to severe intraspecific competition.

Cross-resistance following artificial selection for increased defense against parasitoids in Drosophila melanogaster

An increase in resistance to one natural enemy may result in no correlated change, a positive correlated change, or a negative correlated change in the ability of the host or prey to resist other natural enemies. The type of specificity is important in understanding the evolutionary response to natural enemies and was studied here in a Drosaphila-parasitoid system. Drosophila melanogaster lines selected for increased larval resistance to the endoparasitoid wasps Asobara tabida or Leptopilina boulardi were exposed to attack by A. tabida, L. boulardi and Leptopilina heterotama at 15 degrees C, 20 degrees C, and 25 degrees C. In general, encapsulation ability increased with temperature, with the exception of the lines selected against L. boulardi, which showed the opposite trend. Lines selected against L, boulardi showed large increases in resistance against all three parasitoid species, and showed similar levels of defense against A. tabida to the lines selected against that parasitoid. In contrast, lines selected against A. tabida showed a large increase in resistance to A. tabida and generally to L. heterotoma, but displayed only a small change in their ability to survive attack by L. boulardi. Such asymmetries in correlated responses to selection for increased resistance to natural enemies may influence host-parasitoid community structure.

To 'be', and not to 'have': auxiliary selection in unaccusative verbs in Italian

This paper investigates the characteristics of unaccusative verbs in Italian with respect to the consistency with which these verbs select the auxiliaries ‘be’ (essere) and ‘have’ (avere) in compound tense forms. The study builds on the gradient approach to split intransitivity (Sorace 2000) by exploring the behaviour of 29 intransitive Italian verbs with respect to their core-peripheral features: auxiliary selection acceptability ratings and associated variance measures. Although there is clear support for the gradient approach in relation to the general order of semantic categories along the unaccusativity gradient, the results reveal that the ordering of subclasses within the Change group conflict with that currently proposed in the literature. In addition, the findings demonstrate the aspectual and lexical semantic characteristics of internally-caused change-of-state verbs in Italian require further investigation before their auxiliary selection behaviour can be properly understood. Furthermore, contrary to the gradient account, Existence verbs, the most stative and therefore the most peripheral subclass in the unaccusativity hierarchy, exhibit behaviour more characteristic of core unaccusative verbs. This study examines a wider range of semantic subclasses of unaccusative verbs than has hitherto been reported and identifies the core-peripheral boundary for Italian.1