Pollination and dispersal trait spectra recover faster than the growth form spectrum during spontaneous succession in sandy old‐fields

Question: Spontaneous succession is the most natural and cost‐effective solution for grassland restoration. However, little is known about the time required for the recovery of grassland functionality, i.e., for the recovery of reproductive and vegetative processes typical of pristine grasslands. Since these processes operate at different scales, we addressed the question: do reproductive and vegetative processes require different recovery times during spontaneous succession? Location: Kiskunság sand region (Central Hungary). Methods: As combinations of plant traits can be used to highlight general patterns in ecological processes, we compared reproductive (pollination‐ and dispersal‐related) and vegetative (growth form) traits between recovered grasslands of different age (<10 years old; 10–20 years old; 20–40 years old) and pristine grasslands. Results: During spontaneous succession, the reproductive trait spectra became similar to those of pristine grasslands earlier than the vegetative ones. In arable land abandoned for 10 years, pollination‐ and dispersal‐related trait spectra did not show significant difference to those of pristine grasslands; anemophily and anemochory were the prevailing strategies. Contrarily, significant differences in the growth form spectrum could be observed even after 40 years of abandonment; in recovered grasslands erect leafy species prevailed, while the fraction of dwarf shrubs and tussock‐forming species was significantly lower than in pristine grasslands. Conclusions: The recovery of the ecological processes of pristine grasslands might require different amounts of time, depending on the spatial scale at which they operate. The reproductive trait spectra recovered earlier than the vegetative one, since reproductive attributes first determine plant species sorting at the regional level towards their respective habitats. The recovery of the vegetative trait spectrum needs more time as vegetative‐based interactions operate on a smaller spatial scale. Thus, vegetative traits might be more effective in the long‐term assessment of restoration success than the reproductive ones

Learning biophysically-motivated parameters for alpha helix prediction

<p>Abstract</p> <p>Background</p> <p>Our goal is to develop a state-of-the-art protein secondary structure predictor, with an intuitive and biophysically-motivated energy model. We treat structure prediction as an optimization problem, using parameterizable cost functions representing biological "pseudo-energies". Machine learning methods are applied to estimate the values of the parameters to correctly predict known protein structures.</p> <p>Results</p> <p>Focusing on the prediction of alpha helices in proteins, we show that a model with 302 parameters can achieve a Q_{<it>α </it>}value of 77.6% and an SOV_{<it>α </it>}value of 73.4%. Such performance numbers are among the best for techniques that do not rely on external databases (such as multiple sequence alignments). Further, it is easier to extract biological significance from a model with so few parameters.</p> <p>Conclusion</p> <p>The method presented shows promise for the prediction of protein secondary structure. Biophysically-motivated elementary free-energies can be learned using SVM techniques to construct an energy cost function whose predictive performance rivals state-of-the-art. This method is general and can be extended beyond the all-alpha case described here.</p

High lifetime inbreeding depression counteracts the reproductive assurance benefit of selfing in a mass-flowering shrub

Background Decreases in mate and/or pollinator availability would be expected to affect the selective pressure on plant mating systems. An increase in self-fertilization may evolve to compensate for the negative effects of pollination failure. However, the benefit of selfing in variable pollination environments depends on the relative fitnesses of selfed and outcrossed progeny. We investigated the potential for selfing to provide reproductive assurance over the lifetime of a long-lived perennial species and its variation between plant patches of various sizes. Patch size is likely to affect mate and pollinator availabilities, thereby affecting pollination success and the rate of selfing. We estimated fruit and seed set, reproductive assurance, self-compatibility, the multilocus patch selfing rate and lifetime inbreeding depression in natural patches of Rhododendron ferrugineum (Ericaceae), a mass-flowering species characterized by considerable patch size variation (as estimated by the total number of inflorescences).Results Open seed set declined linearly with increasing patch size, whereas pollinator-mediated seed set (emasculated flowers) was not significantly affected. Progeny array analysis indicated that the selfing rate declined with increasing patch size, consistent with greater reproductive assurance in small sparse patches than in large, dense patches. However, fruit set and adult fitness decreased with decreasing patch size, with an estimated mean lifetime inbreeding depression of 0.9 (obtained by comparing F values in adults and progenies).Conclusions Lifetime inbreeding depression strongly counteracts the advantage of reproductive assurance due to selfing in this long-lived species. The poor fitness of selfed offspring should counteract any evolution towards selfing, despite its potential to alleviate the negative consequences of pollen limitation. This study highlights the need to estimate lifetime inbreeding depression, together with mating system and pollination parameters, if we are to understand the actual benefit of selfing and avoid the overestimation of reproductive assurance

Pollen transfer in fragmented plant populations: insight from the pollen loads of pollinators and stigmas in a mass-flowering species

International audiencePollinator and/or mate scarcity affects pollen transfer, with important ecological and evolutionary consequences for plant reproduction. However, the way in which the pollen loads transported by pollinators and deposited on stigmas are affected by pollination context has been little studied. We investigated the impacts of plant mate and visiting insect availabilities on pollen transport and receipt in a mass-flowering and facultative autogamous shrub (Rhododendron ferrugineum). First, we recorded insect visits to R. ferrugineum in plant patches of diverse densities and sizes. Second, we analyzed the pollen loads transported by R. ferrugineum pollinators and deposited on stigmas of emasculated and intact flowers, in the same patches. Overall, pollinators (bumblebees) transported much larger pollen loads than the ones found on stigmas, and the pollen deposited on stigmas included a high proportion of conspecific pollen. However, comparing pollen loads of emasculated and intact flowers indicated that pollinators contributed only half the conspecific pollen present on the stigma. At low plant density, we found the highest visitation rate and the lowest proportion of conspecific pollen transported and deposited by pollinators. By contrast, at higher plant density and lower visitation rate, pollinators deposited larger proportion of conspecific pollen, although still far from sufficient to ensure that all the ovules were fertilized. Finally, self-pollen completely buffered the detrimental effects on pollination of patch fragmentation and pollinator failure. Our results indicate that pollen loads from pollinators and emasculated flowers should be quantified for an accurate understanding of the relative impacts of pollinator and mate limitation on pollen transfer in facultative autogamous species

The Development of a Phaeocystis Bloom in a Mesocosm Experiment in Relation to Nutrients, Irradiance and Coexisting Algae

A widespread hypothesis is that man-induced eutrophication, an increase in nitrogen and/or phosphorus rather than silicon, gives a competitive advantage to the non-silicon using flagellates against the silicon dependent diatoms. Some authors suggest that such a mechanism could explain the intensification of the Phaeocystis blooms observed in the last decades in the coastal zones of the North Sea. A mesocosm experiment aiming to investigate this mechanism was performed in two 3 m(3) mesocosms. Light climate, mixing regime and nutrient concentrations reproduced conditions in Dutch coastal waters. Silicon was added to ensure the development of a phytoplankton development without Si limitation. Massive blooms of the colony forming Prymnesiophycean Phaeocystis sp. developed in both mesocosms and outcompeted the diatom community. Nutrients were continuously added and no nutrient limitation occurred during the bloom development. After four weeks, the Phaeocystis bloom collapsed and diatoms reappeared in both tanks. The dominance of Phaeocystis in a non silicon-limited environment constitutes an original observation which is in contradiction with the conclusions of some previously published works. [KEYWORDS: Continental coastal zones; dominated spring bloom; dutch tidal inlet; north-sea; pouchetii haptophyceae; ditylum-brightwelli; temora-longicornis; colony formation; english-channel; growth-rate]

Reliable genotyping of samples with very low DNA quantities using PCR.

Our purpose was to identify an experimental procedure using PCR that provides a reliable genotype at a microsatellite locus using only a few picograms of template DNA. Under these circumstances, it is possible (i) that one allele of a heterozygous individual will not be detected and (ii) that PCR-generated alleles or 'false alleles' will arise. A mathematical model has been developed to account for stochastic events when pipetting template DNA in a very dilute DNA extract and computer simulations have been performed. Laboratory experiments were also carried out using DNA extracted from a bear feces sample to determine if experimental results correlate with the mathematical model. The results of 150 typing experiments are consistent with the proposed model. Based on this model and the level of observed false alleles, an experimental procedure using the multiple tubes approach is proposed to obtain reliable genotypes with a confidence level of 99%. This multiple tubes procedure should be systematically used when genotyping nuclear loci of ancient or forensic samples, museum specimens and hair or feces of free ranging animals